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Bastholm CJ, Andersen B, Frisvad JC, Oestergaard SK, Nielsen JL, Madsen AM, Richter J. A novel contaminant in museums? A cross-sectional study on xerophilic Aspergillus growth in climate-controlled repositories. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173880. [PMID: 38857796 DOI: 10.1016/j.scitotenv.2024.173880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 06/12/2024]
Abstract
In the last decade, extensive fungal growth has developed in Danish museums parallel to climate change, challenging occupational health and heritage preservation. The growth was unexpected as the museums strived to control relative humidity below 60 %, and it should exceed 75 % to risk growth. A Danish case study found xerophilic Aspergillus species able to grow at low relative humidity in a museum repository. This cross-sectional study aimed to examine whether xerophilic growth from Aspergillus section Restricti has become a novel contaminant nationally distributed in Danish museum repositories striving to control relative humidity according to international environmental recommendations for heritage collections. The study examined The National Museum of Denmark and eight large State Recognized museums distributed throughout Denmark. It was based on 600 swab and tape-lift samples and 60 MAS100-Eco and filter air samples analyzed for fungi with cultivation and morphological identification, Big-Dye-Sanger sequencing, CaM-Nanopore and ITS-Illumina amplicon sequencing. The study showed growth from seven xerophilic Aspergillus species: A. conicus, A. domesticus, A. glabripes, A. halophilicus, A. magnivesiculatus, A. penicilloides, A. vitricola, of which three are new to Denmark, and 13 xerotolerant Aspergillus species. There was no growth from other fungal species. The multiple detection approach provided a broad characterization; however, there was variance in the detected species depending on the analysis approach. Cultivation and Big-Dye Sanger sequencing showed the highest Aspergillus diversity, detecting 17 species; CaM-Nanopore amplicon sequencing detected 12 species; and ITS-illumina amplicon sequencing detected two species but the highest overall diversity. Cultivation, followed by Big-Dye Sanger and CaM-amplicon sequencing, proved the highest compliance. The study concluded that xerophilic Aspergillus growth is nationally distributed and suggests species from Aspergillus section Restricti as a novel contaminant in climate-controlled museum repositories. To safeguard occupational health and heritage preservation research in sustainable solutions, avoiding xerophilic growth in museum collections is most important.
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Affiliation(s)
- Camilla Jul Bastholm
- Museum ROMU, Roskilde and The National Museum of Denmark, Copenhagen, Denmark; Royal Danish Academy, Copenhagen, Denmark.
| | | | | | | | | | - Anne Mette Madsen
- The National Research Centre for the Working Environment, Copenhagen, Denmark
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Li L, Flores M, Salvador A, Belloch C. Impact of paprika and dextrose addition on dry cured loins microbiota and its effect on aroma development. Int J Food Microbiol 2024; 421:110782. [PMID: 38851175 DOI: 10.1016/j.ijfoodmicro.2024.110782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/24/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
The impact of paprika and dextrose addition on the surface of dry cured loins was analysed attending to differences in microbiota composition and aroma profile. Three different types of loins containing either dextrose (D), paprika (P) or a mixture of dextrose and paprika (DP) were manufactured. The loins were characterized using physic-chemical parameters, free amino acids, volatile compounds and aroma sensorial analysis, as well as applying microbiological counts and metagenomics of the 16S rRNA gene and its rDNA region. The analysis of volatile compounds clearly distinguished all loins, whereas the total content of free amino acids only separated P from D and DP loins. The main sensory differences were linked to paprika addition, which increased the perception of paprika and smoky odors as well as cured, savoury and cheesy notes. Microbial counts analysis could not differentiate between the three loin types; however, metagenomics analysis revealed clear differences in key bacterial and fungal genera among the three loins. Paprika addition favoured dominance of Latilactobacillus in the microbiota of P loins. On the contrary, dextrose addition caused the dominance of Staphylococcus in the microbiota of D loins. In DP loins, both genera were similarly represented in the bacterial community. Regarding fungi, large differences could be observed within the P and D loins, whereas the proportion of Debaryomyces in DP loins increased. The microbiota composition of DP loins controlled the lipid oxidation phenomenon, reducing the generation of derived volatiles producing rancid notes and increase the volatile compounds derived from amino acids such as branched aldehydes, pyrazines and pyrroles, providing particular aroma notes to the loins.
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Affiliation(s)
- Lei Li
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain
| | - Monica Flores
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain
| | - Ana Salvador
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain
| | - Carmela Belloch
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Avda. Agustín Escardino 7, E-46980 Paterna, Valencia, Spain.
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3
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Xia Y, Turner BL, Li Y, Lian P, Yang Z, Fan Y, Yang L, Yang Y. Phosphorus addition enhances heterotrophic respiration but reduces root respiration in a subtropical plantation forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173158. [PMID: 38735329 DOI: 10.1016/j.scitotenv.2024.173158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Soil respiration (Rs) is a major component of the global carbon (C) cycle and is influenced by the availability of nutrients such as phosphorus (P). However, the response of Rs to P addition in P-limited subtropical forest ecosystems and the underlying mechanisms remain poorly understood. To address this, we conducted a P addition experiment (50 kg P ha-1 yr-1) in a subtropical Chinese fir (Cunninghamia lanceolata) plantation forest. We separated Rs into heterotrophic respiration (Rh), root respiration (Rr), and mycorrhizal hyphal respiration (Rm), and quantified soil properties, microbial biomass (phospholipid fatty acid, PLFA), fungal community composition (ITS), and the activity of extracellular enzymes. Phosphorus addition significantly increased Rs and Rh, but decreased Rr and did not influence Rm. Further, P addition increased fungal, bacterial, and total PLFAs, and phenol oxidase activity. Conversely, P application decreased root biomass and did not alter the relative abundance of symbiotrophic fungi. Phosphorus enrichment therefore enhances soil C emissions by promoting organic matter decomposition by heterotrophic activity, rather than via increases in root or mycorrhizal respiration. This advances our mechanistic understanding of the relationship between fertility and soil respiration in subtropical forests, with implications for predicting soil C emissions under global change.
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Affiliation(s)
- Yun Xia
- School of Geographical Science, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350007, China
| | - Benjamin L Turner
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, South Korea
| | - Yiqing Li
- College of Agriculture, Forestry and Natural Resources Management, University of Hawaii, Hilo, HI 96720, USA
| | - Pingping Lian
- School of Design, Fujian University of Technology, Fuzhou 350118, China
| | - Zhijie Yang
- School of Geographical Science, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350007, China
| | - Yuexin Fan
- School of Geographical Science, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350007, China.
| | - Liuming Yang
- School of Geographical Science, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350007, China.
| | - Yusheng Yang
- School of Geographical Science, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Provincial Key Laboratory for Plant Eco-physiology, Fujian Normal University, Fuzhou 350117, China; Institute of Geography, Fujian Normal University, Fuzhou 350007, China
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Ullah S, Huyop F, Wahab RA, Huda N, Oyewusi HA, Sujana IGA, Saloko S, Andriani AASPR, Mohamad MAN, Abdul Hamid AA, Mohd Nasir MH, Antara NS, Gunam IBW. The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island. Sci Rep 2024; 14:14122. [PMID: 38898099 PMCID: PMC11187073 DOI: 10.1038/s41598-024-64838-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024] Open
Abstract
Southern Asian flowers offer honeybees a diversity of nectar. Based on its geographical origin, honey quality varies. Traditional methods are less authentic than DNA-based identification. The origin of honey is determined by pollen, polyphenolic, and macro-microorganisms. In this study, amplicon sequencing targets macro-microorganisms in eDNA using the ITS1 region to explore honey's geographical location and authentication. The variety of honey samples was investigated using ITS1 with Illumina sequencing. For all four honey samples, raw sequence reads showed 979,380 raw ITS1 amplicon reads and 375 ASVs up to the phylum level. The highest total number of 202 ASVs up to phylum level identified Bali honey with 211,189 reads, followed by Banggi honey with 309,207 a total number of 111 ASVs, and Lombok represents only 63 ASVs up to phylum level with several read 458,984. Based on Shannon and Chao1, honey samples from Bali (B2) and (B3) exhibited higher diversity than honey from Lombok (B1) and green honey from Sabah (B4), while the Simpson index showed that Banggi honey (B4) had higher diversity. Honey samples had significant variance in mycobiome taxonomic composition and abundance. Zygosaccharomyces and Aspergillus were the main genera found in Lombok honey, with percentages of 68.81% and 29.76% respectively. Bali honey samples (B2 and B3) were identified as having a significant amount of the genus Aureobasidium, accounting for 40.81% and 25% of the readings, respectively. The microbiome composition of Banggi honey (B4) showed a high presence of Zygosaccharomyces 45.17% and Aureobasidium 35.24%. The ITS1 analysis effectively distinguishes between honey samples of different origins and its potential as a discriminatory tool for honey origin and authentication purposes.
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Affiliation(s)
- Saeed Ullah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia.
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia.
| | - Roswanira Ab Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90509, Sandakan, Sabah, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
- Biochemistry Unit, Department of Science Technology, The Federal Polytechnic, P. M. B 5351, Ado Ekiti, Ekiti State, Nigeria
| | - I Gede Arya Sujana
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia
| | - Satrijo Saloko
- Faculty of Food Technology and Agro Industry, University of Mataram, Mataram, Nusa Tenggara Barat, 83126, Indonesia
| | | | - Mohd Azrul Naim Mohamad
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Mohd Nasir
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Nyoman Semadi Antara
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia
| | - Ida Bagus Wayan Gunam
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia.
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5
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Onetto CA, Ward CM, Van Den Heuvel S, Hale L, Cuijvers K, Borneman AR. Temporal and spatial dynamics within the fungal microbiome of grape fermentation. Environ Microbiol 2024; 26:e16660. [PMID: 38822592 DOI: 10.1111/1462-2920.16660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/10/2024] [Indexed: 06/03/2024]
Abstract
Over 6 years, we conducted an extensive survey of spontaneous grape fermentations, examining 3105 fungal microbiomes across 14 distinct grape-growing regions. Our investigation into the biodiversity of these fermentations revealed that a small number of highly abundant genera form the core of the initial grape juice microbiome. Consistent with previous studies, we found that the region of origin had the most significant impact on microbial diversity patterns. We also discovered that certain taxa were consistently associated with specific geographical locations and grape varieties, although these taxa represented only a minor portion of the overall diversity in our dataset. Through unsupervised clustering and dimensionality reduction analysis, we identified three unique community types, each exhibiting variations in the abundance of key genera. When we projected these genera onto global branches, it suggested that microbiomes transition between these three broad community types. We further investigated the microbial community composition throughout the fermentation process. Our observations indicated that the initial microbial community composition could predict the diversity during the early stages of fermentation. Notably, Hanseniaspora uvarum emerged as the primary non-Saccharomyces species within this large collection of samples.
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Affiliation(s)
- Cristobal A Onetto
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
- School of Wine, Food and Agriculture, The University of Adelaide, Adelaide, South Australia, Australia
| | - Chris M Ward
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | | | - Laura Hale
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Kathleen Cuijvers
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Anthony R Borneman
- The Australian Wine Research Institute, Glen Osmond, South Australia, Australia
- School of Wine, Food and Agriculture, The University of Adelaide, Adelaide, South Australia, Australia
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6
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Yunus A, Mokhtar NM, Raja Ali RA, Ahmad Kendong SM, Ahmad HF. Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues. MethodsX 2024; 12:102623. [PMID: 38435637 PMCID: PMC10907193 DOI: 10.1016/j.mex.2024.102623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Colorectal cancer poses a significant threat to global health, necessitating the development of effective early detection techniques. However, the potential of the fungal microbiome as a putative biomarker for the detection of colorectal adenocarcinoma has not been extensively explored. We analyzed the viability of implementing the fungal mycobiome for this purpose. Biopsies were collected from cancer and polyp patients. The total genomic DNA was extracted from the biopsy samples by utilizing a comprehensive kit to ensure optimal microbial DNA recovery. To characterize the composition and diversity of the fungal mycobiome, high-throughput amplicon sequencing targeting the internal transcribed spacer 1 (ITS1) region was proposed. A comparative analysis revealed discrete fungal profiles among the diseased groups. Here, we also proposed pipelines based on a predictive model using statistical and machine learning algorithms to accurately differentiate colorectal adenocarcinoma and polyp patients from normal individuals. These findings suggest the utility of gut mycobiome as biomarkers for the detection of colorectal adenocarcinoma. Expanding our understanding of the role of the gut mycobiome in disease detection creates novel opportunities for early intervention and personalized therapeutic strategies for colorectal cancer.•Detailed method to identify the gut mycobiome in colorectal cancer patients using ITS-specific amplicon sequencing.•Application of machine learning algorithms to the identification of potential mycobiome biomarkers for non-invasive colorectal cancer screening.•Contribution to the advancement of innovative colorectal cancer diagnostic methods and targeted therapies by applying gut mycobiome knowledge.
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Affiliation(s)
- Aisyah Yunus
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah (UMPSA), Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia (UKM), 56000 Kuala Lumpur, Malaysia
- Gut Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gut Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
- School of Medical and Life Sciences, Sunway University, 47500 Subang Jaya, Selangor, Malaysia
| | - Siti Maryam Ahmad Kendong
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia (UKM), 56000 Kuala Lumpur, Malaysia
- Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah (UMPSA), Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
- Gut Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
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7
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Parente E, Ricciardi A. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 2024; 13:1689. [PMID: 38890917 PMCID: PMC11171936 DOI: 10.3390/foods13111689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.
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Affiliation(s)
- Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy;
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Yang Z, Meng L, Liu Z, Chen J, Wang J, Cui H, Naz B, Wang Y, Xu Y, Song H, An L, Xiao S, Chen S. Warming enhances the negative effects of shrub removal on phosphorus mineralization potential. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171517. [PMID: 38461985 DOI: 10.1016/j.scitotenv.2024.171517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Shrubs have developed various mechanisms for soil phosphorus utilization. Shrub encroachment caused by climate warming alters organic phosphorus mineralization capability by promoting available phosphorus absorption and mediating root exudates. However, few studies have explored how warming regulates the effects of dominant shrubs on soil organic phosphorus mineralization capability. We provide insights into warming, dominant shrub removal, and their interactive effects on the soil organic phosphorus mineralization potential in the Qinghai-Tibetan Plateau. Real-time polymerase chain reaction was used to quantify the soil microbial phosphatase genes (phoC and phoD), which can characterize the soil organic phosphate mineralization potential. We found that warming had no significant effect on the soil organic phosphate-mineralized components (total phosphate, organic phosphate, and available phosphate), genes (phoC and phoD), or enzymes (acid and alkaline phosphatases). Shrub removal negatively influenced the organic phosphate-mineralized components and genes. It significantly decreased soil organic phosphate mineralization gene copy numbers only under warming conditions. Warming increased fungal richness and buffered the effects of shrub removal on bacterial richness and gene copy numbers. However, the change in the microbial community was not the main factor affecting organic phosphate mineralization. We found only phoC copy number had significant correlation to AP. Structural equation modelling revealed that shrub removal and the interaction between warming and shrub removal had a negative direct effect on phoC copy numbers. We concluded that warming increases the negative effect of shrub removal on phosphorus mineralization potential, providing a theoretical basis for shrub encroachment on soil phosphate mineralization under warming conditions.
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Affiliation(s)
- Zi Yang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Lihua Meng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Ziyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jiajia Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hanwen Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Beenish Naz
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Yajun Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Yifeng Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hongxian Song
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Lizhe An
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Shuyan Chen
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China.
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9
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Cusaro CM, Capelli E, Picco AM, Brusoni M. Incidence of resistance to ALS and ACCase inhibitors in Echinochloa species and soil microbial composition in Northern Italy. Sci Rep 2024; 14:10544. [PMID: 38719860 PMCID: PMC11078947 DOI: 10.1038/s41598-024-59856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
The increasing amount of weeds surviving herbicide represents a very serious problem for crop management. The interaction between microbial community of soil and herbicide resistance, along with the potential evolutive consequences, are still poorly known and need to be investigated to better understand the impact on agricultural management. In our study, we analyzed the microbial composition of soils in 32 farms, located in the Northern Italy rice-growing area (Lombardy) with the aim to evaluate the relationship between the microbial composition and the incidence of resistance to acetolactate synthase (ALS) and acetyl-CoA carboxylase (ACCase) inhibiting herbicides in Echinochloa species. We observed that the coverage of weeds survived herbicide treatment was higher than 60% in paddy fields with a low microbial biodiversity and less than 5% in those with a high microbial biodiversity. Fungal communities showed a greater reduction in richness than Bacteria. In soils with a reduced microbial diversity, a significant increase of some bacterial and fungal orders (i.e. Lactobacillales, Malasseziales and Diaporthales) was observed. Interestingly, we identified two different microbial profiles linked to the two conditions: high incidence of herbicide resistance (H-HeR) and low incidence of herbicide resistance (L-HeR). Overall, the results we obtained allow us to make hypotheses on the greater or lesser probability of herbicide resistance occurrence based on the composition of the soil microbiome and especially on the degree of biodiversity of the microbial communities.
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Affiliation(s)
- Carlo Maria Cusaro
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Enrica Capelli
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Anna Maria Picco
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Maura Brusoni
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy.
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10
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Fuentes-Alburquenque S, Olivencia Suez V, Aguilera O, Águila B, Rojas Araya L, Mandakovic D. A Highly Homogeneous Airborne Fungal Community around a Copper Open Pit Mine Reveals the Poor Contribution Made by the Local Aerosolization of Particles. Microorganisms 2024; 12:934. [PMID: 38792765 PMCID: PMC11123957 DOI: 10.3390/microorganisms12050934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Fungi are ubiquitous and metabolically versatile. Their dispersion has important scientific, environmental, health, and economic implications. They can be dispersed through the air by the aerosolization of near surfaces or transported from distant sources. Here, we tested the contribution of local (scale of meters) versus regional (kilometers) sources by analyzing an airborne fungal community by ITS sequencing around a copper mine in the North of Chile. The mine was the regional source, whereas the soil and vegetal detritus were the local sources at each point. The airborne community was highly homogeneous at ca. 2000 km2, impeding the detection of regional or local contributions. Ascomycota was the dominant phylum in the three communities. Soil and vegetal detritus communities had lower alpha diversity, but some taxa had abundance patterns related to the distance from the mine and altitude. On the contrary, the air was compositionally even and unrelated to environmental or spatial factors, except for altitude. The presence of plant pathogens in the air suggests that other distant sources contribute to this region's airborne fungal community and reinforces the complexity of tracking the sources of air microbial communities in a real world where several natural and human activities coexist.
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Affiliation(s)
- Sebastián Fuentes-Alburquenque
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Escuela de Medicina Veterinaria, Facultad de Ciencias Médicas, Universidad Bernardo O’Higgins, Santiago 8370993, Chile;
- Departamento de Matemáticas y Ciencias de la Ingeniería, Escuela de Ingeniaría Civil, Facultad de Ingeniería Ciencia y Tecnología, Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Victoria Olivencia Suez
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Huechuraba 8580745, Chile;
| | - Omayra Aguilera
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Escuela de Medicina Veterinaria, Facultad de Ciencias Médicas, Universidad Bernardo O’Higgins, Santiago 8370993, Chile;
| | - Blanca Águila
- Programa de Doctorado en Microbiología, Universidad de Chile, Ñuñoa 7800003, Chile;
- Fundación Ciencia y Vida, Huechuraba 8580704, Chile
| | - Luis Rojas Araya
- Departamento de Química, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1270709, Chile;
| | - Dinka Mandakovic
- GEMA Genómica, Ecología y Medio Ambiente, Universidad Mayor, Huechuraba 8580745, Chile;
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11
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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12
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Bongaerts D, Bouchez A, De Roos J, Cnockaert M, Wieme AD, Vandamme P, Weckx S, De Vuyst L. Refermentation and maturation of lambic beer in bottles: a necessary step for gueuze production. Appl Environ Microbiol 2024; 90:e0186923. [PMID: 38446583 PMCID: PMC11022581 DOI: 10.1128/aem.01869-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/04/2024] [Indexed: 03/08/2024] Open
Abstract
The production of gueuze beers through refermentation and maturation of blends of lambic beer in bottles is a way for lambic brewers to cope with the variability among different lambic beer batches. The resulting gueuze beers are more carbonated than lambic beers and are supposed to possess a unique flavor profile that varies over time. To map this refermentation and maturation process for gueuze production, a blend of lambic beers was made and bottled, whereby one of them was produced with the old wheat landrace Zeeuwse Witte. Through the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and high-throughput sequencing of bacterial and fungal amplicons, in combination with metabolite target analysis, new insights into gueuze production were obtained. During the initial stages of refermentation, the conditions in the bottles were similar to those encountered during the maturation phase of lambic beer productions in wooden barrels, which was also reflected microbiologically (presence of Brettanomyces species, Pediococcus damnosus, and Acetobacter lambici) and biochemically (ethanol, higher alcohols, lactic acid, acetic acid, volatile phenolic compounds, and ethyl esters). However, after a few weeks of maturation, a switch from a favorable environment to one with nutrient and dissolved oxygen depletion resulted in several changes. Concerning the microbiology, a sequential prevalence of three lactic acid bacterial species occurred, namely, P. damnosus, Lentilactobacillus buchneri, and Lactobacillus acetotolerans, while the diversity of the yeasts decreased. Concerning the metabolites produced, mainly those of the Brettanomyces yeasts determined the metabolic profiles encountered during later stages of the gueuze production.IMPORTANCEGueuze beers are the result of a refermentation and maturation process of a blend of lambic beers carried out in bottles. These gueuze beers are known to have a long shelf life, and their quality typically varies over time. However, knowledge about gueuze production in bottles is scarce. The present study provided more insights into the varying microbial and metabolite composition of gueuze beers during the first 2 years of this refermentation and maturation process. This will allow gueuze producers to gain more information about the influence of the refermentation and maturation time on their beers. These insights can also be used by gueuze producers to better inform their customers about the quality of young and old gueuze beers.
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Affiliation(s)
- Dries Bongaerts
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Arne Bouchez
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonas De Roos
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Margo Cnockaert
- Department of Biochemistry and Microbiology, Laboratory for Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Anneleen D. Wieme
- Department of Biochemistry and Microbiology, Laboratory for Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory for Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Stefan Weckx
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Department of Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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13
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Ren XY, Zheng YL, Liu ZL, Duan GL, Zhu D, Ding LJ. Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133567. [PMID: 38271874 DOI: 10.1016/j.jhazmat.2024.133567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.
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Affiliation(s)
- Xin-Yue Ren
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yu-Ling Zheng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhe-Lun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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14
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Hegde S, Khanipov K, Hornett EA, Nilyanimit P, Pimenova M, Saldaña MA, de Bekker C, Golovko G, Hughes GL. Interkingdom interactions shape the fungal microbiome of mosquitoes. Anim Microbiome 2024; 6:11. [PMID: 38454530 PMCID: PMC10921588 DOI: 10.1186/s42523-024-00298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The mosquito microbiome is an important modulator of vector competence and vectoral capacity. Unlike the extensively studied bacterial microbiome, fungal communities in the mosquito microbiome (the mycobiome) remain largely unexplored. To work towards getting an improved understanding of the fungi associated with mosquitoes, we sequenced the mycobiome of three field-collected and laboratory-reared mosquito species (Aedes albopictus, Aedes aegypti, and Culex quinquefasciatus). RESULTS Our analysis showed both environment and host species were contributing to the diversity of the fungal microbiome of mosquitoes. When comparing species, Ae. albopictus possessed a higher number of diverse fungal taxa than Cx. quinquefasciatus, while strikingly less than 1% of reads from Ae. aegypti samples were fungal. Fungal reads from Ae. aegypti were < 1% even after inhibiting host amplification using a PNA blocker, indicating that this species lacked a significant fungal microbiome that was amplified using this sequencing approach. Using a mono-association mosquito infection model, we confirmed that mosquito-derived fungal isolates colonize Aedes mosquitoes and support growth and development at comparable rates to their bacterial counterparts. Strikingly, native bacterial taxa isolated from mosquitoes impeded the colonization of symbiotic fungi in Ae. aegypti suggesting interkingdom interactions shape fungal microbiome communities. CONCLUSION Collectively, this study adds to our understanding of the fungal microbiome of different mosquito species, that these fungal microbes support growth and development, and highlights that microbial interactions underpin fungal colonization of these medically relevent species.
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Affiliation(s)
- Shivanand Hegde
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK.
- School of Life Sciences, Keele University, Newcastle, UK.
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Emily A Hornett
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Pornjarim Nilyanimit
- Center of Excellence in Clinical Virology, Faculty of Medicine , Chulalongkorn University, Bangkok, Thailand
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Miguel A Saldaña
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Charissa de Bekker
- Microbiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, UK.
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15
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Weaver D, Novak-Frazer L, Palmer M, Richardson M, Bromley M, Bowyer P. Development of a novel mycobiome diagnostic for fungal infection. BMC Microbiol 2024; 24:63. [PMID: 38373963 PMCID: PMC10875777 DOI: 10.1186/s12866-024-03197-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/12/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Amplicon-based mycobiome analysis has the potential to identify all fungal species within a sample and hence could provide a valuable diagnostic assay for use in clinical mycology settings. In the last decade, the mycobiome has been increasingly characterised by targeting the internal transcribed spacer (ITS) regions. Although ITS targets give broad coverage and high sensitivity, they fail to provide accurate quantitation as the copy number of ITS regions in fungal genomes is highly variable even within species. To address these issues, this study aimed to develop a novel NGS fungal diagnostic assay using an alternative amplicon target. METHODS Novel universal primers were designed to amplify a highly diverse single copy and uniformly sized DNA target (Tef1) to enable mycobiome analysis on the Illumina iSeq100 which is a low cost, small footprint and simple to use next-generation sequencing platform. To enable automated analysis and rapid results, a streamlined bioinformatics workflow and sequence database were also developed. Sequencing of mock fungal communities was performed to compare the Tef1 assay and established ITS1-based method. The assay was further evaluated using clinical respiratory samples and the feasibility of using internal spike-in quantitative controls was assessed. RESULTS The Tef1 assay successfully identified and quantified Aspergillus, Penicillium, Candida, Cryptococcus, Rhizopus, Fusarium and Lomentospora species from mock communities. The Tef1 assay was also capable of differentiating closely related species such as A. fumigatus and A. fischeri. In addition, it outperformed ITS1 at identifying A. fumigatus and other filamentous pathogens in mixed fungal communities (in the presence or absence of background human DNA). The assay could detect as few as 2 haploid genome equivalents of A. fumigatus from clinical respiratory samples. Lastly, spike-in controls were demonstrated to enable semi-quantitation of A. fumigatus load in clinical respiratory samples using sequencing data. CONCLUSIONS This study has developed and tested a novel metabarcoding target and found the assay outperforms ITS1 at identifying clinically relevant filamentous fungi. The assay is a promising diagnostic candidate that could provide affordable NGS analysis to clinical mycology laboratories.
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Affiliation(s)
- Danielle Weaver
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK
| | - Lilyann Novak-Frazer
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Maisie Palmer
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Malcolm Richardson
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Mike Bromley
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK.
| | - Paul Bowyer
- Core Technology Facility, University of Manchester, Manchester, M13 9WU, UK.
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16
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Decadt H, Weckx S, De Vuyst L. The microbial and metabolite composition of Gouda cheese made from pasteurized milk is determined by the processing chain. Int J Food Microbiol 2024; 412:110557. [PMID: 38237418 DOI: 10.1016/j.ijfoodmicro.2024.110557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/28/2024]
Abstract
Gouda cheeses of different production batches and ripening times often differ in metabolite composition, which may be due to the starter culture mixture applied or the growth of non-starter lactic acid bacteria (NSLAB) upon maturation. Therefore, a single Gouda cheese production batch was systematically investigated from the thermized milk to the mature cheeses, ripened for up to 100 weeks, to identify the main bacterial species and metabolites and their dynamics during the whole production and ripening. As this seemed to be starter culture strain- and NSLAB-dependent, it requested a detailed, longitudinal, and quantitative investigation. Hereto, microbial colony enumeration, high-throughput full-length 16S rRNA gene sequencing, and a metabolomic approach were combined. Culture-dependently, Lactococcus lactis was the most abundant species from its addition as part of the starter culture up to the first two months of cheese ripening. Afterward, the NSLAB Lacticaseibacillus paracasei became the main species during ripening. The milk was a possible inoculation source for the latter species, despite pasteurization. Culture-independently, the starter LAB Lactococcus cremoris and Lc. lactis were the most abundant species in the cheese core throughout the whole fermentation and ripening phases up to 100 weeks. The cheese rind from 40 until 100 weeks of ripening was characterized by a high relative abundance of the NSLAB Tetragenococcus halophilus and Loigolactobacillus rennini, which both came from the brine. These species were linked with the production of the biogenic amines cadaverine and putrescine. The most abundant volatile organic compound was acetoin, an indicator of citrate and lactose fermentation during the production day, whereas the concentrations of free amino acids were an indicator of the ripening time.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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17
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Pradal I, González-Alonso V, Wardhana YR, Cnockaert M, Wieme AD, Vandamme P, De Vuyst L. Various cold storage-backslopping cycles show the robustness of Limosilactobacillus fermentum IMDO 130101 as starter culture for Type 3 sourdough production. Int J Food Microbiol 2024; 411:110522. [PMID: 38160537 DOI: 10.1016/j.ijfoodmicro.2023.110522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/22/2023] [Accepted: 12/10/2023] [Indexed: 01/03/2024]
Abstract
Type 3 sourdoughs, which are starter culture-initiated and subsequently backslopped, are less studied than other sourdough types. Yet, they can serve as a model to assess how competitive starter culture strains for sourdough production are and how the microbial composition of such sourdoughs may evolve over time. In the present study, Limosilactobacillus fermentum IMDO 130101 was used to produce Type 3 sourdoughs, prepared from wheat and wholemeal wheat flours. Therefore, an initial fermentation of the flour-water mixture was performed at 30 °C for 48 h. This was followed by cold storage-backslopping cycles, consisting of refreshments (50 %, v/v), fermentation steps of 16 h, and storage at 4 °C each week, every three weeks, and every six weeks. The microbial dynamics (culture-dependent and -independent approaches) and metabolite dynamics were measured. In all sourdoughs produced, starter culture strain monitoring, following an amplicon sequence variant approach, showed that Liml. fermentum IMDO 130101 prevailed during one month when the sourdoughs were refreshed each week, during 24 weeks when the sourdoughs were refreshed every three weeks, and during 12 weeks when the sourdoughs were refreshed every six weeks. This suggested the competitiveness and robustness of Liml. fermentum IMDO 130101 for a considerable duration but also showed that the strain is prone to microbial interference. For instance, Levilactobacillus brevis and Pediococcus spp. prevailed upon further cold storage and backslopping. Also, although no yeasts were inoculated into the flour-water mixtures, Kazachstania unispora, Torulaspora delbrueckii, and Wickerhamomyces anomalus were the main yeast species found. They appeared after several weeks of storage and backslopping, which however indicated the importance of an interplay between LAB and yeast species in sourdoughs. The main differences among the mature sourdoughs obtained could be explained by the different flours used, the refreshment conditions applied, and the sampling time (before and after backslopping). Finally, the metabolite quantifications revealed continued metabolite production during the cold storage periods, which may impact the sourdough properties and those of the breads made thereof.
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Affiliation(s)
- Inés Pradal
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Víctor González-Alonso
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Yohanes Raditya Wardhana
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium; BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium; BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
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18
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ullah S, Huda N, Wahab RA, Hamid AAA, Nasir MHM, Mohamad MAN, Ahmad HF, Oyewusi HA, Huyop F. Baseline amplicon sequencing data for the ITS2 region in the green honey of Banggi Island, Sabah. Data Brief 2024; 52:110044. [PMID: 38328502 PMCID: PMC10847015 DOI: 10.1016/j.dib.2024.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Green honey, was discovered on Banggi Island, Sabah, showing high in essential amino acids and chlorophyll derivatives. Despite its lucrative market potential owing to its distinctive color, uncertainties persist regarding its nature. This study leverages amplicon sequencing by targeting micro- and macro-organisms present in honey environmental DNA (eDNA) using Internal Transcribed Spacer 2 (ITS2) region, enabling the identification of floral and microorganism sources that represent the honey's composition. The investigation into green honey from Banggi Island concerns the prevalence of honey adulteration and authenticity for economic gain. Adulteration methods, such as the addition of sugar syrups, compromise honey purity. Using a sequencing approach would help in determining the geographic origin and verifying the authenticity of the honey. The study aims to identify plant species or microorganisms in honey's eDNA. To authenticate honey, we utilized ITS2 with Illumina sequencing, exploring the diversity of green honey samples. Raw sequence reads obtained for the green honey sample revealed 1,438,627 raw reads, with a GC average of 49.22 %. A total of 44 amplicon sequence variances (ASVs) were identified, including three genera: Zygosaccharomyces with two species, Fraxinus with three species, and the genus Ficaria with only one species. Their respective relative abundances were 98.55%, 0.94%, and 0.51%. Zygosaccharomyces rouxii and Zygosaccharomyces mellis were identified as the pre-dominant yeast species in honey, while the Fraxinus and Ficaria genus represent common plant species in Sabah, particularly in Banggi Island. The dominance of Zygosaccharomyces species aligns with their known prevalence in honey, affirming the reliability of our findings. The presence of Fraxinus and Ficaria in the honey sample correlates with its abundance in the local environment. This amplicon sequencing approach not only contributes to our understanding of green honey composition but also serves as a valuable resource for authenticating honey origin in Malaysia, particularly for green honey from Banggi Island, Sabah. Our study pioneers the application of ITS2 amplicon sequencing for green honey amplicon sequencing, providing valuable insights into its composition and origin. This methodology, with a focus on eDNA, contributes to the authentication and quality determination of honey in Malaysia, addressing the pressing concerns of adulteration and variability in production practices.
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Affiliation(s)
- Saeed ullah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90509 Sandakan, Sabah, Malaysia
| | - Roswanira Ab. Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Mohd Nasir
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Azrul Naim Mohamad
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, 26300 Gambang, Pahang, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB 5351, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
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19
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Munch-Andersen CB, Porcellato D, Devold TG, Østlie HM. Isolation, identification, and stability of sourdough microbiota from spontaneously fermented Norwegian legumes. Int J Food Microbiol 2024; 410:110505. [PMID: 38043377 DOI: 10.1016/j.ijfoodmicro.2023.110505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 11/18/2023] [Indexed: 12/05/2023]
Abstract
Fermentation has recently been rediscovered as an attractive technique to process legumes, as it can improve the nutritional quality and value of the end product. This study investigated the dynamics and stability of the microbial communities in spontaneously fermented sourdoughs made from flours of two cultivars of faba beans and two cultivars of peas. Sourdoughs were established by the backslopping technique, and the microbial development at 22 °C and 30 °C was followed by culture dependent and culture independent methods. The utilization of substrates and formation of metabolites were also determined by high-performance liquid chromatography. A stable pH was reached in all the sourdoughs after 11-15 days of daily backslopping. Lactic acid bacteria and yeast from pH stable sourdoughs were isolated, characterized and identified. The fermentation temperature influenced the development of the microbial community and the substrate utilization during spontaneous fermentation. In the 30 °C fermentations, one species dominated (Lactiplantibacillus plantarum/pentosus), a lower pH was achieved, and the available substrates were more extensively converted. The 22 °C fermentation resulted in a more diverse microbial community (Lactiplantibacillus, Leuconostoc, Pediococcus), a higher pH, and more residual substrates were available after fermentation. Yeasts were only detected in one of the pea sourdoughs fermented at 30 °C, with Saccharomyces cerevisiae being the dominant species. Nearly all sourdoughs were depleted of maltose after 24 h fermentation cycles, and higher levels of lactic and acetic acid were detected in 30 °C fermen-tations. This research adds to our understanding of the autochthonous microbial community present in faba beans and peas as well as their natural capacity to establish themselves and ferment legume flours. These findings enhance the possibilities of utilizing and improving plant based protein sources.
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Affiliation(s)
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Tove Gulbrandsen Devold
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Hilde Marit Østlie
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
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20
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Zhang X, Lan T, Jiang H, Ye K, Dai Z. Bacterial community driven nitrogen cycling in coastal sediments of intertidal transition zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168299. [PMID: 37926266 DOI: 10.1016/j.scitotenv.2023.168299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/14/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Microorganisms inhabiting in coastal sediments significantly affect the nitrogen cycling in coastal waters and ecosystems. However, the bacterial community that related to the key active nitrogen transformation processes in intertidal transition zone are still not understood. Across a long flat intertidal zone at depths from 0 to 3 m in Daya Bay, China, the bacterial communities in sediments and their driven nitrogen cycling potential were evaluated with environmental factors and 16S rRNA sequencing. The results showed that the intertidal zone is a divide for environmental factors as pH, salinity and C/N ratio, instead of an average shift from freshwater to salt water. At the same time, the environmental factors influenced the abundance of bacterial community related to nitrogen cycling. Across the intertidal zone, the dominant nitrogen transformation processes were different. At the high tide and middle tide sites, the primary nitrogen cycling process was nitrification that worked with Nitrosomonadaceae, Nitrospiraceae, 0319-6A21, and wb1-A12. At the low tide sites, nitrogen fixation was the dominant function conducted by Bradyrhizobiaceae. The reduction of nitrate was carried out with the help of Xanthomonadales but relatively weak in all sampling sites especially for low tide sites. This was mostly because the richness and evenness of bacterial community were the lowest at the low tide sites. Meanwhile, the pH, Cl-, salinity, NH4+, NO3- and C/N ratio were the important factors that shaped the composition of local bacterial community. Further, the nonmetric multidimensional scaling results indicated that there were significant statistical differences in the composition of bacterial community among samples at different layers. The dominant nitrogen cycling processes in coastal sediments at different tide levels were revealed in this study, which offered an extended concept of nitrogen transformation along the groundwater discharge path in the intertidal transition zone. The distributions and compositions of bacterial communities and predicted functions provided a new insight for coastal environment and ecosystem management.
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Affiliation(s)
- Xiaoying Zhang
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China; College of Construction Engineering, Jilin University, Changchun 130026, China
| | - Tianshan Lan
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China.
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Kexin Ye
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China
| | - Zhenxue Dai
- Institute of Intelligent Simulation and Early Warning for Subsurface Environment, Jilin University, Changchun 130026, China; College of Construction Engineering, Jilin University, Changchun 130026, China.
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21
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Wang Q, Peng L, Wang P, Zhou Z, Li C, Chen C, Wang Y. Changes of atrazine dissipation and microbial community under coexistence of graphene oxide in river water. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132708. [PMID: 37856959 DOI: 10.1016/j.jhazmat.2023.132708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
The coexistence of herbicide atrazine (ATZ) and the nanomaterial graphene oxide (GO) in natural water bodies will be an inevitable scenario due to their widespread application and consequent release into aquatic ecosystems. But the dissipation of ATZ with GO and the response of the microbial community to their combination are still not clear. Here, we investigated the dissipation dynamics and transformation of ATZ with and without GO in river water after 21-d incubation. In the presence of GO, ATZ residue significantly decreased by 11%-43%; the transformation of ATZ markedly increased by 11%-17% when ATZ concentrations were not above 1.0 mg∙L-1. The direct adsorption of ATZ on GO, mainly via π-π interactions, proton transfer and hydrogen bonding, contributed 54%-68% of the total increased ATZ dissipation by GO. ATZ and ATZ+GO exerted effects of similar magnitude on microbial OTU numbers with an increase of bacterial diversity. The coexisting GO increased the relative abundance of ATZ-degradation bacteria and Chitinophagales, thus improving ATZ transformation. This work indicated that the coexistence of GO at environmentally relevant concentrations can effectively reduce ATZ residues and promote the transformation of ATZ to degradation products in river water; nevertheless, the potential risk of GO acting as an ATZ carrier should be given more prominence.
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Affiliation(s)
- Qinghai Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China.
| | - Lei Peng
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China; College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, PR China
| | - Peixin Wang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - Zixin Zhou
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China; College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, PR China
| | - Cui Li
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - Chuansheng Chen
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, PR China
| | - Yu Wang
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
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22
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Chen T, Zhang S, Yang J, Li Y, Kogure E, Zhu Y, Xiong W, Chen E, Shi G. Metabarcoding Analysis of Microorganisms Inside Household Washing Machines in Shanghai, China. Microorganisms 2024; 12:160. [PMID: 38257987 PMCID: PMC10819172 DOI: 10.3390/microorganisms12010160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Washing machines are one of the tools that bring great convenience to people's daily lives. However, washing machines that have been used for a long time often develop issues such as odor and mold, which can pose health hazards to consumers. There exists a conspicuous gap in our understanding of the microorganisms that inhabit the inner workings of washing machines. In this study, samples were collected from 22 washing machines in Shanghai, China, including both water eluted from different parts of washing machines and biofilms. Quantitative qualitative analysis was performed using fluorescence PCR quantification, and microbial communities were characterized by high-throughput sequencing (HTS). This showed that the microbial communities in all samples were predominantly composed of bacteria. HTS results showed that in the eluted water samples, the bacteria mainly included Pseudomonas, Enhydrobacter, Brevibacterium, and Acinetobacter. Conversely, in the biofilm samples, Enhydrobacter and Brevibacterium were the predominant bacterial microorganisms. Correlation analysis results revealed that microbial colonies in washing machines were significantly correlated with years of use and the type of detergent used to clean the washing machine. As numerous pathogenic microorganisms can be observed in the results, effective preventive measures and future research are essential to mitigate these health problems and ensure the continued safe use of these household appliances.
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Affiliation(s)
- Tong Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- KAO (China) Research and Development Center, No. 623, Ziri Road, Minhang District, Shanghai 100098, China (Y.Z.); (W.X.); (E.C.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214000, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Shu Zhang
- KAO (China) Research and Development Center, No. 623, Ziri Road, Minhang District, Shanghai 100098, China (Y.Z.); (W.X.); (E.C.)
| | - Juan Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214000, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214000, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Eiichi Kogure
- Kao Corporation, 1334, Minato, Wakayama 640-8580, Japan
| | - Ye Zhu
- KAO (China) Research and Development Center, No. 623, Ziri Road, Minhang District, Shanghai 100098, China (Y.Z.); (W.X.); (E.C.)
| | - Weiqi Xiong
- KAO (China) Research and Development Center, No. 623, Ziri Road, Minhang District, Shanghai 100098, China (Y.Z.); (W.X.); (E.C.)
| | - Enhui Chen
- KAO (China) Research and Development Center, No. 623, Ziri Road, Minhang District, Shanghai 100098, China (Y.Z.); (W.X.); (E.C.)
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214000, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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23
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Selvarajan R, Sibanda T, Ullah H, Abia ALK. Beach sand mycobiome: The silent threat of pathogenic fungi and toxic metal contamination for beachgoers. MARINE POLLUTION BULLETIN 2024; 198:115895. [PMID: 38101061 DOI: 10.1016/j.marpolbul.2023.115895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/17/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
Emphasis is always placed on bacterial but not fungal pathogens in marine environments. We analysed the fungal diversity, functional predictions, and toxic metals and metalloids contamination in beach sand from different South African locations. Results revealed a diverse fungal community, with Ascomycota, Rozellomycota, and Basidiomycota being the dominant phyla. Functional predictions highlighted fungal metabolic pathways related to of carbohydrates, amino acids, and lipids, in different beach samples. Elevated concentrations of toxic metals and metalloids were detected in Central and Harbour beach sands, likely due to anthropogenic activities. Correlations among different elements were observed, suggesting complex interactions in the coastal environment. Fungal pathogens like Cladosporium, Fusarium, Aspergillus, and Candida in beach sands raise potential public health risk concerns. Therefore, monitoring fungal diversity (including pathogens) alongside bacterial contamination in beach environments is imperative. The results contribute to understanding fungal community dynamics, functional potential, toxic metal and metalloid contamination, and potential risks associated with beach sand ecosystems.
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Affiliation(s)
- Ramganesh Selvarajan
- Institute of Deep Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China; Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida Campus, South Africa.
| | - Timothy Sibanda
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Private Bag 3, Wits 2050, Johannesburg, South Africa
| | - Habib Ullah
- Institute of Deep Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Environmental Research Foundation, Westville 3630, South Africa.
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24
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Plessis C, Jeanne T, Dionne A, Vivancos J, Droit A, Hogue R. ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data. PLANTS (BASEL, SWITZERLAND) 2023; 12:3678. [PMID: 37960035 PMCID: PMC10647208 DOI: 10.3390/plants12213678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
The taxonomic assignment of sequences obtained by high throughput amplicon sequencing poses a limitation for various applications in the biomedical, environmental, and agricultural fields. Identifications are constrained by the length of the obtained sequences and the computational processes employed to efficiently assign taxonomy. Arriving at a consensus is often preferable to uncertain identification for ecological purposes. To address this issue, a new tool called "ASVmaker" has been developed to facilitate the creation of custom databases, thereby enhancing the precision of specific identifications. ASVmaker is specifically designed to generate reference databases for allocating amplicon sequencing data. It uses publicly available reference data and generates specific sequences derived from the primers used to create amplicon sequencing libraries. This versatile tool can complete taxonomic assignments performed with pre-trained classifiers from the SILVA and UNITE databases. Moreover, it enables the generation of comprehensive reference databases for specific genes in cases where no directly applicable database exists for taxonomic classification tools.
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Affiliation(s)
- Clément Plessis
- Institut de Recherche et de Développement en Agroenvironnement, Québec, QC G1P 3W8, Canada
- Computational Biology Laboratory, CHU de Québec—Université Laval Research Center, Québec City, QC G1V 4G2, Canada
| | - Thomas Jeanne
- Institut de Recherche et de Développement en Agroenvironnement, Québec, QC G1P 3W8, Canada
- Computational Biology Laboratory, CHU de Québec—Université Laval Research Center, Québec City, QC G1V 4G2, Canada
| | - Antoine Dionne
- Laboratoire d’Expertise et de Diagnostic en Phytoprotection, Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec (MAPAQ), Québec City, QC G1P 3W6, Canada
| | - Julien Vivancos
- Laboratoire d’Expertise et de Diagnostic en Phytoprotection, Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec (MAPAQ), Québec City, QC G1P 3W6, Canada
| | - Arnaud Droit
- Computational Biology Laboratory, CHU de Québec—Université Laval Research Center, Québec City, QC G1V 4G2, Canada
| | - Richard Hogue
- Institut de Recherche et de Développement en Agroenvironnement, Québec, QC G1P 3W8, Canada
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25
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Renzi S, Nenciarini S, Bacci G, Cavalieri D. Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome. MICROBIOME RESEARCH REPORTS 2023; 3:2. [PMID: 38455081 PMCID: PMC10917621 DOI: 10.20517/mrr.2023.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 03/09/2024]
Abstract
Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
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Affiliation(s)
| | | | | | - Duccio Cavalieri
- Correspondence to: Prof. Duccio Cavalieri, Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino 50019, Italy. E-mail:
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26
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Byers AK, Condron LM, O'Callaghan M, Waller L, Dickie IA, Wakelin SA. Plant species identity and plant-induced changes in soil physicochemistry-but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome. FEMS Microbiol Ecol 2023; 99:fiad126. [PMID: 37816673 PMCID: PMC10589101 DOI: 10.1093/femsec/fiad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.
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Affiliation(s)
- Alexa-Kate Byers
- Bioprotection Aotearoa, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Leo M Condron
- Bioprotection Aotearoa, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | | | - Lauren Waller
- Biosecurity New Zealand, Ministry for Primary Industries, 34-38 Bowen Street, PO Box 2526, Wellington 6140, New Zealand
| | - Ian A Dickie
- Bioprotection Aotearoa, School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch 8140, New Zealand
| | - Steve A Wakelin
- Ecology and Environment, Scion Research Ltd, 10 Kyle Street, Riccarton, Christchurch 8011, Canterbury, New Zealand
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27
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Zhang ZF, Mao J, Cai L. Dispersal Limitation Controlling the Assembly of the Fungal Community in Karst Caves. J Fungi (Basel) 2023; 9:1013. [PMID: 37888269 PMCID: PMC10608104 DOI: 10.3390/jof9101013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
As a unique ecosystem, Karst caves harbor an impressive diversity of specific fungi. However, the factors and mechanisms that shape fungal biodiversity in caves remain elusive. In this study, we explored the assembly patterns of fungal communities based on our previous research in eight representative Karst caves in Southwest China. Our results indicated that dispersal limitation plays a crucial role in shaping the overall fungal community as well as specific communities in rock, sediment, and water samples. However, "Undominated" processes contributed more than dispersal limitation in air samples. Interestingly, the dominant assembly processes varied between caves. Consistently, environmental selection had a minor impact on the assembly of fungal communities. Among the examined spatial and environmental variables, latitude, longitude, altitude, and temperature were found to significantly influence fungal communities irrespective of substrate type. These findings provide valuable insights into the ecological factors governing fungal community assembly in Karst caves.
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Affiliation(s)
- Zhi-Feng Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
| | - Jian Mao
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China;
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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28
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Garg SS, Dubey R, Sharma S, Vyas A, Gupta J. Biological macromolecules-based nanoformulation in improving wound healing and bacterial biofilm-associated infection: A review. Int J Biol Macromol 2023; 247:125636. [PMID: 37392924 DOI: 10.1016/j.ijbiomac.2023.125636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
A chronic wound is a serious complication associated with diabetes mellitus and is difficult to heal due to high glucose levels, oxidative stress, and biofilm-associated microbial infection. The structural complexity of microbial biofilm makes it impossible for antibiotics to penetrate the matrix, hence conventional antibiotic therapies became ineffective in clinical settings. This demonstrates an urgent need to find safer alternatives to reduce the prevalence of chronic wound infection associated with microbial biofilm. A novel approach to address these concerns is to inhibit biofilm formation using biological-macromolecule based nano-delivery system. Higher drug loading efficiency, sustained drug release, enhanced drug stability, and improved bioavailability are advantages of employing nano-drug delivery systems to prevent microbial colonization and biofilm formation in chronic wounds. This review covers the pathogenesis, microbial biofilm formation, and immune response to chronic wounds. Furthermore, we also focus on macromolecule-based nanoparticles as wound healing therapies to reduce the increased mortality associated with chronic wound infections.
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Affiliation(s)
- Sourbh Suren Garg
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Rupal Dubey
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Lovely Professional University, Punjab, India
| | - Sandeep Sharma
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Lovely Professional University, Punjab, India
| | - Ashish Vyas
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Jeena Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India.
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29
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Huang T, Wang Y, Wang X, Ma L, Yang X. Discrepant diversity patterns and function of bacterial and fungal communities on an earthquake-prone mountain gradient in Northwest Sichuan, China. Front Microbiol 2023; 14:1217925. [PMID: 37675421 PMCID: PMC10477999 DOI: 10.3389/fmicb.2023.1217925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
Patterns of microbial diversity on elevational gradients have been extensively studied, but little is known about those patterns during the restoration of earthquake-fractured alpine ecosystems. In this study, soil properties, soil enzyme activities, abundance and diversity of soil bacterial and fungal communities at four positions along a 2.6-km elevational gradient in the Snow Treasure Summit National Nature Reserve, located in Pingwu County, Southwest China. Although there were no significant changes in the soil chemical environment, bacterial and fungal communities were significantly different at different elevations. The overall fungal community presented an N-shaped diversity pattern with increasing elevation, while bacterial diversity decreased significantly with elevation. Changes in microbial diversity were associated with soil phosphorus, plant litter, and variations in dominant microbial taxa. Differences in enzyme activities among elevations were regulated by microbial communities, with changes in catalase and acid phosphatase activities mainly controlled by Acidobacteria and Planctomycetaceae bacteria, respectively (catalase: p < 0.001; acid phosphatase: p < 0.01), and those in β-glucosidase, sucrase, and urease activities mainly controlled by fungi. The β-glucosidase and sucrase were both positively correlated with Herpotrichiellaceae, and urease was positively correlated with Sebacinaceae (p < 0.05). These findings contribute to the conservation and management of mountain ecosystems in the face of changing environmental conditions. Further research can delve into the specific interactions between microbial communities, soil properties, and vegetation to gain deeper insights into the intricate ecological dynamics within earthquake-prone mountain ecosystems.
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Affiliation(s)
- Tianzhi Huang
- Key Laboratory of Ecological Safety and Protection of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Yingyan Wang
- College of Resources and Environmental Engineering, Mianyang Normal University, Mianyang, China
| | - Xuemei Wang
- College of Resources and Environmental Engineering, Mianyang Normal University, Mianyang, China
| | - Li Ma
- College of Resources and Environmental Engineering, Mianyang Normal University, Mianyang, China
| | - Xueting Yang
- Research Center of Sichuan County Economy Development, Mianyang Normal University, Mianyang, China
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Van de Voorde D, Díaz-Muñoz C, Hernandez CE, Weckx S, De Vuyst L. Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof. Front Microbiol 2023; 14:1232323. [PMID: 37621398 PMCID: PMC10445768 DOI: 10.3389/fmicb.2023.1232323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The microbiological and metabolic outcomes of good cocoa fermentation practices can be standardized and influenced through the addition of starter culture mixtures composed of yeast and bacterial strains. The present study performed two spontaneous and 10 starter culture-initiated (SCI) cocoa fermentation processes (CFPs) in Costa Rica with local Trinitario cocoa. The yeast strains Saccharomyces cerevisiae IMDO 050523, Hanseniaspora opuntiae IMDO 020003, and Pichia kudriavzevii IMDO 060005 were used to compose starter culture mixtures in combination with the lactic acid bacterium strain Limosilactobacillus fermentum IMDO 0611222 and the acetic acid bacterium strain Acetobacter pasteurianus IMDO 0506386. The microbial community and metabolite dynamics of the cocoa pulp-bean mass fermentation, the metabolite dynamics of the drying cocoa beans, and the volatile organic compound (VOC) profiles of the chocolate production were assessed. An amplicon sequence variant approach based on full-length 16S rRNA gene sequencing instead of targeting the V4 region led to a highly accurate monitoring of the starter culture strains added, in particular the Liml. fermentum IMDO 0611222 strain. The latter strain always prevailed over the background lactic acid bacteria. A similar approach, based on the internal transcribed spacer (ITS1) region of the fungal rRNA transcribed unit, was used for yeast strain monitoring. The SCI CFPs evolved faster when compared to the spontaneous ones. Moreover, the yeast strains applied did have an impact. The presence of S. cerevisiae IMDO 050523 was necessary for successful fermentation of the cocoa pulp-bean mass, which was characterized by the production of higher alcohols and esters. In contrast, the inoculation of H. opuntiae IMDO 020003 as the sole yeast strain led to underfermentation and a poor VOC profile, mainly due to its low competitiveness. The P. kudriavzevii IMDO 060005 strain tested in the present study did not contribute to a richer VOC profile. Although differences in VOCs could be revealed in the cocoa liquors, no significant effect on the final chocolates could be obtained, mainly due to a great impact of cocoa liquor processing during chocolate-making. Hence, optimization of the starter culture mixture and cocoa liquor processing seem to be of pivotal importance.
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Affiliation(s)
- Dario Van de Voorde
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Carlos Eduardo Hernandez
- Laboratorio de Calidad e Innovación Agroalimentaria, Escuela de Ciencias Agrarias, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Tang L, O'Dwyer J, Kimyon Ö, Manefield MJ. Microbial community composition of food waste before anaerobic digestion. Sci Rep 2023; 13:12703. [PMID: 37543702 PMCID: PMC10404229 DOI: 10.1038/s41598-023-39991-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Anaerobic digestion is widely used to process and recover value from food waste. Commercial food waste anaerobic digestion facilities seek improvements in process efficiency to enable higher throughput. There is limited information on the composition of microbial communities in food waste prior to digestion, limiting rational exploitation of the catalytic potential of microorganisms in pretreatment processes. To address this knowledge gap, bacterial and fungal communities in food waste samples from a commercial anaerobic digestion facility were characterised over 3 months. The abundance of 16S rRNA bacterial genes was approximately five orders of magnitude higher than the abundance of the fungal intergenic spacer (ITS) sequence, suggesting the numerical dominance of bacteria over fungi in food waste before anaerobic digestion. Evidence for the mass proliferation of bacteria in food waste during storage prior to anaerobic digestion is presented. The composition of the bacterial community shows variation over time, but lineages within the Lactobacillaceae family are consistently dominant. Nitrogen content and pH are correlated to community variation. These findings form a foundation for understanding the microbial ecology of food waste and provide opportunities to further improve the throughput of anaerobic digestion.
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Affiliation(s)
- Linjie Tang
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Jack O'Dwyer
- School of Chemical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Önder Kimyon
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Michael J Manefield
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
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Sun Y, Xu Y, Zhang J, Bello A, Li X, Liu W, Egbeagu UU, Zhao L, Han Y, Cheng L, Zhang W, Meng Q, Bi R, Zhao M, Liu X, Sun L, Gai Z, Shi S, Jong C, Xu X. Investigation of underlying links between nitrogen transformation and microorganisms' network modularity in the novel static aerobic composting of dairy manure by "stepwise verification interaction analysis". THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163674. [PMID: 37100152 DOI: 10.1016/j.scitotenv.2023.163674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/21/2023] [Accepted: 04/18/2023] [Indexed: 06/03/2023]
Abstract
Conventional composting is a viable method treating agricultural solid waste, and microorganisms and nitrogen transformation are the two major components of this proces. Unfortunately, conventional composting is time-consuming and laborious, and limited efforts have been made to mitigate these problems. Herein, a novel static aerobic composting technology (NSACT) was developed and employed for the composting of cow manure and rice straw mixtures. During the composting process, physicochemical parameters were analyzed to evaluate the quality of compost products, and microbial abundance dynamics were determined using high-throughput sequencing technique. The results showed that NSACT achieved compost maturity within 17 days as the thermophilic stage (≥55 °C) lasted for 11 days. GI, pH, and C/N were 98.71 %, 8.38, and 19.67 in the top layer, 92.32 %, 8.24, and 22.38 in the middle layer, 102.08 %, 8.33, and 19.95 in the bottom layer. These observations indicate compost products maturated and met the requirements of current legislation. Compared with fungi, bacterial communities dominated NSACT composting system. Based on the stepwise verification interaction analysis (SVIA), the novel combination utilization of multiple statistical analyses (Spearman, RDA/CCA, Network modularity, and Path analyses), bacterial genera Norank Anaerolineaceae (-0.9279*), norank Gemmatimonadetes (1.1959*), norank Acidobacteria (0.6137**) and unclassified Proteobacteria (-0.7998*), and fungi genera Myriococcum thermophilum (-0.0445), unclassified Sordariales (-0.0828*), unclassified Lasiosphaeriaceae (-0.4174**), and Coprinopsis calospora (-0.3453*) were the identified key microbial taxa affecting NH4+-N, NO3--N, TKN and C/N transformation in the NSACT composting matrix respectively. This work revealed that NSACT successfully managed cow manure-rice straw wastes and significantly shorten the composting period. Interestingly, most microorganisms observed in this composting matrix acted in a synergistic manner, promoting nitrogen transformation.
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Affiliation(s)
- Yu Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yonghui Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Jining Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China; College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiang Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Wanying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ugochi Uzoamaka Egbeagu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Liyan Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yue Han
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lijun Cheng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Wenhao Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ruixin Bi
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mingming Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xinda Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Zhaoxue Gai
- School of Public Administration and Law, Northeast Agricultural University, Harbin 150030, China
| | - Shuai Shi
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Chol Jong
- College of Agriculture, Kimjewon Haeju University of Agriculture, Haeju City, Hwanghae South Province 999093, Republic of Korea
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China.
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Belair M, Pensec F, Jany JL, Le Floch G, Picot A. Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding. PLANTS (BASEL, SWITZERLAND) 2023; 12:2383. [PMID: 37376008 DOI: 10.3390/plants12122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.
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Affiliation(s)
- Marie Belair
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Flora Pensec
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Jean-Luc Jany
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Gaétan Le Floch
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Adeline Picot
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
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Gugliucci W, Cirillo V, Maggio A, Romano I, Ventorino V, Pepe O. Valorisation of hydrothermal liquefaction wastewater in agriculture: effects on tobacco plants and rhizosphere microbiota. FRONTIERS IN PLANT SCIENCE 2023; 14:1180061. [PMID: 37342148 PMCID: PMC10277691 DOI: 10.3389/fpls.2023.1180061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023]
Abstract
Industrial wastewater obtained from hydrothermal liquefaction (HTL-WW) of food wastes for biofuels production could represent a source of crop nutrients since it is characterized by a high amount of organic and inorganic compounds. In the present work, the potential use of HTL-WW as irrigation water for industrial crops was investigated. The composition of the HTL-WW was rich in nitrogen, phosphorus, and potassium with high level of organic carbon. A pot experiment with Nicotiana tabacum L. plants was conducted using diluted wastewater to reduce the concentration of some chemical elements below the official accepted threshold values. Plants were grown in the greenhouse under controlled conditions for 21 days and irrigated with diluted HTL-WW every 24 hours. Soils and plants were sampled every seven days to evaluate, over time, the effect of wastewater irrigation both on soil microbial populations, through high-throughput sequencing, and plant growth parameters, through the measurement of different biometric indices. Metagenomic results highlighted that, in the HTL-WW treated rhizosphere, the microbial populations shifted via their mechanisms of adaptation to the new environmental conditions, establishing a new balance among bacterial and fungal communities. Identification of microbial taxa occurring in the rhizosphere of tobacco plants during the experiment highlighted that the HTL-WW application improved the growth of Micrococcaceae, Nocardiaceae and Nectriaceae, which included key species for denitrification, organic compounds degradation and plant growth promotion. As a result, irrigation with HTL-WW improved the overall performance of tobacco plants which showed higher leaf greenness and increased number of flowers compared to irrigated control plants. Overall, these results demonstrate the potential feasibility of using of HTL-WW in irrigated agriculture.
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Affiliation(s)
- Wanda Gugliucci
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy
| | - Valerio Cirillo
- Department of Agricultural Sciences, Division of Plant Biology and Crop Science, University of Naples Federico II, Naples, Italy
| | - Albino Maggio
- Department of Agricultural Sciences, Division of Plant Biology and Crop Science, University of Naples Federico II, Naples, Italy
| | - Ida Romano
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Olimpia Pepe
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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35
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Varela C, Alperstein L, Sundstrom J, Solomon M, Brady M, Borneman A, Jiranek V. A special drop: Characterising yeast isolates associated with fermented beverages produced by Australia's indigenous peoples. Food Microbiol 2023; 112:104216. [PMID: 36906316 DOI: 10.1016/j.fm.2023.104216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Way-a-linah, an alcoholic beverage produced from the fermented sap of Eucalyptus gunnii, and tuba, a fermented drink made from the syrup of Cocos nucifera fructifying bud, are two of several fermented beverages produced by Australian Aboriginal and Torres Strait people. Here we describe the characterisation of yeast isolates from samples associated with the fermentation of way-a-linah and tuba. Microbial isolates were obtained from two different geographical locations in Australia - the Central Plateau in Tasmania, and Erub Island in the Torres Strait. While Hanseniaspora species and Lachancea cidri were the most abundant species in Tasmania, Candida species were the most abundant in Erub Island. Isolates were screened for tolerance to stress conditions found during the production of fermented beverages and for enzyme activities relevant to the appearance, aroma and flavour of these beverages. Based on screening results, eight isolates were evaluated for their volatile profile during the fermentation of wort, apple juice and grape juice. Diverse volatile profiles were observed for beers, ciders and wines fermented with different isolates. These findings reveal the potential of these isolates to produce fermented beverages with unique aroma and flavour profiles and highlight the vast microbial diversity associated with fermented beverages produced by Australia's Indigenous peoples.
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Affiliation(s)
- Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia; Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia.
| | - Lucien Alperstein
- Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Joanna Sundstrom
- Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Mark Solomon
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia
| | - Maggie Brady
- Centre for Aboriginal Economic Policy Research, College of Arts and Social Sciences, The Australian National University, Acton, ACT 2601, Australia
| | - Anthony Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia; Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Vladimir Jiranek
- Department of Wine Science, The University of Adelaide, Glen Osmond, SA 5064, Australia
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36
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Zhang L, Li J, Wang Z, Zhang D, Liu H, Wang J, Wu F, Wang X, Zhou X. Litter mixing promoted decomposition and altered microbial community in common bean root litter. BMC Microbiol 2023; 23:148. [PMID: 37217839 DOI: 10.1186/s12866-023-02871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Decomposition of plant litter is a key driver of carbon and nutrient cycling in terrestrial ecosystems. Mixing litters of different plant species may alter the decomposition rate, but its effect on the microbial decomposer community in plant litter is not fully understood. Here, we tested the effects of mixing with maize (Zea mays L.) and soybean [Glycine max (Linn.) Merr.] stalk litters on the decomposition and microbial decomposer communities of common bean (Phaseolus vulgaris L.) root litter at the early decomposition stage in a litterbag experiment. RESULTS Mixing with maize stalk litter, soybean stalk litter, and both of these litters increased the decomposition rate of common bean root litter at 56 day but not 14 day after incubation. Litter mixing also increased the decomposition rate of the whole liter mixture at 56 day after incubation. Amplicon sequencing found that litter mixing altered the composition of bacterial (at 56 day after incubation) and fungal communities (at both 14 and 56 day after incubation) in common bean root litter. Litter mixing increased the abundance and alpha diversity of fungal communities in common bean root litter at 56 day after incubation. Particularly, litter mixing stimulated certain microbial taxa, such as Fusarium, Aspergillus and Stachybotrys spp. In addition, a pot experiment with adding litters in the soil showed that litter mixing promoted growth of common bean seedlings and increased soil nitrogen and phosphorus contents. CONCLUSIONS This study showed that litter mixing can promote the decomposition rate and cause shifts in microbial decomposer communities, which may positively affect crop growth.
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Affiliation(s)
- Linlin Zhang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Zhilin Wang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Dinghong Zhang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Hui Liu
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Jia Wang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Fengzhi Wu
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Xue Wang
- Northeast Agricultural University Library, Northeast Agricultural University, Harbin, China.
| | - Xingang Zhou
- Department of Horticulture, Northeast Agricultural University, Harbin, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.
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Yue R, Chen H, Xu X, Xia Y, Sun Y, Xia M, Xia D, Sun B. Maternal and infantile gut mycobiome during the weaning period in free ranging Tibetan macaques ( Macaca thibetana). Ecol Evol 2023; 13:e10108. [PMID: 37214608 PMCID: PMC10196218 DOI: 10.1002/ece3.10108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Gut microbiome is critical to the health of mammals. Many previous studies have revealed the gut bacterial microbiomes of mother and infant changed significantly during the weaning period. However, little is known concerning the gut mycobiome of wild primates. Here, we examined the variations on gut mycobiome between weaning and post-weaning for both mother and infant in wild-living Tibetan macaques (Macaca thibetana). Our results showed that the gut mycobiomes of mother and infant were dominated by two phyla Ascomycota and Basidiomycota. For both mother and infant, the ASV richness of gut mycobiome remained relatively steady from weaning to post-weaning periods, while the Shannon indexes increased significant in weaning compared to post-weaning periods. However, no significant difference between mother and infant ASV richness and Shannon indexes during weaning and post-weaning periods respectively. Compared to mothers, we found that much more known taxa of gut fungi were enriched in weaning or post-weaning periods of infants. In particular, we found that the dominant genus Aspergillus was enriched in infants during weaning period. Furthermore, we found that the relative abundance of plant pathogens were significantly higher in the post-weaning period than in the weaning period for infants. Our results indicated that weaning events could affect the gut mycobiome significantly for both mothers and infant in Tibetan macaques, which had a stronger effect on the gut mycobiome of infant monkeys than on their mothers.
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Affiliation(s)
- Ran Yue
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Huijuan Chen
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Xiaojuan Xu
- School of Life SciencesHefei Normal UniversityHefeiChina
| | - Yingna Xia
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Yu Sun
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Mengyi Xia
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
| | - Dongpo Xia
- School of Life SciencesAnhui UniversityHefeiChina
| | - Binghua Sun
- School of Resource and Environmental EngineeringAnhui UniversityHefeiChina
- International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral EcologyAnhui UniversityHefeiChina
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Gounari Z, Bonatsou S, Ferrocino I, Cocolin L, Papadopoulou OS, Panagou EZ. Exploring yeast diversity of dry-salted naturally black olives from Greek retail outlets with culture dependent and independent molecular methods. Int J Food Microbiol 2023; 398:110226. [PMID: 37120943 DOI: 10.1016/j.ijfoodmicro.2023.110226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
In the present study, the physicochemical (pH, water activity, moisture content, salt concentration) classical plate counts (total viable counts, yeasts, lactic acid bacteria, Staphylococcus aureus, Pseudomonas spp., Enterobacteriaceae) and amplicon sequencing of naturally black dry-salted olives obtained from different retail outlets of the Greek market were investigated. According to the results, the values of the physicochemical characteristics presented great variability among the samples. Specifically, pH and water activity (aw) values ranged between 4.0 and 5.0, as well as between 0.58 and 0.91, respectively. Moisture content varied between 17.3 and 56.7 % (g Η2Ο/100 g of olive pulp), whereas salt concentration ranged from 5.26 to 9.15 % (g NaCl/100 g of olive pulp). No lactic acid bacteria, S. aureus, Pseudomonas spp. and Enterobacteriaceae were detected. The mycobiota consisted of yeasts that were further characterized and identified by culture-dependent (rep-PCR, ITS-PCR, and RFLP) and amplicon target sequencing (ATS). Pichia membranifaciens, Candida sorbosivorans, Citeromyces nyonsensis, Candida etchelsii, Wickerhamomyces subpelliculosus, Candida apicola, Wickerhamomyces anomalus, Torulaspora delbrueckii and Candida versatilis were the dominant species according to ITS sequencing (culture-dependent), while ATS revealed the dominance of C. etchelsii, Pichia triangularis, P. membranifaciens, and C. versatilis among samples. The results of this study demonstrated considerable variability in quality attributes among the different commercial samples of dry-salted olives, reflecting a lack of standardization in the processing of this commercial style. However, the majority of the samples were characterized by satisfactory microbiological and hygienic quality and complied with the requirements of the trade standard for table olives of the International Olive Council (IOC) for this processing style in terms of salt concentration. In addition, the diversity of yeast species was elucidated for the first time in commercially available products, increasing our knowledge on the microbial ecology of this traditional food. Further investigation into the technological and multifunctional traits of the dominant yeast species may result in better control during dry-salting and enhance the quality and shelf-life of the final product.
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Affiliation(s)
- Zoe Gounari
- Agricultural University of Athens, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Laboratory of Microbiology and Biotechnology of Foods, Iera Odos 75, Athens 11855, Greece
| | - Stamatoula Bonatsou
- Agricultural University of Athens, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Laboratory of Microbiology and Biotechnology of Foods, Iera Odos 75, Athens 11855, Greece
| | - Ilario Ferrocino
- University of Turin, Department of Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, Torino, Italy
| | - Luca Cocolin
- University of Turin, Department of Agricultural, Forestry and Food Sciences, Largo Paolo Braccini 2, 10095 Grugliasco, Torino, Italy
| | - Olga S Papadopoulou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization DIMITRA, S. Venizelou 1, Lycovrissi 14123, Attiki, Greece
| | - Efstathios Z Panagou
- Agricultural University of Athens, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Laboratory of Microbiology and Biotechnology of Foods, Iera Odos 75, Athens 11855, Greece.
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Kosawang C, Børja I, Herrero ML, Nagy NE, Nielsen LR, Solheim H, Timmermann V, Hietala AM. Fungal succession in decomposing ash leaves colonized by the ash dieback pathogen Hymenoscyphus fraxineus or its harmless relative Hymenoscyphus albidus. Front Microbiol 2023; 14:1154344. [PMID: 37125194 PMCID: PMC10140306 DOI: 10.3389/fmicb.2023.1154344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction The ascomycete Hymenoscyphus fraxineus, originating from Asia, is currently threatening common ash (Fraxinus excelsior) in Europe, massive ascospore production from the saprotrophic phase being a key determinant of its invasiveness. Methods To consider whether fungal diversity and succession in decomposing leaf litter are affected by this invader, we used ITS-1 metabarcoding to profile changes in fungal community composition during overwintering. The subjected ash leaf petioles, collected from a diseased forest and a healthy ash stand hosting the harmless ash endophyte Hymenoscyphus albidus, were incubated in the forest floor of the diseased stand between October 2017 and June 2018 and harvested at 2-3-month intervals. Results Total fungal DNA level showed a 3-fold increase during overwintering as estimated by FungiQuant qPCR. Petioles from the healthy site showed pronounced changes during overwintering; ascomycetes of the class Dothideomycetes were predominant after leaf shed, but the basidiomycete genus Mycena (class Agaricomycetes) became predominant by April, whereas H. albidus showed low prevalence. Petioles from the diseased site showed little change during overwintering; H. fraxineus was predominant, while Mycena spp. showed increased read proportion by June. Discussion The low species richness and evenness in petioles from the diseased site in comparison to petioles from the healthy site were obviously related to tremendous infection pressure of H. fraxineus in diseased forests. Changes in leaf litter quality, owing to accumulation of host defense phenolics in the pathogen challenged leaves, and strong saprophytic competence of H. fraxineus are other factors that probably influence fungal succession. For additional comparison, we examined fungal community structure in petioles collected in the healthy stand in August 2013 and showing H. albidus ascomata. This species was similarly predominant in these petioles as H. fraxineus was in petioles from the diseased site, suggesting that both fungi have similar suppressive effects on fungal richness in petiole/rachis segments they have secured for completion of their life cycle. However, the ability of H. fraxineus to secure the entire leaf nerve system in diseased forests, in opposite to H. albidus, impacts the general diversity and successional trajectory of fungi in decomposing ash petioles.
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Affiliation(s)
- Chatchai Kosawang
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Isabella Børja
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
- Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Maria-Luz Herrero
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Nina E. Nagy
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Lene R. Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg, Denmark
| | - Halvor Solheim
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Volkmar Timmermann
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Ari M. Hietala
- Norwegian Institute of Bioeconomy Research (NIBIO), Steinkjer, Norway
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Ghouili E, Abid G, Hogue R, Jeanne T, D'Astous-Pagé J, Sassi K, Hidri Y, M'Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Muhovski Y. Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley ( Hordeum vulgare L.) Field. BIOLOGY 2023; 12:biology12040546. [PMID: 37106747 PMCID: PMC10135526 DOI: 10.3390/biology12040546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023]
Abstract
Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), Hammam-Lif 2050, PB 901, Tunisia
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), Hammam-Lif 2050, PB 901, Tunisia
| | - Richard Hogue
- Microbial Ecology Laboratory, Research and Development Institute for the Agri-Environment (IRDA), Einstein Street 2700, Québec City, QC G1P 3W8, Canada
| | - Thomas Jeanne
- Microbial Ecology Laboratory, Research and Development Institute for the Agri-Environment (IRDA), Einstein Street 2700, Québec City, QC G1P 3W8, Canada
| | - Joël D'Astous-Pagé
- Microbial Ecology Laboratory, Research and Development Institute for the Agri-Environment (IRDA), Einstein Street 2700, Québec City, QC G1P 3W8, Canada
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène 1082, BP 43, Tunisia
| | - Yassine Hidri
- Olive Tree Institute, Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Cité Mahragène 1082, BP 208, Tunisia
| | - Hatem Cheikh M'Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), University of Carthage, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd., College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79106, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), Hammam-Lif 2050, PB 901, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Hammam-Lif 2050, BP 901, Tunisia
| | - Jouhaina Riahi
- Technical Center for Organic Agriculture, Chott Mariem, Sousse 4042, BP 54, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, 5030 Gembloux, 234 BP, Belgium
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, 5030 Gembloux, 234 BP, Belgium
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41
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Liu H, Yao J, Liu B, Li M, Liu J, Jiang S, Yu W, Zhao Y, Duran R. Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161133. [PMID: 36566868 DOI: 10.1016/j.scitotenv.2022.161133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.
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Affiliation(s)
- Houquan Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China.
| | - Bang Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
| | - Miaomiao Li
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jianli Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shun Jiang
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Wenjing Yu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Yuhui Zhao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
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Metagenomes from Soils along an Agricultural Transect in Ulster County, New York. Microbiol Resour Announc 2023; 12:e0101522. [PMID: 36779724 PMCID: PMC10019288 DOI: 10.1128/mra.01015-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Many modern farming practices negatively impact ecosystems on the local and global scales. Here, we assessed the taxonomic structures of 48 soil microbial communities along an agricultural transect using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. We further characterized the functional structures of a subsample of 12 microbiomes using whole-genome sequencing.
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43
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Verdier-Metz I, Delbès C, Bouchon M, Rifa E, Theil S, Chaucheyras-Durand F, Chevaux E, Dunière L, Chassard C. Dietary Live Yeast Supplementation Influence on Cow’s Milk, Teat and Bedding Microbiota in a Grass-Diet Dairy System. Microorganisms 2023; 11:microorganisms11030673. [PMID: 36985246 PMCID: PMC10053648 DOI: 10.3390/microorganisms11030673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/09/2023] Open
Abstract
The supplementation of animal feed with microbial additives remains questioning for the traditional or quality label raw milk cheeses with regard to microbial transfer to milk. We evaluated the effect of dietary administration of live yeast on performance and microbiota of raw milk, teat skin, and bedding material of dairy cows. Two balanced groups of cows (21 primiparous 114 ± 24 DIM, 18 multiparous 115 ± 33 DIM) received either a concentrate supplemented with Saccharomyces cerevisiae CNCM I-1077 (1 × 1010 CFU/d) during four months (LY group) or no live yeast (C group). The microbiota in individual milk samples, teat skins, and bedding material were analysed using culture dependent techniques and high-throughput amplicon sequencing. The live yeast supplementation showed a numerical increase on body weight over the experiment and there was a tendency for higher milk yield for LY group. A sequence with 100% identity to that of the live yeast was sporadically found in fungal amplicon datasets of teat skin and bedding material but never detected in milk samples. The bedding material and teat skin from LY group presented a higher abundance of Pichia kudriavzevii reaching 53% (p < 0.05) and 10% (p < 0.05) respectively. A significant proportion of bacterial and fungal ASVs shared between the teat skin and the milk of the corresponding individual was highlighted.
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Affiliation(s)
- Isabelle Verdier-Metz
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Céline Delbès
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Matthieu Bouchon
- Université Clermont Auvergne, INRAE, UE 1414 Herbipôle, Domaine de la Borie, 15190 Marcenat, France
| | - Etienne Rifa
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Sébastien Theil
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
| | - Frédérique Chaucheyras-Durand
- Lallemand SAS, 19 rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Eric Chevaux
- Lallemand SAS, 19 rue des Briquetiers, 31702 Blagnac, France
| | - Lysiane Dunière
- Lallemand SAS, 19 rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Site de Theix, 63122 Saint-Genès-Champanelle, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, 20 Côte de Reyne, 15000 Aurillac, France
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44
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Calasso M, Marzano M, Caponio GR, Celano G, Fosso B, Calabrese FM, De Palma D, Vacca M, Notario E, Pesole G, De Angelis M, De Leo F. Shelf-life extension of leavened bakery products by using bio-protective cultures and type-III sourdough. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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45
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Meng Q, Liu S, Guo Y, Hu Y, Yu Z, Bello A, Wang Z, Xu W, Xu X. The co-occurrence network patterns and keystone species of microbial communities in cattle manure-corn straw composting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:20265-20276. [PMID: 36251182 DOI: 10.1007/s11356-022-23599-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Microbes often form complex ecological networks in various habitats. Co-occurrence network analysis allows exploring the complex community interactions beyond the community diversities. This study explores the interspecific relationships within and between bacterial and fungal communities during composting of cow manure using co-occurrence network analysis. Furthermore, the keystone taxa that potentially exert a considerable impact on the microbiome were revealed by network analysis. The networks in the present study harbored more positive links. Specifically, the interactions/coupling within bacterial communities was tighter and the response to changes in external environmental conditions was more quickly during the composting process, while the fungal network had a better buffer capacity for changes in external environmental conditions. Interestingly, this result was authenticated in the bacterial-fungal (BF) network and the Mantel test of major modules and environmental variables. More than that, the Zi-Pi plot revealed that the keystone taxa including "module hubs" and "connectors" were all detected in these networks, which could prevent the dissociation of modules and networks.
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Affiliation(s)
- Qingxin Meng
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Shuang Liu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yue Guo
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Yunlong Hu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Zhidan Yu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Weihui Xu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, 161006, China
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
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Martiniuk JT, Hamilton J, Dodsworth T, Measday V. Grape-associated fungal community patterns persist from berry to wine on a fine geographical scale. FEMS Yeast Res 2023; 23:6967134. [PMID: 36592956 PMCID: PMC9876423 DOI: 10.1093/femsyr/foac067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/30/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Wine grape fungal community composition is influenced by abiotic factors including geography and vintage. Compositional differences may correlate with different wine metabolite composition and sensory profiles, suggesting a microbial role in the shaping of a wine's terroir, or regional character. While grape and wine-associated fungal community composition has been studied extensively at a regional and sub-regional scale, it has not been explored in detail on fine geographical scales over multiple harvests. Over two years, we examined the fungal communities on Vitis Vinifera cv. Pinot noir grape berry surfaces, in crushed grapes, and in lab spontaneous fermentations from three vineyards within a < 1 km radius in Canada's Okanagan Valley wine region. We also evaluated the effect of winery environment exposure on fungal community composition by sampling grapes crushed and fermented in the winery at commercial scale. Spatiotemporal community structure was evident among grape berry surface, crushed grape and fermentation samples, with each vineyard exhibiting a distinct fungal community signature. Crushed grape fungal populations were richer in fermentative yeast species compared to grape berry surface fungal populations. Our study suggests that, as on a regional level, fungal populations may contribute to fine-scale -terroir,' with significant implications for single-vineyard wines.
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Affiliation(s)
- Jonathan T Martiniuk
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jonah Hamilton
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Thomas Dodsworth
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Vivien Measday
- Corresponding author: Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada. E-mail:
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Zheng W, Hu L, Chen Z, Tang J, Pan Y, Yan W, Chen X, Peng Y, Chen L. Effects of perfluorinated compounds homologues on chemical property, microbial composition, richness and diversity of urban forest soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114458. [PMID: 38321677 DOI: 10.1016/j.ecoenv.2022.114458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 02/08/2024]
Abstract
Perfluorinated compounds (PFCs), as an important class of new persistent organic pollutants, are widely distributed in the environment. Yet the effects of different types and concentrations of PFCs on soil microbial community in urban forest ecosystems are remain uncertain. Here, two typical PFCs, perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS), were selected to carry out a pot experiment in greenhouse with singly and joint treatment at different concentrations, to examine their effects on composition and diversity of soil microorganisms and availability of soil macronutrients by using high-throughput Illumina sequencing approach. The results showed both PFOA and PFOS application significantly increased soil NO3--N and NH4+-N content, but did not alter total phosphorus content, compared to the control check (CK) treatments. Total potassium content was reduced in PFOA treatments but increased in PFOS and PFOA×PFOS treatments. The most dominant bacterial phylum was Chloroflexi in low and medium PFCs concentrations and the CK treatments, but it was switched to Acidobacteria in high concentrations. No obvious change was detected for the composition of the dominant fungi community in PFCs treatments compared to the CK treatments. With the increase of PFCs concentrations, soil bacterial richness decreased but its diversity increased, whereas the richness and diversity of fungal community usually decreased. Redundancy analyses revealed that soil fungal community was more sensitive to PFCs pollutants than soil bacterial communities. Further data analysis revealed by structural equation model (SEM) that the PFCs exposed for 60 days indirectly affects the diversity and richness of soil bacteria and fungi by directly affecting NO3--N and NH4+-N content. The results suggested the concentration of PFCs pollutants played a primary role in determining the composition, richness and diversity of forest soil microbial communities.
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Affiliation(s)
- Wei Zheng
- Faculty of Life Science and Technology, Central South University of Forestry & Technology, Changsha 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China
| | - Lei Hu
- Faculty of Life Science and Technology, Central South University of Forestry & Technology, Changsha 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China
| | - Zekai Chen
- Faculty of Life Science and Technology, Central South University of Forestry & Technology, Changsha 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China
| | - Jun Tang
- Faculty of Life Science and Technology, Central South University of Forestry & Technology, Changsha 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China
| | - Yuliang Pan
- Faculty of Life Science and Technology, Central South University of Forestry & Technology, Changsha 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China.
| | - Wende Yan
- Faculty of Life Science and Technology, Central South University of Forestry & Technology, Changsha 410004, China; National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Changsha 410004, China; Laboratory of Urban Forest Ecology of Hunan Province, Changsha, Hunan 410004, China
| | - Xiaoyong Chen
- College of Arts and Science, Governors State University, University Park, IL 60484, USA
| | - Yuanying Peng
- Natural Sciences Division, College of DuPage, Glen Ellyn, IL 60137, USA
| | - Lijun Chen
- Faculty of Forestry, Central South University of Forestry & Technology, Changsha 410004, China.
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Decadt H, Weckx S, De Vuyst L. The rotation of primary starter culture mixtures results in batch-to-batch variations during Gouda cheese production. Front Microbiol 2023; 14:1128394. [PMID: 36876114 PMCID: PMC9978159 DOI: 10.3389/fmicb.2023.1128394] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023] Open
Abstract
Industrial production of Gouda cheeses mostly relies on a rotated use of different mixed-strain lactic acid bacteria starter cultures to avoid phage infections. However, it is unknown how the application of these different starter culture mixtures affect the organoleptic properties of the final cheeses. Therefore, the present study assessed the impact of three different starter culture mixtures on the batch-to-batch variations among Gouda cheeses from 23 different batch productions in the same dairy company. Both the cores and rinds of all these cheeses were investigated after 36, 45, 75, and 100 weeks of ripening by metagenetics based on high-throughput full-length 16S rRNA gene sequencing accompanied with an amplicon sequence variant (ASV) approach as well as metabolite target analysis of non-volatile and volatile organic compounds. Up to 75 weeks of ripening, the acidifying Lactococcus cremoris and Lactococcus lactis were the most abundant bacterial species in the cheese cores. The relative abundance of Leuconostoc pseudomesenteroides was significantly different for each starter culture mixture. This impacted the concentrations of some key metabolites, such as acetoin produced from citrate, and the relative abundance of non-starter lactic acid bacteria (NSLAB). Cheeses with the least Leuc. pseudomesenteroides contained more NSLAB, such as Lacticaseibacillus paracasei that was taken over by Tetragenococcus halophilus and Loigolactobacillus rennini upon ripening time. Taken together, the results indicated a minor role of leuconostocs in aroma formation but a major impact on the growth of NSLAB. The relative abundance of T. halophilus (high) and Loil. rennini (low) increased with ripening time from rind to core. Two main ASV clusters of T. halophilus could be distinguished, which were differently correlated with some metabolites, both beneficial (regarding aroma formation) and undesirable ones (biogenic amines). A well-chosen T. halophilus strain could be a candidate adjunct culture for Gouda cheese production.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Keuschnig C, Martins JMF, Navel A, Simonet P, Larose C. Micro-fractionation shows microbial community changes in soil particles below 20 μm. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1091773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IntroductionMicro-scale analysis of microbes in soil is essential to the overall understanding of microbial organization, interactions, and ecosystem functioning. Soil fractionation according to its aggregated structure has been used to access microbial habitats. While bacterial communities have been extensively described, little is known about the fungal communities at scales relevant to microbial interactions.MethodsWe applied a gentle soil fractionation method to preserve stable aggregated structures within the range of micro-aggregates and studied fungal and bacterial communities as well as nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size fractions (PSFs; >250 μm, 250–63 μm, 63–20 μm, 20–2 μm, <2 μm, and supernatant).ResultsOverall bacterial and fungal community structures changed in PSFs below 20 μm. The relative abundance of Basidiomycota decreased with decreasing particle size over the entire measure range, while Ascomycota showed an increase and Mucoromycota became more prominent in particles below 20 μm. Bacterial diversity was found highest in the < 2 μm fraction, but only a few taxa were washed-off during the procedure and found in supernatant samples. These taxa have been associated with exopolysaccharide production and biofilm formation (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium, and Variovorax). The potential for nitrogen reduction was found elevated in bigger aggregates.DiscussionThe observed changes below 20 μm particle are in line with scales where microbes operate and interact, highlighting the potential to focus on little researched sub-fractions of micro-aggregates. The applied method shows potential for use in studies focusing on the role of microbial biofilms in soil and might also be adapted to research various other soil microbial functions. Technical advances in combination with micro-sampling methods in soil promise valuable output in soil studies when particles below 20 μm are included.
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Tourova TP, Sokolova DS, Semenova EM, Kireev DM, Laptev AB, Nazina TN. Composition of Microbial Fouling on the Surface of Plastics and Steel Exposed in a Pond at a Solid Waste Landfill. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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