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Rodrigues JTD, Margalho LP, Pia AKR, Sierra H, Tavares L, Marquezini MG, Noronha MF, Cabral L, Junior WJFL, Sant'Ana AS. Comprehensive dynamics of bacterial and fungal diversity throughout concentrated chicken broth processing: Integrating culture-dependent and independent techniques. Int J Food Microbiol 2024; 424:110852. [PMID: 39141974 DOI: 10.1016/j.ijfoodmicro.2024.110852] [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: 04/09/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024]
Abstract
This study presents comprehensive insights into the microbiological profile across all concentrated chicken broth processing stages, utilizing a combination of amplicon sequencing based on metataxonomic and culturing techniques. Samples were systematically collected throughout the production chain, with each batch yielding 10 samples per day across eight different dates. These samples underwent thorough analysis, including 16S rRNA and ITS sequencing (n = 30), culture-dependent microbiological tests (n = 40), and physical-chemical characterization (n = 10). Culturing analysis revealed the absence of Listeria monocytogenes and Salmonella spp. at any stage of processing, counts of various microorganisms such as molds, yeasts, Enterobacteria, and others remained below detection limits. Notably, spore counts of selected bacterial groups were observed post-processing, indicating the persistence of certain species, including Bacillus cereus and Clostridium perfringens, albeit in low counts. Furthermore, the study identified a diverse array of bacterial and fungal species throughout the processing chain, with notable occurrence of spore-forming bacteria. The presence of spore-forming bacteria in the final product, despite thermal processing, suggests the need for enhanced strategies to mitigate their introduction and persistence in the processing premises. Thus, this study offers valuable insights into microbial dynamics and diversity through processing concentrated chicken broth.
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Affiliation(s)
- José T D Rodrigues
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Larissa P Margalho
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Arthur K R Pia
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Héctor Sierra
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Louise Tavares
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Míriam G Marquezini
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Melline Fontes Noronha
- Research Informatics Core, Research Resource Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Lucélia Cabral
- Institute of Biological Sciences, University of Brasília, Brasília, DF, Brazil
| | | | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil.
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2
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Romeijn L, Bernatavicius A, Vu D. MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences. Mol Ecol Resour 2024; 24:e14006. [PMID: 39152642 DOI: 10.1111/1755-0998.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/12/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
Efficient and accurate classification of DNA barcode data is crucial for large-scale fungal biodiversity studies. However, existing methods are either computationally expensive or lack accuracy. Previous research has demonstrated the potential of deep learning in this domain, successfully training neural networks for biological sequence classification. We introduce the MycoAI Python package, featuring various deep learning models such as BERT and CNN tailored for fungal Internal Transcribed Spacer (ITS) sequences. We explore different neural architecture designs and encoding methods to identify optimal models. By employing a multi-head output architecture and multi-level hierarchical label smoothing, MycoAI effectively generalizes across the taxonomic hierarchy. Using over 5 million labelled sequences from the UNITE database, we develop two models: MycoAI-BERT and MycoAI-CNN. While we emphasize the necessity of verifying classification results by AI models due to insufficient reference data, MycoAI still exhibits substantial potential. When benchmarked against existing classifiers such as DNABarcoder and RDP on two independent test sets with labels present in the training dataset, MycoAI models demonstrate high accuracy at the genus and higher taxonomic levels, with MycoAI-CNN being the fastest and most accurate. In terms of efficiency, MycoAI models can classify over 300,000 sequences within 5 min. We publicly release the MycoAI models, enabling mycologists to classify their ITS barcode data efficiently. Additionally, MycoAI serves as a platform for developing further deep learning-based classification methods. The source code for MycoAI is available under the MIT Licence at https://github.com/MycoAI/MycoAI.
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Affiliation(s)
- Luuk Romeijn
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, Netherlands
| | - Andrius Bernatavicius
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, Netherlands
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Duong Vu
- Westerdijk Fungal Biodiveristy Institute, Utrecht, Netherlands
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3
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Brtnicky M, Pecina V, Kucerik J, Hammerschmiedt T, Mustafa A, Kintl A, Sera J, Koutny M, Baltazar T, Holatko J. Biodegradation of poly-3-hydroxybutyrate after soil inoculation with microbial consortium: Soil microbiome and plant responses to the changed environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174328. [PMID: 38945229 DOI: 10.1016/j.scitotenv.2024.174328] [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: 02/07/2024] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
Biodegradable plastics play a vital role in addressing global plastics disposal challenges. Poly-3-hydroxybutyrate (P3HB) is a biodegradable bacterial intracellular storage polymer with substantial usage potential in agriculture. Poly-3-hydroxybutyrate and its degradation products are non-toxic; however, previous studies suggest that P3HB biodegradation negatively affects plant growth because the microorganisms compete with plants for nutrients. One possible solution to this issue could be inoculating soil with a consortium of plant growth-promoting and N-fixing microorganisms. To test this hypothesis, we conducted a pot experiment using lettuce (Lactuca sativa L. var. capitata L.) grown in soil amended with two doses (1 % and 5 % w/w) of P3HB and microbial inoculant (MI). We tested five experimental variations: P3HB 1 %, P3HB 1 % + MI, P3HB 5 %, P3HB 5 % + MI, and MI, to assess the impact of added microorganisms on plant growth and P3HB biodegradation. The efficient P3HB degradation, which was directly dependent on the amount of bioplastics added, was coupled with the preferential utilization of P3HB as a carbon (C) source. Due to the increased demand for nutrients in P3HB-amended soil by microbial degraders, respiration and enzyme activities were enhanced. This indicated an increased mineralisation of C as well as nitrogen (N), sulphur (S), and phosphorus (P). Microbial inoculation introduced specific bacterial taxa that further improved degradation efficiency and nutrient turnover (N, S, and P) in P3HB-amended soil. Notably, soil acidification related to P3HB was not the primary factor affecting plant growth inhibition. However, despite plant growth-promoting rhizobacteria and N2-fixing microorganisms originating from MI, plant biomass yield remained limited, suggesting that these microorganisms were not entirely successful in mitigating the growth inhibition caused by P3HB.
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Affiliation(s)
- Martin Brtnicky
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Vaclav Pecina
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic; Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Jiri Kucerik
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.
| | - Tereza Hammerschmiedt
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Adnan Mustafa
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Antonin Kintl
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic; Agricultural Research, Ltd., 664 41 Troubsko, Czech Republic
| | - Jana Sera
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, Nad Ovcirnou 3685, 760 01 Zlin, Czech Republic
| | - Marek Koutny
- Department of Environmental Protection Engineering, Faculty of Technology, Tomas Bata University in Zlin, Nad Ovcirnou 3685, 760 01 Zlin, Czech Republic
| | - Tivadar Baltazar
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Jiri Holatko
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
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Murray MLH, Dopheide A, Leonard J, Padamsee M, Schwendenmann L. Phyllosphere of Agathis australis Leaves and the Impact of the Soil-Borne Pathogen Phytophthora agathidicida. MICROBIAL ECOLOGY 2024; 87:125. [PMID: 39382674 PMCID: PMC11481638 DOI: 10.1007/s00248-024-02441-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 10/01/2024] [Indexed: 10/10/2024]
Abstract
Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand's endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.
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Affiliation(s)
| | - Andrew Dopheide
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand
| | - Jenny Leonard
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand
| | - Mahajabeen Padamsee
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, 1010, New Zealand.
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand.
| | - Luitgard Schwendenmann
- School of Environment, University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
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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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Jaswal K, Todd OA, Flores Audelo RC, Santus W, Paul S, Singh M, Miao J, Underhill DM, Peters BM, Behnsen J. Commensal Yeast Promotes Salmonella Typhimurium Virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.606421. [PMID: 39211098 PMCID: PMC11360897 DOI: 10.1101/2024.08.08.606421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Enteric pathogens engage in complex interactions with the host and the resident microbiota to establish gut colonization. Although mechanistic interactions between enteric pathogens and bacterial commensals have been extensively studied, whether and how commensal fungi affect pathogenesis of enteric infections remains largely unknown. Here we show that colonization with the common human gut commensal fungus Candida albicans worsened infections with the enteric pathogen Salmonella enterica serovar Typhimurium. Presence of C. albicans in the mouse gut increased Salmonella cecum colonization and systemic dissemination. We investigated the underlying mechanism and found that Salmonella binds to C. albicans via Type 1 fimbriae and uses its Type 3 Secretion System (T3SS) to deliver effector proteins into C. albicans . A specific effector, SopB, was sufficient to manipulate C. albicans metabolism, triggering increased arginine biosynthesis in C. albicans and the release of millimolar amounts of arginine into the extracellular environment. The released arginine, in turn, induced T3SS expression in Salmonella , increasing its invasion of epithelial cells. C. albicans deficient in arginine production was unable to increase Salmonella virulence in vitro or in vivo . In addition to modulating pathogen invasion, arginine also directly influenced the host response to infection. Arginine-producing C. albicans dampened the inflammatory response during Salmonella infection, whereas C. albicans deficient in arginine production did not. Arginine supplementation in the absence of C. albicans increased the systemic spread of Salmonella and decreased the inflammatory response, phenocopying the presence of C. albicans . In summary, we identified C. albicans colonization as a susceptibility factor for disseminated Salmonella infection, and arginine as a central metabolite in the cross-kingdom interaction between fungi, bacteria, and host.
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Gajdošová Z, Caboň M, Kolaříková Z, Sudová R, Rydlová J, Turisová I, Turis P, Kučera J, Slovák M. Environmental heterogeneity structures root-associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats. Mol Ecol 2024; 33:e17441. [PMID: 38923648 DOI: 10.1111/mec.17441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/04/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Rocky habitats, globally distributed ecosystems, harbour diverse biota, including numerous endemic and endangered species. Vascular plants thriving in these environments face challenging abiotic conditions, requiring diverse morphological and physiological adaptations. Their engagement with the surrounding microbiomes is, however, equally vital for their adaptation, fitness, and long-term survival. Nevertheless, there remains a lack of understanding surrounding this complex interplay within this fascinating biotic ecosystem. Using microscopic observations and metabarcoding analyses, we examined the fungal abundance and diversity in the root system of the rock-dwelling West Carpathian endemic shrub, Daphne arbuscula (Thymelaeaceae). We explored the diversification of root-associated fungal communities in relation to microclimatic variations across the studied sites. We revealed extensive colonization of the Daphne roots by diverse taxonomic fungal groups attributed to different ecological guilds, predominantly plant pathogens, dark septate endophytes (DSE), and arbuscular mycorrhizal fungi (AMF). Notably, differences in taxonomic composition and ecological guilds emerged between colder and warmer microenvironments. Apart from omnipresent AMF, warmer sites exhibited a prevalence of plant pathogens, while colder sites were characterized by a dominance of DSE. This mycobiome diversification, most likely triggered by the environment, suggests that D. arbuscula populations in warmer areas may be more vulnerable to fungal diseases, particularly in the context of global climate change.
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Affiliation(s)
- Zuzana Gajdošová
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Caboň
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Kolaříková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Radka Sudová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Jana Rydlová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Ingrid Turisová
- Department of Biology, Ecology and Environment, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Banská Bystrica, Slovakia
| | - Peter Turis
- Department of Biology, Ecology and Environment, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Banská Bystrica, Slovakia
| | - Jaromír Kučera
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Slovák
- Plant Sciences and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Praha, Czech Republic
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Hashimoto A, Shibata S, Hirooka Y, Ohkuma M. Phylogenetic and morphological re-evaluation of Camptophora. Antonie Van Leeuwenhoek 2024; 117:109. [PMID: 39083124 DOI: 10.1007/s10482-024-01990-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: 08/23/2023] [Accepted: 06/17/2024] [Indexed: 10/16/2024]
Abstract
The genetic variety and habitats of Camptophora species, generally known as black yeast, have not been clarified. In this study, we re-evaluated Camptophora based on morphological observations and phylogenetic analyses. Because prior investigations on Camptophora only included a few strains/specimens, 24 Camptophora-related strains were newly obtained from 13 leaf samples of various plant species to redefine the genetic and species concepts of Camptophora. Their molecular phylogenetic relationships were examined using small subunit nuclear ribosomal DNA (nSSU, 18S rDNA), the internal transcribed spacer (ITS) rDNA operon, the large subunit nuclear ribosomal DNA (LSU, 28S rDNA), β-tubulin, the second largest subunit of RNA polymerase II (rpb2), and mitochondrial small subunit DNA (mtSSU). Single- and multi-locus analyses using nSSU-ITS-LSU-rpb2-mtSSU revealed a robust phylogenetic relationship among Camptophora species within Chaetothyriaceae. Camptophora species could be distinguished from other chaetothyriaceous genera by their snake-shaped conidia with microcyclic conidiation and loosely interwoven mycelial masses. Based on the results of phylogenetic analyses, two undescribed lineages were recognized, and Ca. schimae was excluded from the genus. ITS sequence comparison with environmental DNA sequences revealed that the distribution of the genus is restricted to the Asia-Pacific region. Camptophora has been isolated or detected from abrupt sources, and this was attributed to its microcycle. The mechanisms driving genetic diversity within species are discussed with respect to their phyllosphere habitats.
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Affiliation(s)
- Akira Hashimoto
- Japan Collection of Microorganisms RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Saho Shibata
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, Koganei, Tokyo, 184-8584, Japan
- Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
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Hale B, Watts C, Conatser M, Brown E, Wijeratne AJ. Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing. ENVIRONMENTAL MICROBIOME 2024; 19:46. [PMID: 38997772 PMCID: PMC11241880 DOI: 10.1186/s40793-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. RESULTS Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. CONCLUSIONS This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.
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Affiliation(s)
- Brett Hale
- AgriGro Incorporated, Doniphan, MO, USA
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA
- College of Science and Mathematics, Arkansas State University, State University, AR, USA
| | - Caitlin Watts
- College of Agriculture, Arkansas State University, State University, AR, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew Conatser
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Edward Brown
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Asela J Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA.
- College of Science and Mathematics, Arkansas State University, State University, AR, USA.
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10
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Robin-Soriano A, Maurice K, Boivin S, Bourceret A, Laurent-Webb L, Youssef S, Nespoulous J, Boussière I, Berder J, Damasio C, Vincent B, Boukcim H, Ducousso M, Gros-Balthazard M. Absence of Gigasporales and rarity of spores in a hot desert revealed by a multimethod approach. MYCORRHIZA 2024; 34:251-270. [PMID: 39023766 DOI: 10.1007/s00572-024-01160-w] [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: 03/14/2024] [Accepted: 06/29/2024] [Indexed: 07/20/2024]
Abstract
Hot deserts impose extreme conditions on plants growing in arid soils. Deserts are expanding due to climate change, thereby increasing the vulnerability of ecosystems and the need to preserve them. Arbuscular mycorrhizal fungi (AMF) improve plant fitness by enhancing plant water/nutrient uptake and stress tolerance. However, few studies have focused on AMF diversity and community composition in deserts, and the soil and land use parameters affecting them. This study aimed to comprehensively describe AMF ecological features in a 5,000 km2 arid hyperalkaline region in AlUla, Saudi Arabia. We used a multimethod approach to analyse over 1,000 soil and 300 plant root samples of various species encompassing agricultural, old agricultural, urban and natural ecosystems. Our method involved metabarcoding using 18S and ITS2 markers, histological techniques for direct AMF colonization observation and soil spore extraction and observation. Our findings revealed a predominance of AMF taxa assigned to Glomeraceae, regardless of the local conditions, and an almost complete absence of Gigasporales taxa. Land use had little effect on the AMF richness, diversity and community composition, while soil texture, pH and substantial unexplained stochastic variance drove these compositions in AlUla soils. Mycorrhization was frequently observed in the studied plant species, even in usually non-mycorrhizal plant taxa (e.g. Amaranthaceae, Urticaceae). Date palms and Citrus trees, representing two major crops in the region, however, displayed a very low mycorrhizal frequency and intensity. AlUla soils had a very low concentration of spores, which were mostly small. This study generated new insight on AMF and specific behavioral features of these fungi in arid environments.
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Affiliation(s)
| | - Kenji Maurice
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Stéphane Boivin
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | - Amelia Bourceret
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, Paris, France
| | - Liam Laurent-Webb
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, Paris, France
| | - Sami Youssef
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | - Jérôme Nespoulous
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | - Inès Boussière
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Julie Berder
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
| | | | - Bryan Vincent
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
| | - Hassan Boukcim
- Department of Research and Development, VALORHIZ, Montferrier sur Lez, France
- ASARI, Mohammed VI Polytechnic University, Laâyoune, Morocco
| | - Marc Ducousso
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier, France
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11
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Neumann CJ, Pausan MR, Haid V, Weiss EC, Kolovetsiou-Kreiner V, Amtmann B, Winkler P, Mahnert A, Jantscher-Krenn E, Moissl-Eichinger C. The dynamics of the female microbiome: unveiling abrupt changes of microbial domains across body sites from prepartum to postpartum phases. Microbiol Spectr 2024; 12:e0014724. [PMID: 38917430 PMCID: PMC11302012 DOI: 10.1128/spectrum.00147-24] [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: 01/16/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
The microbial ecosystem of women undergoes enormous changes during pregnancy and the perinatal period. Little is known about the extent of changes in the maternal microbiome beyond the vaginal cavity and its recovery after birth. In this study, we followed pregnant women [maternal prepartum (mpre), n = 30] into the postpartum period [1 month postpartum, maternal postpartum (mpost), n = 30]. We profiled their oral, urinary, and vaginal microbiome; archaeome; mycobiome; and urinary metabolome and compared them with those of nonpregnant (np) women (n = 29). Overall, pregnancy status (np, mpre, and mpost) had a smaller effect on the microbiomes than body site, but massive transitions were observed for the oral and urogenital (vaginal and urinary) microbiomes. While the oral microbiome fluctuates during pregnancy but stabilizes rapidly within the first month postpartum, the urogenital microbiome is characterized by a major remodeling caused by a massive loss of Lactobacillus and thus a shift from Vaginal Community State Type (CST) I (40% of women) to CST IV (85% of women). The urinary metabolome rapidly reached an np-like composition after delivery, apart from lactose and oxaloacetic acid, which were elevated during active lactation. Fungal and archaeal profiles were indicative of pregnancy status. Methanobacterium signatures were found mainly in np women, and Methanobrevibacter showed an opposite behavior in the oral cavity (increased) and vagina (decreased) during pregnancy. Our findings suggest that the massive remodeling of the maternal microbiome and metabolome needs more attention and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies. IMPORTANCE The perinatal microbiome is of specific interest for the health of the mother and infant. We therefore investigate the dynamics of the female microbiome from nonpregnant over prepartum to the postpartum period in urine and the oral and vaginal cavities. A specific focus of this study is put not only on the bacterial part of the microbiome but also on the underinvestigated contribution of fungi and archaea. To our knowledge, we present the first study highlighting those aspects. Our findings suggest that the massive remodeling of the maternal microbiome and metabolome needs more attention and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies.
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Affiliation(s)
- Charlotte J. Neumann
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Manuela-Raluca Pausan
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Victoria Haid
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Eva-Christine Weiss
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | | | - Bettina Amtmann
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | - Petra Winkler
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Evelyn Jantscher-Krenn
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Graz, Styria, Austria
- BioTechMed, Graz, Styria, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
- BioTechMed, Graz, Styria, Austria
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12
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Zhu YQ, Li XL, Zhao DX, Wei YL, Yuan HS. Four New Species of Tomentella (Thelephorales, Basidiomycota) from Subtropical Forests in Southwestern China. J Fungi (Basel) 2024; 10:440. [PMID: 39057325 PMCID: PMC11278398 DOI: 10.3390/jof10070440] [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: 05/20/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
Species of the basidiomycetous genus Tomentella are widely distributed throughout temperate forests. Numerous studies on the taxonomy and phylogeny of Tomentella have been conducted from the temperate zone in the Northern hemisphere, but few have been from subtropical forests. In this study, four new species, T. casiae, T. guiyangensis, T. olivaceomarginata and T. rotundata from the subtropical mixed forests of Southwestern China, are described and illustrated based on morphological characteristics and phylogenetic analyses of the internal transcribed spacer regions (ITS) and the large subunit of the nuclear ribosomal RNA gene (LSU). Molecular analyses using Maximum Likelihood and Bayesian analysis confirmed the phylogenetic positions of these four new species. Anatomical comparisons among the closely related species in phylogenetic and morphological features are discussed. Four new species could be distinguished by the characteristics of basidiocarps, the color of the hymenophoral surface, the size of the basidia, the shape of the basidiospores and some other features.
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Affiliation(s)
- Ya-Quan Zhu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China; (Y.-Q.Z.); (D.-X.Z.); (Y.-L.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue-Long Li
- Institute of Edible Fungi, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China;
| | - Dong-Xue Zhao
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China; (Y.-Q.Z.); (D.-X.Z.); (Y.-L.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu-Lian Wei
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China; (Y.-Q.Z.); (D.-X.Z.); (Y.-L.W.)
| | - Hai-Sheng Yuan
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China; (Y.-Q.Z.); (D.-X.Z.); (Y.-L.W.)
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13
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Bomberg M, Miettinen H, Kinnunen P. Seasonal variation in metabolic profiles and microbial communities in a subarctic ore processing plant. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13284. [PMID: 38922785 PMCID: PMC11194043 DOI: 10.1111/1758-2229.13284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/30/2024] [Indexed: 06/28/2024]
Abstract
The mining industry strives to reduce its water footprint by recycling water in ore processing. This leads to build-up of ions, flotation chemicals and microbial biomass, which may affect the process. The Boliden Kevitsa mine in Northern Finland is exposed to seasonal change and recycles up to 90% of the process water. We studied the variation in size, composition and putative functions of microbial communities in summer and winter in the ore processing plant. The raw water, Cu and Ni thickener overflow waters had statistically significantly higher bacterial numbers in winter compared to summer, and specific summer and winter communities were identified. Metagenomic analysis indicated that Cu and Hg resistance genes, sulphate/thiosulphate, molybdate, iron(III) and zinc ABC transporters, nitrate reduction, denitrification, thiosulphate oxidation and methylotrophy were more common in winter than in summer. Raw water drawn from the nearby river did not affect the microbial communities in the process samples, indicating that the microbial communities and metabolic capacities develop within the process over time in response to the conditions in the processing plant, water chemistry, used chemicals, ore properties and seasonal variation. We propose that the microbial community structures are unique to the Boliden Kevitsa mine and processing plant.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland Ltd.EspooFinland
| | | | - Päivi Kinnunen
- VTT Technical Research Centre of Finland Ltd.TampereFinland
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14
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Camacho-Sanchez M. A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria. Int Microbiol 2024; 27:719-730. [PMID: 37672116 DOI: 10.1007/s10123-023-00422-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Metabarcoding is a powerful tool to characterize biodiversity in biological samples. The interpretation of taxonomic profiles from metabarcoding data has been hindered by their compositional nature. Several strategies have been proposed to transform compositional data into quantitative data, but they have intrinsic limitations. Here, I propose a workflow based on bacterial and fungal cellular internal standards (spike-ins) for absolute quantification of the microbiota in soil samples. These standards were added to the samples before DNA extraction in amounts estimated after qPCRs, to target around 1-2% coverage in the sequencing run. In bacteria, proportions of spike-in reads in the sequencing run were very similar (< 2-fold change) to those predicted by the qPCR assessment, and for fungi they differed up to 40-fold. The low variation among replicates highlights the reproducibility of the method. Estimates based on multiple bacterial spike-ins were highly correlated (r = 0.99). Procrustes analysis evidenced significant biological effects on the community composition when normalizing compositional data. A protocol based on qPCR estimation of input amounts of cellular spikes is proposed as a cheap and reliable strategy for quantitative metabarcoding of biological samples.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA) Centro Las Torres, Alcalá del Río, 41200, Seville, Spain.
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15
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Nishisaka CS, Ventura JP, Bais HP, Mendes R. Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly. ENVIRONMENTAL MICROBIOME 2024; 19:33. [PMID: 38745256 DOI: 10.1186/s40793-024-00567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/07/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps-TasA, which is defective in exopolysaccharide (EPS) and TasA protein production. RESULTS qPCR revealed that the B. subtilis UD1022eps-TasA- strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis. CONCLUSION This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.
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Affiliation(s)
- Caroline Sayuri Nishisaka
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - João Paulo Ventura
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center (BPI), Newark, DE, USA
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16
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Yuu EY, Bührer C, Eckmanns T, Fulde M, Herz M, Kurzai O, Lindstedt C, Panagiotou G, Piro VC, Radonic A, Renard BY, Reuss A, Siliceo SL, Thielemann N, Thürmer A, Vorst KV, Wieler LH, Haller S. The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis. Gut Pathog 2024; 16:27. [PMID: 38735967 PMCID: PMC11089716 DOI: 10.1186/s13099-024-00616-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/13/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing. RESULTS The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants. CONCLUSIONS Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.
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Affiliation(s)
- Elizabeth Y Yuu
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | | | | | - Marcus Fulde
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michaela Herz
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | | | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07745, Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vitor C Piro
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | | | - Bernhard Y Renard
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | - Annicka Reuss
- Robert Koch Institute, Berlin, Germany
- Ministry of Justice and Health, Schleswig-Holstein, Kiel , Germany
| | - Sara Leal Siliceo
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | - Nadja Thielemann
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | | | - Kira van Vorst
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Lothar H Wieler
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Robert Koch Institute, Berlin, Germany
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17
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Richter FJ, Suter M, Lüscher A, Buchmann N, El Benni N, Feola Conz R, Hartmann M, Jan P, Klaus VH. Effects of management practices on the ecosystem-service multifunctionality of temperate grasslands. Nat Commun 2024; 15:3829. [PMID: 38714701 PMCID: PMC11076620 DOI: 10.1038/s41467-024-48049-y] [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: 06/14/2023] [Accepted: 04/19/2024] [Indexed: 05/10/2024] Open
Abstract
Human wellbeing depends on ecosystem services, highlighting the need for improving the ecosystem-service multifunctionality of food and feed production systems. We study Swiss agricultural grasslands to assess how employing and combining three widespread aspects of grassland management and their interactions can enhance 22 plot-level ecosystem service indicators, as well as ecosystem-service multifunctionality. The three management aspects we assess are i) organic production system, ii) an eco-scheme prescribing extensive management (without fertilization), and iii) harvest type (pasture vs. meadow). While organic production system and interactions between the three management aspects play a minor role, the main effects of eco-scheme and harvest type considerably shape single services. Moreover, the eco-scheme 'extensive management' and the harvest type 'pasture' enhance plot-scale ecosystem-service multifunctionality, mostly through facilitating cultural services at the expense of provisioning services. These changes in ecosystem-service supply occur mainly via changes in land-use intensity, i.e., reduced fertilizer input and harvest frequency. In conclusion, diversifying grassland management where this is currently homogeneous across farms and landscapes depicts an important first step to improve landscape-scale multifunctionality for sustainable grassland systems. To meet societal ecosystem services demand, the three studied management aspects can be systematically combined to increase ecosystem services that are in short supply.
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Affiliation(s)
- Franziska J Richter
- Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland.
| | - Matthias Suter
- Forage Production and Grassland Systems, Agroscope, Zürich, Switzerland
| | - Andreas Lüscher
- Forage Production and Grassland Systems, Agroscope, Zürich, Switzerland
| | - Nina Buchmann
- Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Nadja El Benni
- Sustainability Assessment and Agricultural Management, Agroscope, Ettenhausen, Switzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Pierrick Jan
- Managerial Economics in Agriculture, Agroscope, Ettenhausen, Switzerland
| | - Valentin H Klaus
- Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forage Production and Grassland Systems, Agroscope, Zürich, Switzerland
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18
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Strawsine M, van Galen LG, Lord JM, Larcombe MJ. Trophic facilitation in forest restoration: Can Nothofagus trees use ectomycorrhizal fungi of the pioneer shrub Leptospermum? Ecol Evol 2024; 14:e11442. [PMID: 38803610 PMCID: PMC11128459 DOI: 10.1002/ece3.11442] [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: 02/11/2024] [Revised: 04/21/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
The benefits of plant-to-plant facilitation in ecological restoration are well recognized, yet the potential for indirect trophic facilitation remains understudied. Nothofagus (southern beech; Nothofagaceae) is an iconic southern hemisphere tree genus that is frequently the focus of ecological restoration efforts. One aspect of Nothofagus ecology that may limit restoration success is the availability of appropriate ectomycorrhizal fungi. It has been suggested that pioneer dual-mycorrhizal hosts such as Leptospermum species (Myrtaceae) could facilitate Nothofagus establishment by providing fungal inoculum, but the capacity for Nothofagus to use Leptospermum ectomycorrhizal fungi is unknown. To investigate potential indirect facilitation, we conducted a common garden pot trial to determine if Nothofagus cliffortioides (mountain beech) can use symbionts from Leptospermum scoparium (mānuka) ectomycorrhizal communities. Nothofagus and Leptospermum seedlings were grown in monoculture and mixed pairs with reciprocal "home" and "away" soil fungal inoculum. ITS2 metabarcoding of eDNA from hyphal ingrowth bags revealed that Nothofagus and Leptospermum inoculum contained different ectomycorrhizal fungal communities, but that half of the common ectomycorrhizal taxa identified were found in both soil types, suggesting generalist fungi exist. Nothofagus was able to form associations with some fungal species originating from Leptospermum inoculum, however, probable spore contamination meant that the proportion of root colonization associated with those species was ambiguous. Root ectomycorrhizal colonization rates were positively associated with seedling biomass, and there was some evidence of a home soil inoculum advantage in Nothofagus, but these effects were minor. Additionally, we found evidence that home inoculum provides a protective advantage against drought stress for Leptospermum seedlings. Our results indicate the potential for using Leptospermum to promote Nothofagus establishment in restoration plantings and highlight the possible benefits of considering fungal mutualists in ecological restoration projects.
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Affiliation(s)
- Merissa Strawsine
- Department of BotanyUniversity of OtagoDunedinNew Zealand
- Present address:
Shasta‐Trinity National ForestReddingCaliforniaUSA
| | - Laura G. van Galen
- Department of BotanyUniversity of OtagoDunedinNew Zealand
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Society for the Protection of Underground Networks (SPUN)DoverDelawareUSA
| | - Janice M. Lord
- Department of BotanyUniversity of OtagoDunedinNew Zealand
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19
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Wei H, Liu J, Liu M, Zhang H, Chen Y. Rumen fermentation and microbial diversity of sheep fed a high-concentrate diet supplemented with hydroethanolic extract of walnut green husks. Anim Biosci 2024; 37:655-667. [PMID: 37946420 PMCID: PMC10915217 DOI: 10.5713/ab.23.0213] [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: 06/10/2023] [Revised: 08/16/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE This study aimed to assess the impact of a hydroethanolic extract of walnut green husks (WGH) on rumen fermentation and the diversity of bacteria, methanogenic archaea, and fungi in sheep fed a high-concentrate diet. METHODS Five healthy small-tailed Han ewes with permanent rumen fistula were selected and housed in individual pens. This study adopted a self-controlled and crossover design with a control period and an experimental period. During the control period, the animals were fed a basal diet (with a ratio of concentrate to roughage of 65:35), while during the treatment period, the animals were fed the basal diet supplemented with 0.5% hydroethanolic extract of WGH. Fermentation parameters, digestive enzyme activities, and microbial diversity in rumen fluid were analyzed. RESULTS Supplementation of hydroethanolic extract of WGH had no significant effect on feed intake, concentrations of total volatile fatty acids, isovalerate, ammonia nitrogen, and microbial protein (p>0.05). However, the ruminal pH, concentrations of acetate, butyrate and isobutyrate, the ratio of acetate to propionate, protozoa count, and the activities of filter paper cellulase and cellobiase were significantly increased (p<0.05), while concentrations of propionate and valerate were significantly decreased (p<0.05). Moreover, 16S rRNA gene sequencing revealed that the relative abundance of rumen bacteria Christensenellaceae R7 group, Saccharofermentans, and Ruminococcaceae NK4A214 group were significantly increased, while Ruminococcus gauvreauii group, Prevotella 7 were significantly decreased (p<0.05). The relative abundance of the fungus Pseudomonas significantly increased, while Basidiomycota, Fusarium, and Alternaria significantly decreased (p<0.05). However, there was no significant change in the community structure of methanogenic archaea. CONCLUSION Supplementation of hydroethanolic extract of WGH to a high-concentrate diet improved the ruminal fermentation, altered the structure of ruminal bacterial and fungal communities, and exhibited beneficial effects in alleviating subacute rumen acidosis of sheep.
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Affiliation(s)
- Huan Wei
- Laboratory of Nutrition for Meat & Dairy Herbivore, College of Animal Science, Xinjiang Agricultural University, Urumqi 830052,
China
| | - Jiancheng Liu
- Laboratory of Nutrition for Meat & Dairy Herbivore, College of Animal Science, Xinjiang Agricultural University, Urumqi 830052,
China
| | - Mengjian Liu
- Laboratory of Nutrition for Meat & Dairy Herbivore, College of Animal Science, Xinjiang Agricultural University, Urumqi 830052,
China
| | - Huiling Zhang
- Laboratory of Nutrition for Meat & Dairy Herbivore, College of Animal Science, Xinjiang Agricultural University, Urumqi 830052,
China
| | - Yong Chen
- Laboratory of Nutrition for Meat & Dairy Herbivore, College of Animal Science, Xinjiang Agricultural University, Urumqi 830052,
China
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20
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Arunan B, Talukdar D, Swain S, Varadarajan A, Sarda R, Singh G, Nischal N, Soneja M, Bakshi S, Jana P, Tanwar S, Sikka K, Verma H, Subramanian A, Xess I, Wig N, Das B, Ray A. Metagenomic insights into fungal community composition of the nasopharyngeal region of COVID-19 associated mucormycosis patients from India. J Med Virol 2024; 96:e29601. [PMID: 38597375 DOI: 10.1002/jmv.29601] [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: 02/13/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024]
Abstract
Coronavirus disease 2019 (COVID-19) associated mucormycosis (CAM) was reported predominantly from India during the second wave of COVID-19 and has a high mortality rate. The present study aims to understand the fungal community composition of the nasopharyngeal region of CAM-infected individuals and compare it with severe COVID-19 patients and healthy controls. The fungal community composition was decoded by analyzing the sequence homology of the internal transcribed spacer-2-(ITS-2) region of metagenomic DNA extracted from the upper respiratory samples. The alpha-diversity indices were found to be significantly altered in CAM patients (p < 0.05). Interestingly, a higher abundance of Candida africana, Candida haemuloni, Starmerella floris, and Starmerella lactiscondensi was observed exclusively in CAM patients. The interindividual changes in mycobiome composition were well supported by beta-diversity analysis (p < 0.05). The current study provides insights into the dysbiosis of the nasal mycobiome during CAM infection. In conclusion, our study shows that severe COVID-19 and CAM are associated with alteration in mycobiome as compared to healthy controls. However, the sequential alteration in the fungal flora which ultimately leads to the development of CAM needs to be addressed by future studies.
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Affiliation(s)
| | - Daizee Talukdar
- Functional Genomics Laboratory, BRIC-THSTI, Faridabad, Haryana, India
| | - Satish Swain
- Department of Medicine, AIIMS, New Delhi, Delhi, India
| | | | - Radhika Sarda
- Department of Medicine, AIIMS, New Delhi, Delhi, India
| | | | | | - Manish Soneja
- Department of Medicine, AIIMS, New Delhi, Delhi, India
| | - Susmita Bakshi
- Functional Genomics Laboratory, BRIC-THSTI, Faridabad, Haryana, India
| | - Pradipta Jana
- Functional Genomics Laboratory, BRIC-THSTI, Faridabad, Haryana, India
| | - Subhash Tanwar
- Functional Genomics Laboratory, BRIC-THSTI, Faridabad, Haryana, India
| | - Kapil Sikka
- Department of Otorhinolaryngology, AIIMS, New Delhi, Delhi, India
| | - Hitesh Verma
- Department of Otorhinolaryngology, AIIMS, New Delhi, Delhi, India
| | | | | | - Naveet Wig
- Department of Medicine, AIIMS, New Delhi, Delhi, India
| | - Bhabatosh Das
- Functional Genomics Laboratory, BRIC-THSTI, Faridabad, Haryana, India
| | - Animesh Ray
- Department of Medicine, AIIMS, New Delhi, Delhi, India
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21
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Pineda-Mendoza RM, Gutiérrez-Ávila JL, Salazar KF, Rivera-Orduña FN, Davis TS, Zúñiga G. Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae). Front Microbiol 2024; 15:1360488. [PMID: 38525076 PMCID: PMC10959539 DOI: 10.3389/fmicb.2024.1360488] [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: 12/23/2023] [Accepted: 02/15/2024] [Indexed: 03/26/2024] Open
Abstract
The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts.
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Affiliation(s)
- Rosa María Pineda-Mendoza
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge Luis Gutiérrez-Ávila
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Kevin F. Salazar
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Flor N. Rivera-Orduña
- Laboratorio de Ecología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Thomas S. Davis
- Department of Forest and Rangeland Stewardship, Warner College of Natural Resources, Colorado State University, Fort Collins, CO, United States
| | - Gerardo Zúñiga
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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22
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Schrader L, Trautner J, Tebbe CC. Identifying environmental factors affecting the microbial community composition on outdoor structural timber. Appl Microbiol Biotechnol 2024; 108:254. [PMID: 38446240 PMCID: PMC10917859 DOI: 10.1007/s00253-024-13089-3] [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: 12/21/2023] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/07/2024]
Abstract
Timber wood is a building material with many positive properties. However, its susceptibility to microbial degradation is a major challenge for outdoor usage. Although many wood-degrading fungal species are known, knowledge on their prevalence and diversity causing damage to exterior structural timber is still limited. Here, we sampled 46 decaying pieces of wood from outdoor constructions in the area of Hamburg, Germany; extracted their DNA; and investigated their microbial community composition by PCR amplicon sequencing of the fungal ITS2 region and partial bacterial 16S rRNA genes. In order to establish a link between the microbial community structure and environmental factors, we analysed the influence of wood species, its C and N contents, the effect of wood-soil contact, and the importance of its immediate environment (city, forest, meadow, park, respectively). We found that fungal and bacterial community composition colonising exterior timber was similar to fungi commonly found in forest deadwood. Of all basidiomycetous sequences retrieved, some, indicative for Perenniporia meridionalis, Dacrymyces capitatus, and Dacrymyces stillatus, were more frequently associated with severe wood damage. Whilst the most important environmental factor shaping fungal and bacterial community composition was the wood species, the immediate environment was important for fungal species whilst, for the occurrence of bacterial taxa, soil contact had a high impact. No influence was tangible for variation of the C or N content. In conclusion, our study demonstrates that wood colonising fungal and bacterial communities are equally responsive in their composition to wood species, but respond differently to environmental factors. KEY POINTS: • Perenniporia meridionalis and Dacrymyces are frequently associated with wood damage • Fungal community composition on timber is affected by its surrounding environment • Bacterial community composition on structural timber is affected by soil contact.
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Affiliation(s)
- Lauritz Schrader
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Jochen Trautner
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, 38116, Brunswick, Germany.
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23
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VanderRoest JP, Fowler JA, Rhoades CC, Roth HK, Broeckling CD, Fegel TS, McKenna AM, Bechtold EK, Boot CM, Wilkins MJ, Borch T. Fire Impacts on the Soil Metabolome and Organic Matter Biodegradability. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4167-4180. [PMID: 38385432 DOI: 10.1021/acs.est.3c09797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Global wildfire activity has increased since the 1970s and is projected to intensify throughout the 21st century. Wildfires change the composition and biodegradability of soil organic matter (SOM) which contains nutrients that fuel microbial metabolism. Though persistent forms of SOM often increase postfire, the response of more biodegradable SOM remains unclear. Here we simulated severe wildfires through a controlled "pyrocosm" approach to identify biodegradable sources of SOM and characterize the soil metabolome immediately postfire. Using microbial amplicon (16S/ITS) sequencing and gas chromatography-mass spectrometry, heterotrophic microbes (Actinobacteria, Firmicutes, and Protobacteria) and specific metabolites (glycine, protocatechuate, citric cycle intermediates) were enriched in burned soils, indicating that burned soils contain a variety of substrates that support microbial metabolism. Molecular formulas assigned by 21 T Fourier transform ion cyclotron resonance mass spectrometry showed that SOM in burned soil was lower in molecular weight and featured 20 to 43% more nitrogen-containing molecular formulas than unburned soil. We also measured higher water extractable organic carbon concentrations and higher CO2 efflux in burned soils. The observed enrichment of biodegradable SOM and microbial heterotrophs demonstrates the resilience of these soils to severe burning, providing important implications for postfire soil microbial and plant recolonization and ecosystem recovery.
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Affiliation(s)
- Jacob P VanderRoest
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Julie A Fowler
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Holly K Roth
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Corey D Broeckling
- Bioanalysis and Omics Center, Analytical Resources Core, Colorado State University, Fort Collins, 80521, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Emily K Bechtold
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Claudia M Boot
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
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24
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Ferlian O, Goldmann K, Bonkowski M, Dumack K, Wubet T, Eisenhauer N. Invasive earthworms shift soil microbial community structure in northern North American forest ecosystems. iScience 2024; 27:108889. [PMID: 38322986 PMCID: PMC10844042 DOI: 10.1016/j.isci.2024.108889] [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: 08/18/2023] [Revised: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Invasive earthworms colonize ecosystems around the globe. Compared to other species' invasions, earthworm invasions have received little attention. Previous studies indicated their tremendous effects on resident soil biota representing a major part of the terrestrial biodiversity. We investigated effects of earthworm invasion on soil microbial communities in three forests in North America by conducting DNA sequencing of soil bacteria, fungi, and protists in two soil depths. Our study shows that microbial diversity was lower in highly invaded forest areas. While bacterial diversity was strongly affected compared to fungi and protists, fungal community composition and family dominance were strongly affected compared to bacteria and protists. We found most species specialized on invasion in fungi, mainly represented by saprotrophs. Comparably, few protist species, mostly bacterivorous, were specialized on invasion. As one of the first observational studies, we investigated earthworm invasion on three kingdoms showing distinct taxa- and trophic level-specific responses to earthworm invasion.
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Affiliation(s)
- Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Kezia Goldmann
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
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25
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Hotopp AM, Olsen BJ, Ishaq SL, Frey SD, Kovach AI, Kinnison MT, Gigliotti FN, Roeder MR, Cammen KM. Plumage microorganism communities of tidal marsh sparrows. iScience 2024; 27:108668. [PMID: 38230264 PMCID: PMC10790016 DOI: 10.1016/j.isci.2023.108668] [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: 06/16/2023] [Revised: 11/02/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024] Open
Abstract
Microorganism communities can shape host phenotype evolution but are often comprised of thousands of taxa with varied impact on hosts. Identification of taxa influencing host evolution relies on first describing microorganism communities and acquisition routes. Keratinolytic (keratin-degrading) microorganisms are hypothesized to be abundant in saltmarsh sediments and to contribute to plumage evolution in saltmarsh-adapted sparrows. Metabarcoding was used to describe plumage bacterial (16S rRNA) and fungal (ITS) communities in three sparrow species endemic to North America's Atlantic coast saltmarshes. Results describe limited within-species variability and moderate host species-level patterns in microorganism diversity and community composition. A small percentage of overall microorganism diversity was comprised of potentially keratinolytic microorganisms, warranting further functional studies. Distinctions between plumage and saltmarsh sediment bacteria, but not fungal, communities were detected, suggesting multiple bacterial acquisition routes and/or vertebrate host specialization. This research lays groundwork for future testing of causal links between microorganisms and avian host evolution.
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Affiliation(s)
- Alice M. Hotopp
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Brian J. Olsen
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Suzanne L. Ishaq
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Serita D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael T. Kinnison
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Franco N. Gigliotti
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Kristina M. Cammen
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
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26
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Silva JPD, Veloso TGR, Costa MD, Souza JJLLD, Soares EMB, Gomes LC, Schaefer CEGR. Microbial successional pattern along a glacier retreat gradient from Byers Peninsula, Maritime Antarctica. ENVIRONMENTAL RESEARCH 2024; 241:117548. [PMID: 37939803 DOI: 10.1016/j.envres.2023.117548] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
The retreat of glaciers in Antarctica has increased in the last decades due to global climate change, influencing vegetation expansion, and soil physico-chemical and biological attributes. However, little is known about soil microbiology diversity in these periglacial landscapes. This study characterized and compared bacterial and fungal diversity using metabarcoding of soil samples from the Byers Peninsula, Maritime Antarctica. We identified bacterial and fungal communities by amplification of bacterial 16 S rRNA region V3-V4 and fungal internal transcribed spacer 1 (ITS1). We also applied 14C dating on soil organic matter (SOM) from six profiles. Physico-chemical analyses and attributes associated with SOM were evaluated. A total of 14,048 bacterial ASVs were obtained, and almost all samples had 50% of their sequences assigned to Actinobacteriota and Proteobacteria. Regarding the fungal community, Mortierellomycota, Ascomycota and Basidiomycota were the main phyla from 1619 ASVs. We found that soil age was more relevant than the distance from the glacier, with the oldest soil profile (late Holocene soil profile) hosting the highest bacterial and fungal diversity. The microbial indices of the fungal community were correlated with nutrient availability, soil reactivity and SOM composition, whereas the bacterial community was not correlated with any soil attribute. The bacterial diversity, richness, and evenness varied according to presence of permafrost and moisture regime. The fungal community richness in the surface horizon was not related to altitude, permafrost, or moisture regime. The soil moisture regime was crucial for the structure, high diversity and richness of the microbial community, specially to the bacterial community. Further studies should examine the relationship between microbial communities and environmental factors to better predict changes in this terrestrial ecosystem.
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Affiliation(s)
- Jônatas Pedro da Silva
- Graduate Program in Soils and Plant Nutrition, Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil
| | | | - Maurício Dutra Costa
- Microbiology Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Bolsista Pesquisador Do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
| | - José João Lelis Leal de Souza
- Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Bolsista Pesquisador Do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
| | | | | | - Carlos Ernesto G R Schaefer
- Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Bolsista Pesquisador Do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
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27
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Wetzel S, Müller A, Kohnert E, Mehrbarzin N, Huber R, Häcker G, Kreutz C, Lederer AK, Badr MT. Longitudinal dynamics of gut bacteriome and mycobiome interactions pre- and post-visceral surgery in Crohn's disease. Front Cell Infect Microbiol 2024; 13:1275405. [PMID: 38287975 PMCID: PMC10822897 DOI: 10.3389/fcimb.2023.1275405] [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: 08/09/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Alterations of the gut microbiome are involved in the pathogenesis of Crohn's disease (CD). The role of fungi in this context is unclear. This study aimed to determine postoperative changes in the bacterial and fungal gut communities of CD patients undergoing intestinal resection, and to evaluate interactions between the bacteriome and mycobiome and their impact on the patients' outcome. Methods We report a subgroup analysis of a prospective cohort study, focusing on 10 CD patients whose fecal samples were collected for bacterial 16S rRNA and fungal ITS2 genes next-generation sequencing the day before surgery and on the 5th or 6th postoperative day. Results No significant differences in bacterial and fungal diversity were observed between preoperative and postoperative stool samples. By in-depth analysis, significant postoperative abundance changes of bacteria and fungi and 17 interkingdom correlations were detected. Network analysis identified 13 microbial clusters in the perioperative gut communities, revealing symbiotic and competitive interactions. Relevant factors were gender, age, BMI, lifestyle habits (smoking, alcohol consumption) and surgical technique. Postoperative abundance changes and identified clusters were associated with clinical outcomes (length of hospital stay, complications) and levels of inflammatory markers. Conclusions Our findings highlight the importance of dissecting the interactions of gut bacterial and fungal communities in CD patients and their potential influence on postoperative and disease outcomes.
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Affiliation(s)
- Simon Wetzel
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexander Müller
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Negin Mehrbarzin
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roman Huber
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Ann-Kathrin Lederer
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of General, Visceral and Transplant Surgery, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Aufdecken gemeinsamer Prinzipien immunvermittelter Erkrankungen: von der Grundlagenwissenschaft zu neuen Therapien (IMM-PACT)-Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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28
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Maurice K, Bourceret A, Youssef S, Boivin S, Laurent-Webb L, Damasio C, Boukcim H, Selosse MA, Ducousso M. Anthropic disturbances impact the soil microbial network structure and stability to a greater extent than natural disturbances in an arid ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167969. [PMID: 37914121 DOI: 10.1016/j.scitotenv.2023.167969] [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: 08/16/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Growing pressure from climate change and agricultural land use is destabilizing soil microbial community interactions. Yet little is known about microbial community resistance and adaptation to disturbances over time. This hampers our ability to determine the recovery latency of microbial interactions after disturbances, with fundamental implications for ecosystem functioning and conservation measures. Here we examined the response of bacterial and fungal community networks in the rhizosphere of Haloxylon salicornicum (Moq.) Bunge ex Boiss. over the course of soil disturbances resulting from a history of different hydric constraints involving flooding-drought successions. An anthropic disturbance related to past agricultural use, with frequent successions of flooding and drought, was compared to a natural disturbance, i.e., an evaporation basin, with yearly flooding-drought successions. The anthropic disturbance resulted in a specific microbial network topology characterized by lower modularity and stability, reflecting the legacy of past agricultural use on soil microbiome. In contrast, the natural disturbance resulted in a network topology and stability close to those of natural environments despite the lower alpha diversity, and a different community composition compared to that of the other sites. These results highlighted the temporality in the response of the microbial community structure to disturbance, where long-term adaptation to flooding-drought successions lead to a higher stability than disturbances occurring over a shorter timescale.
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Affiliation(s)
- Kenji Maurice
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France.
| | - Amélia Bourceret
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France
| | - Sami Youssef
- Department of Research and Development, VALORHIZ, 1900, Boulevard de la Lironde, PSIII, Parc Scientifique Agropolis, F34980 Montferrier sur Lez, France
| | - Stéphane Boivin
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
| | - Liam Laurent-Webb
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France
| | - Coraline Damasio
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
| | - Hassan Boukcim
- Department of Research and Development, VALORHIZ, 1900, Boulevard de la Lironde, PSIII, Parc Scientifique Agropolis, F34980 Montferrier sur Lez, France; ASARI, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid Ben Guerir, 43150, Morocco
| | - Marc-André Selosse
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France; Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland; Institut Universitaire de France, Paris, France
| | - Marc Ducousso
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
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Bambi M, Galla G, Donati C, Rovero F, Hauffe HC, Barelli C. Gut microbiota variations in wild yellow baboons (Papio cynocephalus) are associated with sex and habitat disturbance. Sci Rep 2024; 14:869. [PMID: 38195759 PMCID: PMC10776872 DOI: 10.1038/s41598-023-50126-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Although male and female mammals differ in biological traits and functional needs, the contribution of this sexual dimorphism to variations in gut bacteria and fungi (gut microbiota) in relation to habitat type has not been fully examined. To understand whether the combination of sex and habitat affects gut microbiota variation, we analyzed 40 fecal samples of wild yellow baboons (Papio cynocephalus) living in contrasting habitat types (intact, well-protected vs. fragmented, less protected forests) in the Udzungwa Mountains of Tanzania. Sex determination was performed using the marker genes SRY (Sex-determining Region Y) and DDX3X-DDX3Y (DEAD-Box Helicase 3). Samples were attributed to 34 individuals (19 females and 15 males) belonging to five social groups. Combining the results of sex determination with two amplicon sequencing datasets on bacterial (V1-V3 region of the 16S rRNA gene) and fungal (ITS2) gut communities, we found that overall, baboon females had a significantly higher gut bacterial richness compared to males. Beta diversity estimates indicated that bacterial composition was significantly different between males and females, and this was true for individuals from both well- and less protected forests. Our results highlight the combined role of sex and habitat type in shaping variation in gut microbial communities in wild non-human primates.
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Affiliation(s)
- Marina Bambi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Donati
- Computational Biology Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Francesco Rovero
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Heidi C Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudia Barelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
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Abarenkov K, Nilsson RH, Larsson KH, Taylor AS, May T, Frøslev TG, Pawlowska J, Lindahl B, Põldmaa K, Truong C, Vu D, Hosoya T, Niskanen T, Piirmann T, Ivanov F, Zirk A, Peterson M, Cheeke T, Ishigami Y, Jansson A, Jeppesen T, Kristiansson E, Mikryukov V, Miller J, Oono R, Ossandon F, Paupério J, Saar I, Schigel D, Suija A, Tedersoo L, Kõljalg U. The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered. Nucleic Acids Res 2024; 52:D791-D797. [PMID: 37953409 PMCID: PMC10767974 DOI: 10.1093/nar/gkad1039] [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: 09/14/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.
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Affiliation(s)
- Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
| | - Karl-Henrik Larsson
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
- Natural History Museum, University of Oslo, Box 1172 Blindern, 0318 Oslo, Norway
| | - Andy F S Taylor
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - Tobias Guldberg Frøslev
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Björn Lindahl
- Swedish University of Agricultural Sciences, Department of Soil and Environment, Box 7014, SE-750 07 Uppsala, Sweden
| | - Kadri Põldmaa
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Camille Truong
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, The Netherlands
| | | | - Tuula Niskanen
- Botany Unit, Finnish Museum of Natural History, P.O.Box 7, 00014 University of Helsinki, Finland
| | - Timo Piirmann
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Filipp Ivanov
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Allan Zirk
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Marko Peterson
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Tanya E Cheeke
- School of Biological Sciences, Washington State University, 2710 Crimson Way, Richland, WA 9935, USA
| | - Yui Ishigami
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Arnold Tobias Jansson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 453, 405 30 Göteborg, Sweden
| | - Thomas Stjernegaard Jeppesen
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Joseph T Miller
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California at Santa Barbara, USA
| | | | - Joana Paupério
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Irja Saar
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Dmitry Schigel
- Global Biodiversity Information Facility (GBIF), Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ave Suija
- Natural History Museum, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
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Zhou W, Shi W, Soltis PS, Soltis DE, Xiang QY(J. Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation. FRONTIERS IN PLANT SCIENCE 2023; 14:1274746. [PMID: 38192694 PMCID: PMC10773735 DOI: 10.3389/fpls.2023.1274746] [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: 08/08/2023] [Accepted: 10/27/2023] [Indexed: 01/10/2024]
Abstract
Introduction The well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America. Methods Metagenomic sequencing of fungal ITS and bacterial-archaeal 16S rDNA was used to capture the foliar endophytic communities. Alpha and beta diversity of fungi and bacteria were compared at multiple scales and dimensions to gain insights into the relative roles of historical geographic isolation, host identity, phylogeny, and environment from samples at different sites in shaping endophytic diversity patterns. Results We found that beta diversity of endophytes varied greatly among plant individuals within species and between species among genera at the same sampling site, and among three sampling sites, but little variation between region-of-origin of all plant species (EA vs ENA) and between EA-ENA disjunct counterparts within genera. Various numbers of indicator fungal species differing in abundance were identified for each plant genus and Cornus species. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance of plants was detected among the disjunct genera but not among species of Cornus. However, significant correlations between beta diversities at different taxonomic scales of endophytes and phylogenetic distances of Cornus species were observed. Discussion Our results suggest important roles of host identity and environment (sampling sites), and a likely minor role of phylogenetic divergence and historical biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera and Cornus. The results lead to a hypothesis that the sister taxa in EA and ENA likely differ in FEF and FEB when growing in native habitats due to differences in local environments, which may potentially drive allopatric divergence of the functional features of species.
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Affiliation(s)
- Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Wei Shi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Qiu-Yun (Jenny) Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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O'Connell LM, Mann AE, Osagie E, Akhigbe P, Blouin T, Soule A, Obuekwe O, Omoigberale A, Burne RA, Coker MO, Richards VP. Supragingival mycobiome of HIV-exposed-but-uninfected children reflects a stronger correlation with caries-free-associated taxa compared to HIV-infected or uninfected children. Microbiol Spectr 2023; 11:e0149123. [PMID: 37874172 PMCID: PMC10715047 DOI: 10.1128/spectrum.01491-23] [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: 04/21/2023] [Accepted: 09/15/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Globally, caries is among the most frequent chronic childhood disease, and the fungal component of the microbial community responsible is poorly studied despite evidence that fungi contribute to increased acid production exacerbating enamel demineralization. HIV infection is another global health crisis. Perinatal HIV exposure with infection are caries risk factors; however, the caries experience in the context of perinatal HIV exposure without infection is less clear. Using high-throughput amplicon sequencing, we find taxonomic differences that become pronounced during late-stage caries. Notably, we show a stronger correlation with health-associated taxa for HIV-exposed-but-uninfected children when compared to unexposed and uninfected children. This aligns with a lower incidence of caries in primary teeth at age 6 or less for exposed yet uninfected children. Ultimately, these findings could contribute to improved risk assessment, intervention, and prevention strategies such as biofilm disruption and the informed design of pro-, pre-, and synbiotic oral therapies.
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Affiliation(s)
- Lauren M. O'Connell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Allison E. Mann
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Esosa Osagie
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Paul Akhigbe
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Thomas Blouin
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Ashlyn Soule
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Ozoemene Obuekwe
- Department of Oral and Maxillofacial Surgery, University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | - Augustine Omoigberale
- Department of Child Health, University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | - Robert A. Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Modupe O. Coker
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Department of Oral Biology, School of Dental Medicine, Rutgers University, Newark, New Jersey, USA
| | - Vincent P. Richards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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Arnolds KL, Higgins RC, Crandall J, Li G, Linger JG, Guarnieri MT. Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform. MICROBIAL ECOLOGY 2023; 87:12. [PMID: 38072911 PMCID: PMC10710964 DOI: 10.1007/s00248-023-02321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.
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Affiliation(s)
- Kathleen L Arnolds
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Riley C Higgins
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jennifer Crandall
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Gabriella Li
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jeffrey G Linger
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA.
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401, USA.
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.
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Bomberg M, Miettinen H. Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples. J Microbiol Methods 2023; 215:106850. [PMID: 37907119 DOI: 10.1016/j.mimet.2023.106850] [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: 04/24/2023] [Revised: 09/04/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
Abstract
Microorganisms in flotation and minerals processing may significantly affect the grade and yield of metal concentrates. However, studying the phenomena requires working techniques to detach microorganisms and their DNA from mineral particles to which they strongly adhere. We developed a new method utilizing the competitive properties of anionic nanocellulose to block sorption of DNA to and detach microbial cells from mineral particles from ore processing. In general, up to one ng DNA mL-1 sample was obtained with the custom anionic nanocellulose method (CM) compared to DNA amounts below the Qubit assay's detection limit for extractions with a commercial kit (KIT). Similarly, 0.5-4 orders of magnitude more bacterial 16S and fungal 5.8S rRNA gene copies were detected by qPCR from CM treated samples compared to KIT extractions. A clear difference in the detected microbial community structure between CM and KIT extracted samples was also observed. Commercial kits optimized for mineral soils are easy to use and time efficient but may miss a considerable part of the microbial communities. A competing agent such as anionic nanocellulose may decrease the interaction between microorganisms or their DNA and minerals and provide a comprehensive view into the microbial communities in mineral processing environments.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland.
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland
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Sandall EL, Maureaud AA, Guralnick R, McGeoch MA, Sica YV, Rogan MS, Booher DB, Edwards R, Franz N, Ingenloff K, Lucas M, Marsh CJ, McGowan J, Pinkert S, Ranipeta A, Uetz P, Wieczorek J, Jetz W. A globally integrated structure of taxonomy to support biodiversity science and conservation. Trends Ecol Evol 2023; 38:1143-1153. [PMID: 37684131 DOI: 10.1016/j.tree.2023.08.004] [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: 10/31/2022] [Revised: 07/30/2023] [Accepted: 08/04/2023] [Indexed: 09/10/2023]
Abstract
All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.
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Affiliation(s)
- Emily L Sandall
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA.
| | - Aurore A Maureaud
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, USA.
| | - Robert Guralnick
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Melodie A McGeoch
- Securing Antarctica's Environmental Future, Department of Environment and Genetics, LaTrobe University, Melbourne, Australia
| | - Yanina V Sica
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Matthew S Rogan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Douglas B Booher
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Robert Edwards
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; Cleveland Museum of Natural History, Cleveland, OH, USA
| | - Nico Franz
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Kate Ingenloff
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Maisha Lucas
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Charles J Marsh
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Jennifer McGowan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; The Nature Conservancy, Arlington, VA, USA
| | - Stefan Pinkert
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; Department of Conservation Ecology, University of Marburg, Marburg, Germany
| | - Ajay Ranipeta
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA
| | - Peter Uetz
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA
| | - John Wieczorek
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06520, USA; Center for Biodiversity & Global Change, Yale University, New Haven, CT 06520, USA; E.O. Wilson Biodiversity Foundation, Durham, NC, USA
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36
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Thamm M, Reiß F, Sohl L, Gabel M, Noll M, Scheiner R. Solitary Bees Host More Bacteria and Fungi on Their Cuticle than Social Bees. Microorganisms 2023; 11:2780. [PMID: 38004791 PMCID: PMC10673014 DOI: 10.3390/microorganisms11112780] [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: 10/10/2023] [Revised: 11/01/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Bees come into contact with bacteria and fungi from flowering plants during their foraging trips. The Western honeybee (Apis mellifera) shows a pronounced hygienic behavior with social interactions, while the solitary red mason bee (Osmia bicornis) lacks a social immune system. Since both visit the same floral resources, it is intriguing to speculate that the body surface of a solitary bee should harbor a more complex microbiome than that of the social honeybee. We compared the cuticular microbiomes of A. mellifera (including three European subspecies) and O. bicornis for the first time by bacterial 16S rRNA and fungal ITS gene-based high-throughput amplicon sequencing. The cuticular microbiome of the solitary O. bicornis was significantly more complex than that of the social A. mellifera. The microbiome composition of A. mellifera subspecies was very similar. However, we counted significantly different numbers of fungi and a higher diversity in the honeybee subspecies adapted to warmer climates. Our results suggest that the cuticular microbiome of bees is strongly affected by visited plants, lifestyle and adaptation to temperature, which have important implications for the maintenance of the health of bees under conditions of global change.
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Affiliation(s)
- Markus Thamm
- Behavioral Physiology and Sociobiology, Julius-Maximilians-Universität Würzburg, 97070 Würzburg, Germany; (M.T.); (M.G.)
| | - Fabienne Reiß
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; (F.R.); (L.S.)
| | - Leon Sohl
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; (F.R.); (L.S.)
| | - Martin Gabel
- Behavioral Physiology and Sociobiology, Julius-Maximilians-Universität Würzburg, 97070 Würzburg, Germany; (M.T.); (M.G.)
- Landesbetrieb Landwirtschaft Hessen, Bee Institute Kirchhain, 35274 Kirchhain, Germany
| | - Matthias Noll
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany; (F.R.); (L.S.)
- Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ricarda Scheiner
- Behavioral Physiology and Sociobiology, Julius-Maximilians-Universität Würzburg, 97070 Würzburg, Germany; (M.T.); (M.G.)
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de Morais JS, Cabral L, Bezerril FF, Uhlmann LO, Dos Santos Lima M, Noronha MF, Dos Santos SA, Madruga MS, Olegario LS, Wagner R, Sant'Ana AS, Magnani M. Farming system impacts the bioactive compounds, microbial diversity, aroma and color in edible red mini-roses (Rosa chinensis Jacq.). Food Res Int 2023; 173:113233. [PMID: 37803548 DOI: 10.1016/j.foodres.2023.113233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/15/2023] [Accepted: 06/27/2023] [Indexed: 10/08/2023]
Abstract
Mini-roses (Rosa chinensis Jacq.) is largely used in salty dishes and desserts. This study evaluated instrumental color, sugars, organic acids, phenolics, volatiles, and the indigenous microbiota (fungi and bacteria) in edible mini-roses farmed in discarded fruits biocompost and animal manure systems. A descriptive sensory analysis of flowers was also performed. Mini-roses farmed in biocompost had higher luminosity and intensity of instrumental red color, a higher concentration of phenolic compounds, including anthocyanins related to red color, and fructose than mini-roses farmed in animal manure (p < 0.05). Furthermore, mini-roses farmed in biocompost had higher concentrations of various volatiles (p < 0.05), including hexyl acetate and cis-3 -hexenyl butyrate related to the fruity aroma. Bacterial groups related to plant growth-promoting such as Stenotrophomonas and endophilic fungal groups such as Eurotiales sp, Pleosporales sp were found in higher abundance (p < 0.05) in mini-roses farmed in biocompost. Mini-rose farmed in biocompost also received higher score (p < 0.05) for fruity aroma and red color than mini-rose mini-roses farmed in animal manure. Results indicate that farming mini-roses using biocompost from discarded fruits impacts the synthesis of phenolics and volatiles, resulting in a more intense fruity aroma and red color. Findings also suggest that the microbiota of mini-roses farmed in biocompost or animal manure do not represent a major risk for the safety of these products.
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Affiliation(s)
- Janne Santos de Morais
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Center of Technology, Federal University of Paraíba, Campus I, 58051-900 João Pessoa, Paraíba, Brazil
| | - Lucélia Cabral
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Center of Technology, Federal University of Paraíba, Campus I, 58051-900 João Pessoa, Paraíba, Brazil
| | - Fabricia França Bezerril
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Center of Technology, Federal University of Paraíba, Campus I, 58051-900 João Pessoa, Paraíba, Brazil
| | - Lilian Osmari Uhlmann
- Department of Phytotechnics, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Marcos Dos Santos Lima
- Department of Food Technology, Federal Institute of Sertão Pernambucano, Petrolina, Pernambuco, Brazil
| | - Melline F Noronha
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Silvana Alves Dos Santos
- Empresa Paraibana de Abastecimento e Serviços Agrícolas - EMPASA, João Pessoa, Paraíba 58071-000, Brazil
| | - Marta Suely Madruga
- Laboratory of Flavor Analysis, Department of Food Engineering, Center of Technology, Federal University of Paraíba, João Pessoa, Brazil
| | - Lary Souza Olegario
- Laboratory of Flavor Analysis, Department of Food Engineering, Center of Technology, Federal University of Paraíba, João Pessoa, Brazil
| | - Roger Wagner
- Department of Food Science Technology, Federal University Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, State of São Paulo, Brazil
| | - Marciane Magnani
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Center of Technology, Federal University of Paraíba, Campus I, 58051-900 João Pessoa, Paraíba, Brazil.
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Reiß F, Schuhmann A, Sohl L, Thamm M, Scheiner R, Noll M. Fungicides and insecticides can alter the microbial community on the cuticle of honey bees. Front Microbiol 2023; 14:1271498. [PMID: 37965543 PMCID: PMC10642971 DOI: 10.3389/fmicb.2023.1271498] [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: 08/03/2023] [Accepted: 09/28/2023] [Indexed: 11/16/2023] Open
Abstract
Honey bees are crucial for our ecosystems as pollinators, but the intensive use of plant protection products (PPPs) in agriculture poses a risk for them. PPPs do not only affect target organisms but also affect non-targets, such as the honey bee Apis mellifera and their microbiome. This study is the first of its kind, aiming to characterize the effect of PPPs on the microbiome of the cuticle of honey bees. We chose PPPs, which have frequently been detected in bee bread, and studied their effects on the cuticular microbial community and function of the bees. The effects of the fungicide Difcor® (difenoconazole), the insecticide Steward® (indoxacarb), the combination of both (mix A) and the fungicide Cantus® Gold (boscalid and dimoxystrobin), the insecticide Mospilan® (acetamiprid), and the combination of both (mix B) were tested. Bacterial 16S rRNA gene and fungal transcribed spacer region gene-based amplicon sequencing and quantification of gene copy numbers were carried out after nucleic acid extraction from the cuticle of honey bees. The treatment with Steward® significantly affected fungal community composition and function. The fungal gene copy numbers were lower on the cuticle of bees treated with Difcor®, Steward®, and PPP mix A in comparison with the controls. However, bacterial and fungal gene copy numbers were increased in bees treated with Cantus® Gold, Mospilan®, or PPP mix B compared to the controls. The bacterial cuticular community composition of bees treated with Cantus® Gold, Mospilan®, and PPP mix B differed significantly from the control. In addition, Mospilan® on its own significantly changed the bacterial functional community composition. Cantus® Gold significantly affected fungal gene copy numbers, community, and functional composition. Our results demonstrate that PPPs show adverse effects on the cuticular microbiome of honey bees and suggest that PPP mixtures can cause stronger effects on the cuticular community than a PPP alone. The cuticular community composition was more diverse after the PPP mix treatments. This may have far-reaching consequences for the health of honey bees.
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Affiliation(s)
- Fabienne Reiß
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Antonia Schuhmann
- Behavioral Physiology and Sociobiology, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Leon Sohl
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Markus Thamm
- Behavioral Physiology and Sociobiology, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Ricarda Scheiner
- Behavioral Physiology and Sociobiology, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Matthias Noll
- Institute of Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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De-la-Vega-Camarillo E, Hernández-García JA, Villa-Tanaca L, Hernández-Rodríguez C. Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents. FRONTIERS IN PLANT SCIENCE 2023; 14:1247814. [PMID: 37860235 PMCID: PMC10582567 DOI: 10.3389/fpls.2023.1247814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.
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Affiliation(s)
| | | | | | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
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Arrieta-Echeverri MC, Fernandez GJ, Duarte-Riveros A, Correa-Álvarez J, Bardales JA, Villanueva-Mejía DF, Sierra-Zapata L. Multi-omics characterization of the microbial populations and chemical space composition of a water kefir fermentation. Front Mol Biosci 2023; 10:1223863. [PMID: 37849822 PMCID: PMC10577418 DOI: 10.3389/fmolb.2023.1223863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
In recent years, the popularity of fermented foods has strongly increased based on their proven health benefits and the adoption of new trends among consumers. One of these health-promoting products is water kefir, which is a fermented sugary beverage based on kefir grains (symbiotic colonies of yeast, lactic acid and acetic acid bacteria). According to previous knowledge and the uniqueness of each water kefir fermentation, the following project aimed to explore the microbial and chemical composition of a water kefir fermentation and its microbial consortium, through the integration of culture-dependent methods, compositional metagenomics, and untargeted metabolomics. These methods were applied in two types of samples: fermentation grains (inoculum) and fermentation samples collected at different time points. A strains culture collection of ∼90 strains was established by means of culture-dependent methods, mainly consisting of individuals of Pichia membranifaciens, Acetobacter orientalis, Lentilactobacillus hilgardii, Lacticaseibacillus paracasei, Acetobacter pomorum, Lentilactobacillus buchneri, Pichia kudriavzevii, Acetobacter pasteurianus, Schleiferilactobacillus harbinensis, and Kazachstania exigua, which can be further studied for their use in synthetic consortia formulation. In addition, metabarcoding of each fermentation time was done by 16S and ITS sequencing for bacteria and yeast, respectively. The results show strong population shifts of the microbial community during the fermentation time course, with an enrichment of microbial groups after 72 h of fermentation. Metataxonomics results revealed Lactobacillus and Acetobacter as the dominant genera for lactic acid and acetic acid bacteria, whereas, for yeast, P. membranifaciens was the dominant species. In addition, correlation and systematic analyses of microbial growth patterns and metabolite richness allowed the recognition of metabolic enrichment points between 72 and 96 h and correlation between microbial groups and metabolite abundance (e.g., Bile acid conjugates and Acetobacter tropicalis). Metabolomic analysis also evidenced the production of bioactive compounds in this fermented matrix, which have been associated with biological activities, including antimicrobial and antioxidant. Interestingly, the chemical family of Isoschaftosides (C-glycosyl flavonoids) was also found, representing an important finding since this compound, with hepatoprotective and anti-inflammatory activity, had not been previously reported in this matrix. We conclude that the integration of microbial biodiversity, cultured species, and chemical data enables the identification of relevant microbial population patterns and the detection of specific points of enrichment during the fermentation process of a food matrix, which enables the future design of synthetic microbial consortia, which can be used as targeted probiotics for digestive and metabolic health.
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Affiliation(s)
| | - Geysson Javier Fernandez
- Infectious Diseases Biology and Control Group (BCEI), Universidad de Antioquia UdeA, Medellín, Colombia
| | | | - Javier Correa-Álvarez
- Research Group CIBIOP, School of Applied Sciences and Engineering, Universidad EAFIT, Medellín, Antioquia, Colombia
| | | | | | - Laura Sierra-Zapata
- Research Group CIBIOP, School of Applied Sciences and Engineering, Universidad EAFIT, Medellín, Antioquia, Colombia
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Pagani DM, Ventura SPR, Vu D, Mendes-Pereira T, Ribeiro Tomé LM, de Carvalho DS, Costa-Rezende DH, Kato RB, García GJY, Geml J, Robert V, They NH, Brenig B, Azevedo V, Scroferneker ML, Valente P, Góes-Neto A. Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon. J Fungi (Basel) 2023; 9:890. [PMID: 37754998 PMCID: PMC10532596 DOI: 10.3390/jof9090890] [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: 07/25/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.
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Affiliation(s)
- Danielle Machado Pagani
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Stefânia P. R. Ventura
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Thairine Mendes-Pereira
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Luiz Marcelo Ribeiro Tomé
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Daniel Santana de Carvalho
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
| | - Diogo Henrique Costa-Rezende
- Departamento de Ciências Biológicas, Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Feira de Santana 44036-900, BA, Brazil;
| | - Rodrigo Bentes Kato
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - Glen Jasper Yupanqui García
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
| | - József Geml
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka U. 6, 3300 Eger, Hungary;
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (D.V.); (V.R.)
| | - Ng Haig They
- Laboratório de Ecologia Aquática Microbiana, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Departamento Interdisciplinar, Centro de Estudos Costeiros, Limnológicos e Marinhos, Universidade Federal do Rio Grande do Sul, Campus Litoral Norte, Tramandaí 95590-000, RS, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Goettingen, 37073 Göttingen, Germany;
| | - Vasco Azevedo
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Laboratory of Cellular and Molecular Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Maria Lúcia Scroferneker
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil;
| | - Patricia Valente
- Programa de Pós-Graduação em Microbiologia Agrícola e do Ambiente, Universidade Federal do Rio Grande do Sul, Porto Alegre 90010-150, RS, Brazil; (D.M.P.); (P.V.)
| | - Aristóteles Góes-Neto
- Programa de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (S.P.R.V.); (R.B.K.); (G.J.Y.G.); (V.A.)
- Programa de Pós-Graduação em Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (T.M.-P.); (L.M.R.T.); (D.S.d.C.)
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Correia P, Azevedo E, Caeiro MF. Redefining the Genus Corollospora Based on Morphological and Phylogenetic Approaches. J Fungi (Basel) 2023; 9:841. [PMID: 37623612 PMCID: PMC10455288 DOI: 10.3390/jof9080841] [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: 06/06/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
The present study, initially to resolve the cryptic species within Corollospora maritima, is to determine how to attain taxonomic discrimination at species and generic levels. Multiple sequence alignments (MSAs) of the ITS, 28S, and 18S regions of the nuclear ribosomal cistron were separately subjected to pairwise distance assessments, Bayesian, and Maximum likelihood phylogenetic analyses. Morphological descriptions of 15 type strains of Corollospora species, along with MSAs involving representatives of the whole genus Corollospora (268 isolates, many from C. maritima sensu lato) totaling 355 published sequences, allowed phylogenetic assessments conducted to the following p-distance thresholds in the ITS/28S regions: ≥3%/1% for species segregation and ≥8%/2% for generic segregation. This resulted in the introduction of 10 new genera encompassing 13 new combinations of current Corollospora species: Ajigaurospora pseudopulchella, Corollosporella anglusa, Corollosporella ramulosa, Corollosporopsis portsaidica, Garethelia parvula, Honshuriella fusca, Keraliethelia pulcehlla, Nakagariella filiformis, Paracorollospora angusta, Paracorollospora luteola, Paracorollospora marina, Shirahamella gracilis, and Tokuratelia colossa. Furthermore, seven undefined genera considered putative new genera (pNGenus A to G), and 16 undefined putative new species (seven spp. come from the resolution of the C. maritima complex), await re-assessment of their morphology and additional molecular data, which may result in the recognition of new taxa.
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Affiliation(s)
- Pedro Correia
- Centro de Ecologia, Evolução e Alterações Climáticas (ce3c), Faculdade de Ciências da Universidade de Lisboa (FCUL), DBV, C2, Campo Grande, 1749-016 Lisboa, Portugal; (P.C.); (E.A.)
| | - Egídia Azevedo
- Centro de Ecologia, Evolução e Alterações Climáticas (ce3c), Faculdade de Ciências da Universidade de Lisboa (FCUL), DBV, C2, Campo Grande, 1749-016 Lisboa, Portugal; (P.C.); (E.A.)
- Centro de Estudos do Ambiente e do Mar (CESAM Lisboa), Faculdade de Ciências da Universidade de Lisboa (FCUL), DBV, C2, Campo Grande, 1749-016 Lisboa, Portugal
| | - Maria F. Caeiro
- Centro de Estudos do Ambiente e do Mar (CESAM Lisboa), Faculdade de Ciências da Universidade de Lisboa (FCUL), DBV, C2, Campo Grande, 1749-016 Lisboa, Portugal
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Mishcherikova V, Lynikienė J, Marčiulynas A, Gedminas A, Prylutskyi O, Marčiulynienė D, Menkis A. Biogeography of Fungal Communities Associated with Pinus sylvestris L. and Picea abies (L.) H. Karst. along the Latitudinal Gradient in Europe. J Fungi (Basel) 2023; 9:829. [PMID: 37623600 PMCID: PMC10455207 DOI: 10.3390/jof9080829] [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: 07/05/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
We assessed the diversity and composition of fungal communities in different functional tissues and the rhizosphere soil of Pinus sylvestris and Picea abies stands along the latitudinal gradient of these tree species distributions in Europe to model possible changes in fungal communities imposed by climate change. For each tree species, living needles, shoots, roots, and the rhizosphere soil were sampled and subjected to high-throughput sequencing. Results showed that the latitude and the host tree species had a limited effect on the diversity and composition of fungal communities, which were largely explained by the environmental variables of each site and the substrate they colonize. The mean annual temperature and mean annual precipitation had a strong effect on root fungal communities, isothermality on needle fungal communities, mean temperature of the warmest quarter and precipitation of the driest month on shoot fungal communities, and precipitation seasonality on soil fungal communities. Fungal communities of both tree species are predicted to shift to habitats with a lower annual temperature amplitude and with increasing precipitation during the driest month, but the suitability of these habitats as compared to the present conditions is predicted to decrease in the future.
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Affiliation(s)
- Valeriia Mishcherikova
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, V.N. Karazin Kharkiv National University, Svobody Sq., 61022 Kharkiv, Ukraine;
| | - Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
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Eriksen E, Madsen AM, Afanou AK, Straumfors A, Eiler A, Graff P. Occupational exposure to inhalable pathogenic microorganisms in waste sorting. Int J Hyg Environ Health 2023; 253:114240. [PMID: 37633050 DOI: 10.1016/j.ijheh.2023.114240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
This study assessed microorganisms in personal inhalable work air samples aiming to identify potential human pathogens, and correlate exposure to adverse health outcomes in waste workers. Full-shift personal exposure was measured in six different waste sorting plants. Microbial concentrations in inhalable air samples were analysed using MALDI-TOF MS for cultivable, and next generation sequencing (NGS) for non-cultivable microorganisms. Concentrations of bacterial and fungal CFUs varied substantially within and between waste sorting plants, ranging from no identifiable organisms to a maximum concentration in the order of 105 CFU/m3. Bacillus and Staphylococcus were among the most abundant bacterial genera, whilst fungal genera were dominated by Aspergillus and Penicillium. Approximately 15% of all identified species were human pathogens classified in risk group 2, whereas 7% belonged to risk group 1. Furthermore, significant correlations between concentrations of fungi in risk group 1 and self-reported adverse symptoms, such as wheezing were identified in exposed workers. The combination of culture-based methods and NGS facilitated the investigation of infectious microbial species with potential pathophysiological properties as well as non-infectious biological agents in inhalable work air samples and thereby contributed to the risk assessment of occupational exposure in waste sorting.
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Affiliation(s)
- Elke Eriksen
- STAMI, National Institute of Occupational Health, Gydas Vei 8, 0363, Oslo, Norway; Section for Aquatic Biology and Toxicology, Department of Biosciences, Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway.
| | - Anne Mette Madsen
- The National Research Center for Work Environment, Lersø Parkallé 105, 2100, Copenhagen, Denmark
| | - Anani Komlavi Afanou
- STAMI, National Institute of Occupational Health, Gydas Vei 8, 0363, Oslo, Norway
| | - Anne Straumfors
- STAMI, National Institute of Occupational Health, Gydas Vei 8, 0363, Oslo, Norway
| | - Alexander Eiler
- Section for Aquatic Biology and Toxicology, Department of Biosciences, Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Pål Graff
- STAMI, National Institute of Occupational Health, Gydas Vei 8, 0363, Oslo, Norway
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45
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Sun P, Li Z, Zhang B. Characterization of disease-associated microbiota in hepatocellular carcinoma. J Cancer Res Ther 2023; 19:881-891. [PMID: 37675712 DOI: 10.4103/jcrt.jcrt_139_22] [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] [Indexed: 09/08/2023]
Abstract
Aims This study aimed to investigate the differences in the composition of microbial communities and related functions in hepatocellular carcinoma (HCC) tumours and matched normal tissues were investigated. Methods and Material Tumour tissues and matched normal samples were collected from 30 HCC patients. Genomic DNA was collected and subjected to sequencing of the V3 + V4 region of the 16S rRNA gene. The microbial community profiles and metabolic pathway predictions of the different groups were characterized and compared. Results Tumour and adjacent tissues had similar microbiota compositions but differed in abundance. Proteobacteria and Firmicutes abundance decreased and Cyanobacteria and Acidobacteria abundance increased in the tumour tissue. The microbial community diversity was higher in the tumour tissues than in adjacent samples, with potentially more dominant taxa in the adjacent tissues, including Firmicutes, Proteobacteria, and Actinobacteria. Acidobacteria, Cyanobacteria, and Chloroflexi were the dominant microbes in tumour tissues. A total of 46 metabolic pathways were identified. Global and overview maps were the most abundant pathways, followed by carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport. The top 50 most highly correlated microbial genera included Klebsiella, Rhodococcus, Ochrobactrum, and Azoarcus. Fonticella, Haloimpatiens, Brevibacterium, and Acidothermus were positively correlated with other microbial genera. The microbiota of adjacent tissues was more robust in the network analysis. Conclusions This study revealed differences in microbial composition between HCC tumour tissues and normal tissues and differences in microbial abundance associated with different metabolic functions. Cyanobacteria, Proteobacteria, and Actinobacteria may play important roles in HCC.
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Affiliation(s)
- Pengfei Sun
- Department of Hepatobiliary and Pancreatic Surgery, Shandong Cancer Hospital and Institute, Shandong Fist Medical University and Shandong Academy of Medical Sciences, Jinan City, Shandong Province, China
| | - Zhongchao Li
- Department of Hepatobiliary and Pancreatic Surgery, Shandong Cancer Hospital and Institute, Shandong Fist Medical University and Shandong Academy of Medical Sciences, Jinan City, Shandong Province, China
| | - Bo Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Shandong Cancer Hospital and Institute, Shandong Fist Medical University and Shandong Academy of Medical Sciences, Jinan City, Shandong Province, China
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46
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Janowski D, Leski T. Landscape-scale mapping of soil fungal distribution: proposing a new NGS-based approach. Sci Rep 2023; 13:10280. [PMID: 37355666 PMCID: PMC10290699 DOI: 10.1038/s41598-023-37538-7] [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: 04/12/2023] [Accepted: 06/23/2023] [Indexed: 06/26/2023] Open
Abstract
Soil fungi play an indispensable role in the functioning of terrestrial habitats. Most landscape-scale studies of soil fungal diversity try to identify the fungal taxa present at a study site and define the relationships between their abundance and environmental factors. The specific spatial distribution of these fungi over the site, however, is not addressed. Our study's main objective is to propose a novel approach to landscape-scale mapping of soil fungi distribution using next generation sequencing and geographic information system applications. Furthermore, to test the proposed approach and discuss its performance, we aimed to conduct a case study mapping the spatial distribution of soil fungi on the Wielka Żuława island. The case study was performed on the Wielka Żuława island in northern Poland, where soil samples were collected every 100 m in an even grid. The fungal taxa and their relative abundance in each sample were assessed using the Illumina platform. Using the data obtained for the sampled points, maps of soil fungi spatial distribution were generated using three common interpolators: inverted distance weighted (IDW), B-spline, and ordinary Kriging. The proposed approach succeeded in creating maps of fungal distribution on Wielka Żuława. The most abundant groups of soil fungi were Penicillium on the genus level, Aspergillaceae on the family level, and ectomycorrhizal fungi on the trophic group level. Ordinary Kriging proved to be the most accurate at predicting relative abundance values for the groups of fungi significantly spatially autocorrelated at the sampled scale. For the groups of fungi not displaying spatial autocorrelation at the sampled scale, IDW provided the most accurate predictions of their relative abundance. Although less accurate at predicting exact relative abundance values, B-spline performed best in delineating the spatial patterns of soil fungi distribution. The proposed approach to landscape-scale mapping of soil fungi distribution could provide new insights into the ecology of soil fungi and terrestrial ecosystems in general. Producing maps of predicted fungal distribution in landscape-scale soil fungi diversity studies would also facilitate the reusability and replicability of the results. Outside the area of research, mapping the distribution of soil fungi could prove helpful in areas such as agriculture and forestry, nature conservation, and urban planning.
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Affiliation(s)
- Daniel Janowski
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland.
- Department of Natural Environmental Studies, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Tomasz Leski
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
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47
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van Galen LG, Orlovich DA, Lord JM, Nilsen AR, Dutoit L, Larcombe MJ. Correlated evolution in an ectomycorrhizal host-symbiont system. THE NEW PHYTOLOGIST 2023; 238:1215-1229. [PMID: 36751898 DOI: 10.1111/nph.18802] [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: 11/06/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.
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Affiliation(s)
- Laura G van Galen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - David A Orlovich
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Janice M Lord
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Andy R Nilsen
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
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Szulc J, Okrasa M, Ryngajłło M, Pielech-Przybylska K, Gutarowska B. Markers of Chemical and Microbiological Contamination of the Air in the Sport Centers. Molecules 2023; 28:molecules28083560. [PMID: 37110794 PMCID: PMC10144153 DOI: 10.3390/molecules28083560] [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: 03/27/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
This study aimed to assess the markers of chemical and microbiological contamination of the air at sport centers (e.g., the fitness center in Poland) including the determination of particulate matter, CO2, formaldehyde (DustTrak™ DRX Aerosol Monitor; Multi-functional Air Quality Detector), volatile organic compound (VOC) concentration (headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry), the number of microorganisms in the air (culture methods), and microbial biodiversity (high-throughput sequencing on the Illumina platform). Additionally the number of microorganisms and the presence of SARS-CoV-2 (PCR) on the surfaces was determined. Total particle concentration varied between 0.0445 mg m-3 and 0.0841 mg m-3 with the dominance (99.65-99.99%) of the PM2.5 fraction. The CO2 concentration ranged from 800 ppm to 2198 ppm, while the formaldehyde concentration was from 0.005 mg/m3 to 0.049 mg m-3. A total of 84 VOCs were identified in the air collected from the gym. Phenol, D-limonene, toluene, and 2-ethyl-1-hexanol dominated in the air at the tested facilities. The average daily number of bacteria was 7.17 × 102 CFU m-3-1.68 × 103 CFU m-3, while the number of fungi was 3.03 × 103 CFU m-3-7.34 × 103 CFU m-3. In total, 422 genera of bacteria and 408 genera of fungi representing 21 and 11 phyla, respectively, were detected in the gym. The most abundant bacteria and fungi (>1%) that belonged to the second and third groups of health hazards were: Escherichia-Shigella, Corynebacterium, Bacillus, Staphylococcus, Cladosporium, Aspergillus, and Penicillium. In addition, other species that may be allergenic (Epicoccum) or infectious (Acinetobacter, Sphingomonas, Sporobolomyces) were present in the air. Moreover, the SARS-CoV-2 virus was detected on surfaces in the gym. The monitoring proposal for the assessment of the air quality at a sport center includes the following markers: total particle concentration with the PM2.5 fraction, CO2 concentration, VOCs (phenol, toluene, and 2-ethyl-1-hexanol), and the number of bacteria and fungi.
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Affiliation(s)
- Justyna Szulc
- Department of Environmental Biotechnology, Lodz University of Technology, 90-530 Łódź, Poland
| | - Małgorzata Okrasa
- Department of Personal Protective Equipment, Central Institute for Labour Protection-National Research Institute, 90-133 Łódź, Poland
| | - Małgorzata Ryngajłło
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-573 Łódź, Poland
| | | | - Beata Gutarowska
- Department of Environmental Biotechnology, Lodz University of Technology, 90-530 Łódź, Poland
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Nguyen NH, Nguyen PT, Otake H, Nagata A, Hirano N, Imanishi-Shimizu Y, Shimizu K. Biodiversity of Basidiomycetous Yeasts Associated with Cladonia rei Lichen in Japan, with a Description of Microsporomyces cladoniophilus sp. nov. J Fungi (Basel) 2023; 9:jof9040473. [PMID: 37108927 PMCID: PMC10145395 DOI: 10.3390/jof9040473] [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: 12/28/2022] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
For more than a century, lichens have been used as an example of dual-partner symbiosis. Recently, this has been challenged by the discovery of various basidiomycetous yeasts that coexist in multiple lichen species, among which Cladonia lichens from Europe and the United States were discovered to be highly specifically associated with the basidiomycetous yeast of the family Microsporomycetaceae. To verify this highly specific relationship, we investigated the diversity of basidiomycetous yeasts associated with Cladonia rei, a widely distributed lichen in Japan, by applying two approaches: yeast isolation from the lichen thalli and meta-barcoding analysis. We obtained 42 cultures of Cystobasidiomycetous yeast which were grouped into six lineages within the family Microsporomycetaceae. Unexpectedly, although the cystobasidiomycetes-specific primer was used, not only the cystobasidiomycetous yeasts but species from other classes were also detected via the meta-barcoding dataset; in particular, pucciniomycetous yeasts were found at a high frequency in some samples. Further, Halobasidium xiangyangense, which was detected in every sample with high abundance, is highly likely a generalist epiphytic fungus that has the ability to associate with C. rei. In the pucciniomycetous group, most of the detected species belong to the scale insect-associated yeast Septobasidium genus. In conclusion, even though Microsporomyces species are not the only yeast group associated with Cladonia lichen, our study demonstrated that the thalli of Cladonia rei lichen could be a suitable habit for them.
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Affiliation(s)
- Ngoc-Hung Nguyen
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Phuong-Thao Nguyen
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Hitomi Otake
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Ayana Nagata
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Nobuharu Hirano
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
| | - Yumi Imanishi-Shimizu
- College of Science and Engineering, Kanto Gakuin University, Mutsuura-higashi 1-50-1, Kanazawa-ku, Yokohama 236-8501, Kanagawa, Japan
| | - Kiminori Shimizu
- Department of Biological Science and Technology, Tokyo University of Science, Niijuku 6-3-1, Katsushika, Tokyo 125-8585, Japan
- Medical Mycology Research Center, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8673, Chiba, Japan
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50
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Couvillion SP, Danczak RE, Cao X, Yang Q, Keerthisinghe TP, McClure RS, Bitounis D, Burnet MC, Fansler SJ, Richardson RE, Fang M, Qian WJ, Demokritou P, Thrall BD. Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model. NANOIMPACT 2023; 30:100463. [PMID: 37060994 DOI: 10.1016/j.impact.2023.100463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
Graphene oxide (GO) nanomaterials have unique physicochemical properties that make them highly promising for biomedical, environmental, and agricultural applications. There is growing interest in the use of GO and extensive in vitro and in vivo studies have been conducted to assess its nanotoxicity. Although it is known that GO can alter the composition of the gut microbiota in mice and zebrafish, studies on the potential impacts of GO on the human gut microbiome are largely lacking. This study addresses an important knowledge gap by investigating the impact of GO exposure- at low (25 mg/L) and high (250 mg/L) doses under both fed (nutrient rich) and fasted (nutrient deplete) conditions- on the gut microbial communitys' structure and function, using an in vitro model. This model includes simulated oral, gastric, small intestinal phase digestion of GO followed by incubation in a colon bioreactor. 16S rRNA amplicon sequencing revealed that GO exposure resulted in a restructuring of community composition. 25 mg/L GO induced a marked decrease in the Bacteroidota phylum and increased the ratio of Firmicutes to Bacteroidota (F/B). Untargeted metabolomics on the supernatants indicated that 25 mg/L GO impaired microbial utilization and metabolism of substrates (amino acids, carbohydrate metabolites) and reduced production of beneficial microbial metabolites such as 5-hydroxyindole-3-acetic acid and GABA. Exposure to 250 mg/L GO resulted in community composition and metabolome profiles that were very similar to the controls that lacked both GO and digestive enzymes. Differential abundance analyses revealed that 3 genera from the phylum Bacteroidota (Bacteroides, Dysgonomonas, and Parabacteroides) were more abundant after 250 mg/L GO exposure, irrespective of feed state. Integrative correlation network analysis indicated that the phylum Bacteroidota showed strong positive correlations to multiple microbial metabolites including GABA and 3-indoleacetic acid, are much larger number of correlations compared to other phyla. These results show that GO exposure has a significant impact on gut microbial community composition and metabolism at both low and high GO concentrations.
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Affiliation(s)
- Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Robert E Danczak
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xiaoqiong Cao
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Qin Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Tharushi P Keerthisinghe
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Ryan S McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rachel E Richardson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore; Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA.
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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