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Wang M, Li D, Frey B, Gao D, Liu X, Chen C, Sui X, Li M. Land use modified impacts of global change factors on soil microbial structure and function: A global hierarchical meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173286. [PMID: 38772492 DOI: 10.1016/j.scitotenv.2024.173286] [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: 03/17/2024] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 05/23/2024]
Abstract
Nitrogen cycling in terrestrial ecosystems is critical for biodiversity, vegetation productivity and biogeochemical cycling. However, little is known about the response of functional nitrogen cycle genes to global change factors in soils under different land uses. Here, we conducted a multiple hierarchical mixed effects meta-analyses of global change factors (GCFs) including warming (W+), mean altered precipitation (MAP+/-), elevated carbon dioxide concentrations (eCO2), and nitrogen addition (N+), using 2706 observations extracted from 200 peer-reviewed publications. The results showed that GCFs had significant and different effects on soil microbial communities under different types of land use. Under different land use types, such as Wetland, Tundra, Grassland, Forest, Desert and Agriculture, the richness and diversity of soil microbial communities will change accordingly due to differences in vegetation cover, soil management practices and environmental conditions. Notably, soil bacterial diversity is positively correlated with richness, but soil fungal diversity is negatively correlated with richness, when differences are driven by GCFs. For functional genes involved in nitrification, eCO2 in agricultural soils and the interaction of N+ with other GCFs in grassland soils stimulate an increase in the abundance of the AOA-amoA gene. In agricultural soil, MAP+ increases the abundance of nifH. W+ in agricultural soils and N+ in grassland soils decreased the abundance of nifH. The abundance of the genes nirS and nirK, involved in denitrification, was mainly negatively affected by W+ and positively affected by eCO2 in agricultural soil, but negatively affected by N+ in grassland soil. This meta-analysis was important for subsequent research related to global climate change. Considering data limitations, it is recommended to conduct multiple long-term integrated observational experiments to establish a scientific basis for addressing global changes in this context.
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Affiliation(s)
- Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Detian Li
- Griffith School of Environment and Science and the Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Beat Frey
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Decai Gao
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, PR China
| | - Xiangyu Liu
- Griffith School of Environment and Science and the Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Chengrong Chen
- Griffith School of Environment and Science and the Australian Rivers Institute, Griffith University, Nathan, QLD, Australia
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China.
| | - Maihe Li
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland; Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, PR China; School of Life Science, Hebei University, Baoding, China.
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Gadd GM, Fomina M, Pinzari F. Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation. Microbiol Mol Biol Rev 2024; 88:e0020022. [PMID: 38179930 PMCID: PMC10966957 DOI: 10.1128/mmbr.00200-22] [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: 05/30/2023] [Accepted: 09/11/2023] [Indexed: 01/06/2024] Open
Abstract
SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.
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Affiliation(s)
- Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, College of Chemical Engineering and Environment, China University of Petroleum, Beijing, China
| | - Marina Fomina
- Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- National Reserve “Sophia of Kyiv”, Kyiv, Ukraine
| | - Flavia Pinzari
- Institute for Biological Systems (ISB), Council of National Research of Italy (CNR), Monterotondo (RM), Italy
- Natural History Museum, London, United Kingdom
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Barnés-Guirado M, Stchigel AM, Cano-Lira JF. A New Genus of the Microascaceae (Ascomycota) Family from a Hypersaline Lagoon in Spain and the Delimitation of the Genus Wardomyces. J Fungi (Basel) 2024; 10:236. [PMID: 38667907 PMCID: PMC11051006 DOI: 10.3390/jof10040236] [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: 02/13/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The Saladas de Sástago-Bujaraloz is an endorheic and arheic complex of lagoons located in the Ebro Basin and protected by the Ramsar Convention on Wetlands. Due to the semi-arid climate of the region and the high salinity of their waters, these lagoons constitute an extreme environment. We surveyed the biodiversity of salt-tolerant and halophilic fungi residents of the Laguna de Pito, a lagoon belonging to this complex. Therefore, we collected several samples of water, sediments, and soil of the periphery. Throughout the study, we isolated 21 fungal species, including a strain morphologically related to the family Microascaceae. However, this strain did not morphologically match any of genera within this family. After an in-depth morphological characterization and phylogenetic analysis using a concatenated sequence dataset of four phylogenetically informative molecular markers (the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA (nrDNA); the D1-D2 domains of the 28S gene of the nuclear ribosomal RNA (LSU); and a fragment of the translation elongation factor 1-alpha (EF-1α) and the β-tubulin (tub2) genes), we established the new genus Dactyliodendromyces, with Dactyliodendromyces holomorphus as its species. Additionally, as a result of our taxonomic study, we reclassified the paraphyletic genus Wardomyces into three different genera: Wardomyces sensu stricto, Parawardomyces gen. nov., and Pseudowardomyces gen. nov., with Parawardomyces ovalis (formerly Wardomyces ovalis) and Pseudowardomyces humicola (formerly Wardomyces humicola) as the type species of their respective genera. Furthermore, we propose new combinations, including Parawardomyces giganteus (formerly Wardomyces giganteus) and Pseudowardomyces pulvinatus (formerly Wardomyces pulvinatus).
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Affiliation(s)
| | - Alberto Miguel Stchigel
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain; (M.B.-G.); (J.F.C.-L.)
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4
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Gostinčar C, Gunde-Cimerman N. Black yeasts in hypersaline conditions. Appl Microbiol Biotechnol 2024; 108:252. [PMID: 38441672 PMCID: PMC10914880 DOI: 10.1007/s00253-024-13052-2] [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: 12/08/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 03/07/2024]
Abstract
Extremotolerant and extremophilic fungi are an important part of microbial communities that thrive in extreme environments. Among them, the black yeasts are particularly adaptable. They use their melanized cell walls and versatile morphology, as well as a complex set of molecular adaptations, to survive in conditions that are lethal to most other species. In contrast to extremophilic bacteria and archaea, these fungi are typically extremotolerant rather than extremophilic and exhibit an unusually wide ecological amplitude. Some extremely halotolerant black yeasts can grow in near-saturated NaCl solutions, but can also grow on normal mycological media. They adapt to the low water activity caused by high salt concentrations by sensing their environment, balancing osmotic pressure by accumulating compatible solutes, removing toxic salt ions from the cell using membrane transporters, altering membrane composition and remodelling the highly melanized cell wall. As protection against extreme conditions, halotolerant black yeasts also develop different morphologies, from yeast-like to meristematic. Genomic studies of black yeasts have revealed a variety of reproductive strategies, from clonality to intense recombination and the formation of stable hybrids. Although a comprehensive understanding of the ecological role and molecular adaptations of halotolerant black yeasts remains elusive and the application of many experimental methods is challenging due to their slow growth and recalcitrant cell walls, much progress has been made in deciphering their halotolerance. Advances in molecular tools and genomics are once again accelerating the research of black yeasts, promising further insights into their survival strategies and the molecular basis of their adaptations. KEY POINTS: • Black yeasts show remarkable adaptability to environmental stress • Black yeasts are part of microbial communities in hypersaline environments • Halotolerant black yeasts utilise various molecular and morphological adaptations.
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Affiliation(s)
- Cene Gostinčar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
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Hernando AV, Sun W, Abitbol T. "You Are What You Eat": How Fungal Adaptation Can Be Leveraged toward Myco-Material Properties. GLOBAL CHALLENGES (HOBOKEN, NJ) 2024; 8:2300140. [PMID: 38486929 PMCID: PMC10935908 DOI: 10.1002/gch2.202300140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/01/2023] [Indexed: 03/17/2024]
Abstract
Fungi adapt to their surroundings, modifying their behaviors and composition under different conditions like nutrient availability and environmental stress. This perspective examines how a basic understanding of fungal genetics and the different ways that fungi can be influenced by their surroundings can be leveraged toward the production of functional mycelium materials. Simply put, within the constraints of a given genetic script, both the quality and quantity of fungal mycelium are shaped by what they eat and where they grow. These two levers, encompassing their global growth environment, can be turned toward different materials outcomes. The final properties of myco-materials are thus intimately shaped by the conditions of their growth, enabling the design of new biobased and biodegradable material constructions for applications that have traditionally relied on petroleum-based chemicals.This perspective highlights aspects of fungal genetics and environmental adaptation that have potential materials science implications, along the way touching on key studies, both to situate the state of the art within the field and to punctuate the viewpoints of the authors. Finally, this work ends with future perspectives, reinforcing key topics deemed important to consider in emerging myco-materials research.
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Affiliation(s)
- Alicia Vivas Hernando
- Institute of Materials (IMX)École Polytechnique Fédérale de Lausanne (EPFL)Lausanne1015Switzerland
| | - Wenjing Sun
- Institute of Materials (IMX)École Polytechnique Fédérale de Lausanne (EPFL)Lausanne1015Switzerland
| | - Tiffany Abitbol
- Institute of Materials (IMX)École Polytechnique Fédérale de Lausanne (EPFL)Lausanne1015Switzerland
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6
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Georgieva ML, Bilanenko EN, Ponizovskaya VB, Kokaeva LY, Georgiev AA, Efimenko TA, Markelova NN, Kuvarina AE, Sadykova VS. Haloalkalitolerant Fungi from Sediments of the Big Tambukan Saline Lake (Northern Caucasus): Diversity and Antimicrobial Potential. Microorganisms 2023; 11:2587. [PMID: 37894245 PMCID: PMC10609068 DOI: 10.3390/microorganisms11102587] [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: 09/12/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
We have performed a characterization of cultivated haloalkalitolerant fungi from the sediments of Big Tambukan Lake in order to assess their biodiversity and antimicrobial activity. This saline, slightly alkaline lake is known as a source of therapeutic sulfide mud used in sanatoria of the Caucasian Mineral Waters, Russia. Though data on bacteria and algae observed in this lake are available in the literature, data on fungi adapted to the conditions of the lake are lacking. The diversity of haloalkalitolerant fungi was low and represented by ascomycetes of the genera Acremonium, Alternaria, Aspergillus, Chordomyces, Emericellopsis, Fusarium, Gibellulopsis, Myriodontium, Penicillium, and Pseudeurotium. Most of the fungi were characterized by moderate alkaline resistance, and they tolerated NaCl concentrations up to 10% w/v. The analysis of the antimicrobial activity of fungi showed that 87.5% of all strains were active against Bacillus subtilis, and 39.6% were also determined to be effective against Escherichia coli. The majority of the strains were also active against Aspergillus niger and Candida albicans, about 66.7% and 62.5%, respectively. These studies indicate, for the first time, the presence of polyextremotolerant fungi in the sediments of Big Tambukan Lake, which probably reflects their involvement in the formation of therapeutic muds.
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Affiliation(s)
- Marina L. Georgieva
- Gause Institute of New Antibiotics, St. Bolshaya Pirogovskaya 11, 119021 Moscow, Russia; (T.A.E.); (N.N.M.); (A.E.K.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234 Moscow, Russia; (E.N.B.); (V.B.P.); (L.Y.K.); (A.A.G.)
| | - Elena N. Bilanenko
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234 Moscow, Russia; (E.N.B.); (V.B.P.); (L.Y.K.); (A.A.G.)
| | - Valeria B. Ponizovskaya
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234 Moscow, Russia; (E.N.B.); (V.B.P.); (L.Y.K.); (A.A.G.)
| | - Lyudmila Y. Kokaeva
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234 Moscow, Russia; (E.N.B.); (V.B.P.); (L.Y.K.); (A.A.G.)
- Faculty of Soil Sciences, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Anton A. Georgiev
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119234 Moscow, Russia; (E.N.B.); (V.B.P.); (L.Y.K.); (A.A.G.)
| | - Tatiana A. Efimenko
- Gause Institute of New Antibiotics, St. Bolshaya Pirogovskaya 11, 119021 Moscow, Russia; (T.A.E.); (N.N.M.); (A.E.K.)
| | - Natalia N. Markelova
- Gause Institute of New Antibiotics, St. Bolshaya Pirogovskaya 11, 119021 Moscow, Russia; (T.A.E.); (N.N.M.); (A.E.K.)
| | - Anastasia E. Kuvarina
- Gause Institute of New Antibiotics, St. Bolshaya Pirogovskaya 11, 119021 Moscow, Russia; (T.A.E.); (N.N.M.); (A.E.K.)
| | - Vera S. Sadykova
- Gause Institute of New Antibiotics, St. Bolshaya Pirogovskaya 11, 119021 Moscow, Russia; (T.A.E.); (N.N.M.); (A.E.K.)
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Abstract
Hypersaline waters and glacial ice are inhospitable environments that have low water activity and high concentrations of osmolytes. They are inhabited by diverse microbial communities, of which extremotolerant and extremophilic fungi are essential components. Some fungi are specialized in only one of these two environments and can thrive in conditions that are lethal to most other life-forms. Others are generalists, highly adaptable species that occur in both environments and tolerate a wide range of extremes. Both groups efficiently balance cellular osmotic pressure and ion concentration, stabilize cell membranes, remodel cell walls, and neutralize intracellular oxidative stress. Some species use unusual reproductive strategies. Further investigation of these adaptations with new methods and carefully designed experiments under ecologically relevant conditions will help predict the role of fungi in hypersaline and glacial environments affected by climate change, decipher their stress resistance mechanisms and exploit their biotechnological potential.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
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8
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Dos Santos MSN, Ody LP, Kerber BD, Araujo BA, Oro CED, Wancura JHC, Mazutti MA, Zabot GL, Tres MV. New frontiers of soil fungal microbiome and its application for biotechnology in agriculture. World J Microbiol Biotechnol 2023; 39:287. [PMID: 37632593 DOI: 10.1007/s11274-023-03728-8] [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: 06/21/2023] [Accepted: 08/10/2023] [Indexed: 08/28/2023]
Abstract
The fungi-based technology provided encouraging scenarios in the transition from a conventionally based economic system to the potential security of sources closely associated with the agricultural sphere such as the agriculture. In recent years, the intensification of fungi-based processes has generated significant gains, additionally to the production of materials with significant benefits and strong environmental importance. Furthermore, the growing concern for human health, especially in the agriculture scenario, has fostered the investigation of organisms with high biological and beneficial potential for use in agricultural systems. Accordingly, this study offered a comprehensive review of the diversity of the soil fungal microbiome and its main applications in a biotechnological approach aimed at agriculture and food chain-related areas. Moreover, the spectrum of opportunities and the extensive optimization platform for obtaining fungi compounds and metabolites are discussed. Finally, future perspectives regarding the insurgency of innovations and challenges on the broad rise of visionary solutions applied to the biotechnology context are provided.
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Affiliation(s)
- Maicon S N Dos Santos
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria (UFSM),, 1040, Sete de Setembro St., Center DC, Cachoeira do Sul, RS 96508-010, Brazil
| | - Lissara P Ody
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria (UFSM),, 1040, Sete de Setembro St., Center DC, Cachoeira do Sul, RS 96508-010, Brazil
| | - Bruno D Kerber
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria (UFSM),, 1040, Sete de Setembro St., Center DC, Cachoeira do Sul, RS 96508-010, Brazil
| | - Beatriz A Araujo
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria (UFSM),, 1040, Sete de Setembro St., Center DC, Cachoeira do Sul, RS 96508-010, Brazil
| | - Carolina E D Oro
- Department of Food Engineering, Integrated Regional University of Alto Uruguay and Missions, 1621, Sete de Setembro Av., Fátima, Erechim, RS 99709-910, Brazil
| | - João H C Wancura
- Department of Chemical Engineering, Federal University of Santa Maria (UFSM), 1000, Roraima Av., Camobi, Santa Maria, RS 97105-900, Brazil
| | - Marcio A Mazutti
- Department of Chemical Engineering, Federal University of Santa Maria (UFSM), 1000, Roraima Av., Camobi, Santa Maria, RS 97105-900, Brazil
| | - Giovani L Zabot
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria (UFSM),, 1040, Sete de Setembro St., Center DC, Cachoeira do Sul, RS 96508-010, Brazil
| | - Marcus V Tres
- Laboratory of Agroindustrial Processes Engineering (LAPE), Federal University of Santa Maria (UFSM),, 1040, Sete de Setembro St., Center DC, Cachoeira do Sul, RS 96508-010, Brazil.
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9
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Thitla T, Kumla J, Hongsanan S, Senwanna C, Khuna S, Lumyong S, Suwannarach N. Exploring diversity rock-inhabiting fungi from northern Thailand: a new genus and three new species belonged to the family Herpotrichiellaceae. Front Cell Infect Microbiol 2023; 13:1252482. [PMID: 37692164 PMCID: PMC10485699 DOI: 10.3389/fcimb.2023.1252482] [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: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023] Open
Abstract
Members of the family Herpotrichiellaceae are distributed worldwide and can be found in various habitats including on insects, plants, rocks, and in the soil. They are also known to be opportunistic human pathogens. In this study, 12 strains of rock-inhabiting fungi that belong to Herpotrichiellaceae were isolated from rock samples collected from forests located in Lamphun and Sukhothai provinces of northern Thailand during the period from 2021 to 2022. On the basis of the morphological characteristics, growth temperature, and multi-gene phylogenetic analyses of a combination of the internal transcribed spacer, the large subunit, and the small subunit of ribosomal RNA, beta tubulin and the translation elongation factor 1-a genes, the new genus, Petriomyces gen. nov., has been established to accommodate the single species, Pe. obovoidisporus sp. nov. In addition, three new species of Cladophialophora have also been introduced, namely, Cl. rupestricola, Cl. sribuabanensis, and Cl. thailandensis. Descriptions, illustrations, and a phylogenetic trees indicating the placement of these new taxa are provided. Here, we provide updates and discussions on the phylogenetic placement of other fungal genera within Herpotrichiellaceae.
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Affiliation(s)
- Tanapol Thitla
- Master of Science Program in Applied Microbiology (International Program), Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Sinang Hongsanan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Chanokned Senwanna
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Surapong Khuna
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
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Moreno-Perlin T, Valdés-Muñoz G, Jiménez-Gómez I, Gunde-Cimerman N, Yarzábal Rodríguez LA, Sánchez-Carbente MDR, Vargas-Fernández A, Gutiérrez-Cepeda A, Batista-García RA. Extremely chaotolerant and kosmotolerant Aspergillus atacamensis - a metabolically versatile fungus suitable for recalcitrant biosolid treatment. Front Microbiol 2023; 14:1191312. [PMID: 37455742 PMCID: PMC10338856 DOI: 10.3389/fmicb.2023.1191312] [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: 03/21/2023] [Accepted: 05/09/2023] [Indexed: 07/18/2023] Open
Abstract
Obligate halophily is extremely rare in fungi. Nevertheless, Aspergillus atacamensis (strain EXF-6660), isolated from a salt water-exposed cave in the Coastal Range hills of the hyperarid Atacama Desert in Chile, is an obligate halophile, with a broad optimum range from 1.5 to 3.4 M of NaCl. When we tested its ability to grow at varied concentrations of both kosmotropic (NaCl, KCl, and sorbitol) and chaotropic (MgCl2, LiCl, CaCl2, and glycerol) solutes, stereoscopy and laser scanning microscopy revealed the formation of phialides and conidia. A. atacamensis EXF-6660 grew up to saturating levels of NaCl and at 2.0 M concentration of the chaotropic salt MgCl2. Our findings confirmed that A. atacamensis is an obligate halophile that can grow at substantially higher MgCl2 concentrations than 1.26 M, previously considered as the maximum limit supporting prokaryotic life. To assess the fungus' metabolic versatility, we used the phenotype microarray technology Biolog FF MicroPlates. In the presence of 2.0 M NaCl concentration, strain EXF-6660 metabolism was highly versatile. A vast repertoire of organic molecules (~95% of the substrates present in Biolog FF MicroPlates) was metabolized when supplied as sole carbon sources, including numerous polycyclic aromatic hydrocarbons, benzene derivatives, dyes, and several carbohydrates. Finally, the biotechnological potential of A. atacamensis for xenobiotic degradation and biosolid treatment was investigated. Interestingly, it could remove biphenyls, diphenyl ethers, different pharmaceuticals, phenols, and polyaromatic hydrocarbons. Our combined findings show that A. atacamensis EXF-6660 is a highly chaotolerant, kosmotolerant, and xerotolerant fungus, potentially useful for xenobiotic and biosolid treatments.
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Affiliation(s)
- Tonatiuh Moreno-Perlin
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Gisell Valdés-Muñoz
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Irina Jiménez-Gómez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Alfaniris Vargas-Fernández
- Instituto de Investigación en Salud, Facultad de Ciencias de la Salud, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
- Instituto de Química, Facultad de Ciencias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Adrián Gutiérrez-Cepeda
- Instituto de Investigación en Salud, Facultad de Ciencias de la Salud, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
- Instituto de Química, Facultad de Ciencias, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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11
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Wijayawardene NN, Boonyuen N, Ranaweera CB, de Zoysa HKS, Padmathilake RE, Nifla F, Dai DQ, Liu Y, Suwannarach N, Kumla J, Bamunuarachchige TC, Chen HH. OMICS and Other Advanced Technologies in Mycological Applications. J Fungi (Basel) 2023; 9:688. [PMID: 37367624 DOI: 10.3390/jof9060688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.
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Affiliation(s)
- Nalin N Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, General Sir John Kotelawala Defence University Sri Lanka, Kandawala Road, Rathmalana 10390, Sri Lanka
| | - Heethaka K S de Zoysa
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Rasanie E Padmathilake
- Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Pulliyankulama, Anuradhapura 50000, Sri Lanka
| | - Faarah Nifla
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Dong-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Yanxia Liu
- Guizhou Academy of Tobacco Science, No.29, Longtanba Road, Guanshanhu District, Guiyang 550000, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thushara C Bamunuarachchige
- Department of Bioprocess Technology, Faculty of Technology, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
| | - Huan-Huan Chen
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Key Laboratory of Insect-Pollinator Biology of Ministry of Agriculture and Rural Affairs, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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Cittadino GM, Andrews J, Purewal H, Estanislao Acuña Avila P, Arnone JT. Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya. J Fungi (Basel) 2023; 9:jof9050523. [PMID: 37233234 DOI: 10.3390/jof9050523] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.
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Affiliation(s)
- Gina M Cittadino
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Johnathan Andrews
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Harpreet Purewal
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | | | - James T Arnone
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
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13
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Paiva DS, Fernandes L, Pereira E, Trovão J, Mesquita N, Tiago I, Portugal A. Exploring Differences in Culturable Fungal Diversity Using Standard Freezing Incubation-A Case Study in the Limestones of Lemos Pantheon (Portugal). J Fungi (Basel) 2023; 9:jof9040501. [PMID: 37108954 PMCID: PMC10143818 DOI: 10.3390/jof9040501] [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: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
In this study, we explored the biodiversity and abundance of culturable fungi in four samples associated with different biodeterioration outlines collected from the Lemos Pantheon, a limestone-built artwork in Portugal. We compared the results from prolonged standard freezing with those previously obtained from fresh samples to analyze differences in the obtained community and assess the effectiveness of the standard freezing incubation protocol in uncovering a different segment of culturable fungal diversity. Our results showed a slight decrease in culturable diversity, but over 70% of the obtained isolates were not present in the previously studied fresh samples. We also identified a high number of potential new species with this procedure. Moreover, the use of a wide variety of selective culture media positively influenced the diversity of the cultivable fungi obtained in this study. These findings highlight the importance of developing new protocols under varying conditions to accurately characterize the culturable fraction in a given sample. The identification and study of these communities and their possible contribution to the biodeterioration process is crucial knowledge for formulating effective conservation and restoration plans to prevent further damage to valuable cultural heritage assets.
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Affiliation(s)
- Diana S Paiva
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Emília Pereira
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
| | - Nuno Mesquita
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Igor Tiago
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António Portugal
- Centre for Functional Ecology (CFE)-Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab-Laboratory for Phytopathology, Instituto Pedro Nunes, Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA-Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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14
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Are dark septate endophytes an ancestral ecological state in the evolutionary history of the order Chaetothyriales? Arch Microbiol 2023; 205:55. [PMID: 36607426 DOI: 10.1007/s00203-023-03401-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023]
Abstract
Dark septate endophytes (DSE) are pigmented fungi that colonize plant roots. They represent a morpho-functional status composed of many species belonging to the phylum Ascomycota, distributed in different orders. The order Chaetothyriales has representatives with diverse lifestyles, among which the rock-inhabiting one has been proposed to be the ancestral ecological character state. However, all taxa have the phenotypic characteristic of being highly melanized. This trait has been considered relevant in most Chaetothyriales because it allows them to tolerate extreme or toxic environmental conditions. In the present study, aiming to reconstruct the evolutionary history of this order, we analyzed the contribution of the DSE habit to the diversification of the Chaetothyriales. We also report the distribution of the DSE habit among the main families and/or clades within the order. Our results suggest that DSE had a key position in the evolution of the order Chaetothyriales, both as an ancestral ecological character and as a character from which other specialized forms such as Domatium probably derived.
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15
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Krah F, March‐Salas M. eDNA
metabarcoding reveals high soil fungal diversity and variation in community composition among Spanish cliffs. Ecol Evol 2022; 12:e9594. [DOI: 10.1002/ece3.9594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Franz‐Sebastian Krah
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Conservation Biology Goethe University Frankfurt Frankfurt am Main Germany
| | - Martí March‐Salas
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Plant Evolutionary Ecology Goethe University Frankfurt Frankfurt am Main Germany
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16
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Coleine C, Delgado-Baquerizo M. Unearthing terrestrial extreme microbiomes for searching terrestrial-like life in the Solar System. Trends Microbiol 2022; 30:1101-1115. [PMID: 35568658 DOI: 10.1016/j.tim.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 01/13/2023]
Abstract
The possibility of life elsewhere in the universe has fascinated humankind for ages. To the best of our knowledge, life, as we know it, is limited to planet Earth; yet current investigation suggests that life might be more common than previously thought. In this review, we explore extreme terrestrial analogue environments in the search for some notable examples of extreme organisms, including overlooked microbial groups such as viruses, fungi, and protists, associated with limits of life on Earth. This knowledge is integral to provide the foundational principles needed to predict what sort of Earth-like organisms we might find in the Solar System and beyond, and to understand the future and origins of life on Earth.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain; Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013 Sevilla, Spain.
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17
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Cai S, Snyder AB. Genomic characterization of polyextremotolerant black yeasts isolated from food and food production environments. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:928622. [PMID: 37746166 PMCID: PMC10512282 DOI: 10.3389/ffunb.2022.928622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/04/2022] [Indexed: 09/26/2023]
Abstract
Black yeasts have been isolated from acidic, low water activity, and thermally processed foods as well as from surfaces in food manufacturing plants. The genomic basis for their relative tolerance to food-relevant environmental stresses has not been well defined. In this study, we performed whole genome sequencing (WGS) on seven black yeast strains including Aureobasidium (n=5) and Exophiala (n=2) which were isolated from food or food production environments. These strains were previously characterized for their tolerance to heat, hyperosmotic pressure, high pressure processing, hypochlorite sanitizers, and ultraviolet light. Based on the WGS data, three of the strains previously identified as A. pullulans were reassigned as A. melanogenum. Both haploid and diploid A. melanogenum strains were identified in this collection. Single-locus phylogenies based on beta tubulin, RNA polymerase II, or translation elongation factor protein sequences were compared to the phylogeny produced through SNP analysis, revealing that duplication of the fungal genome in diploid strains complicates the use of single-locus phylogenetics. There was not a strong association between phylogeny and either environmental source or stress tolerance phenotype, nor were trends in the copy numbers of stress-related genes associated with extremotolerance within this collection. While there were obvious differences between the genera, the heterogenous distribution of stress tolerance phenotypes and genotypes suggests that food-relevant black yeasts may be ubiquitous rather than specialists associated with particular ecological niches. However, further evaluation of additional strains and the potential impact of gene sequence modification is necessary to confirm these findings.
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Affiliation(s)
| | - Abigail B. Snyder
- Department of Food Science, Cornell University, Ithaca, NY, United States
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18
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Cao D, Lou Y, Jiang X, Zhang D, Liu J. Fungal Diversity in Barley Under Different Storage Conditions. Front Microbiol 2022; 13:895975. [PMID: 35814699 PMCID: PMC9257103 DOI: 10.3389/fmicb.2022.895975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
The diversity of fungi in barley in simulated storage environments was analyzed. Barley was stored at different temperatures (15, 25, 35°C) and relative humidity (55, 65, 75, 85 RH) for 180 and 360 days. Alpha diversity, beta diversity, species composition, and species differences were analyzed using Illumina HiSeq technology. The fungal communities in all barley samples before and after storage belonged to 3 phyla, 18 classes, 39 orders, 71 families, 103 genera, and 152 species. The relative abundance of the dominant phylum Ascomycota was 77.98–99.19%. The relative abundance of Basidiomycota was 0.77–21.96%. At the genus level, the dominant genera of fungi in barley initially included Fusarium, Aspergillus, Microdochium, Alternaria, and Epicoccum. After 360 days of storage, the dominant genera became Epicoccum, Alternaria, Bipolar, Cladosporium, Fusarium, and Aspergillus. According to Venn diagrams and principal coordinates analysis, the fungal community diversity in barley initially was much higher than in barley stored at different temperatures and humidity. The application of PLS-DA could accurately distinguish between barley stored for 180 and 360 days. Some high-temperature and high-humidity environments accelerated storage. The dominant genera differed in different storage conditions and constantly changed with increasing storage duration. Epicoccum was one of the dominant genera after longer storage periods. This study provides theoretical support for optimizing safe storage conditions in barley.
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Affiliation(s)
- Dongmei Cao
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
- Key Laboratory of Agro-Products Processing and Quality Safety of Heilongjiang Province, Daqing, China
- Heilongjiang Engineering Research Center for Coarse Cereals Processing and Quality Safety, Daqing, China
| | - Yuhao Lou
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiujie Jiang
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dongjie Zhang
- College of Food Science, Heilongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing, China
- Key Laboratory of Agro-Products Processing and Quality Safety of Heilongjiang Province, Daqing, China
- Heilongjiang Engineering Research Center for Coarse Cereals Processing and Quality Safety, Daqing, China
- Heilongjiang Province Cultivating Collaborative Innovation Center for the Beidahuang Modern Agricultural Industry Technology, Daqing, China
- *Correspondence: Dongjie Zhang,
| | - Junmei Liu
- College of Food Science, Jilin Agricultural University, Daqing, China
- Junmei Liu,
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19
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Yang X, Bao Y, Shao T, Wang W, Ma P, Wang W, Gallo A, Yuan X. Altitudinal Distribution Patterns of Phyllosphere Microbial Communities and Their Contribution to Silage Fermentation of Kobresia pygmaea Along the Elevation Gradient on the Tibetan Plateau. Front Microbiol 2022; 13:874582. [PMID: 35685941 PMCID: PMC9173736 DOI: 10.3389/fmicb.2022.874582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
The study aimed to reveal altitudinal distribution patterns of phyllosphere microbial communities and silage fermentation of Kobresia pygmaea along the elevation gradient on the Tibetan Plateau. The K. pygmaea was individually collected from 2,500, 3,000, 4,000, 4,500, and 5,000 m above sea level (a.s.l.) on the Tibetan Plateau and ensiled for 60 days, respectively. The phyllosphere bacterial diversity increased while fungal diversity decreased along the elevation gradient, and bacterial and fungal richness showed a unimodal distribution with peak abundance at 4,000 and 3,000 m a.s.l., respectively. After 60 days of ensiling, the bacterial and fungal community composition changed but did not exhibit clear altitudinal distribution patterns. All K. pygmaea underwent a weak fermentation indicated by pH above 5.0 and low ratio of lactic/acetic acid (LA/AA). The S5000 and S3000 showed the highest and lowest pH, respectively. Although Lactobacillus dominated S4000 after 60 days of ensiling, S4000 still exhibited poor fermentation quality as well as silages from the other four regions. The higher ammonia N concentrations in S3000 and S4000 than the other silages were consistent with the detectable butyric acid in S3000 and S4000. The silage fermentation of K. pygmaea collected from five regions exhibited poor fermentation quality, thereby inoculating lactic acid bacteria to K. pygmaea before ensiling is highly recommended to improve fermentation quality on the Tibetan Plateau.
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Affiliation(s)
- Xin Yang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Yuhong Bao
- State Key Laboratory of Germplasm Resources and Genetic Improvement of Tibetan Barley and Yak, Lhasa, China
- Institute of Grass Science, TAR Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Wenkang Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Pengfei Ma
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Wenbo Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Antonio Gallo
- Department of Animal Science, Food and Nutrition (DIANA), Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Xianjun Yuan
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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20
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Snyder AB. The role of heat resistance in yeast spoilage of thermally processed foods: highlighting the need for a probabilistic, systems-based approach to microbial quality. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Black Fungi and Stone Heritage Conservation: Ecological and Metabolic Assays for Evaluating Colonization Potential and Responses to Traditional Biocides. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12042038] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Identifying species involved in biodeterioration processes is helpful, however further effort is needed to assess their ecological requirements and actual activity. Black fungi (BF) represent one of the most underestimated threats to stone cultural heritage in the Mediterranean basin; they are difficult to kill or remove due to their ability to grow inside the rock and cope with several stresses. Despite this, little is known about BF and factors favoring their growth on stone surfaces. Eighteen BF species were here investigated for temperature and salt tolerance, and metabolic traits by plate assays. The relation between some highly damaged monuments and their BF settlers was assessed using X-ray diffraction analysis, mercury intrusion porosimetry, and SEM. The sensitiveness to four commonly used traditional biocides was also tested. All strains were able to grow within the range of 5–25 °C and in the presence of 3.5% NaCl. Instrumental analyses were fundamental in discovering the relation between halophilic strains and weathered marble sculptures. The acid, cellulase, esterase, and protease production recorded proved BF’s potential to produce a chemical action on carbonate stones and likely affect other materials/historical artefacts. Besides, the use of carboxymethylcellulose and Tween 20 should be evaluated in restoration practice to prevent tertiary bioreceptivity. Agar diffusion tests helped identify the most resistant species to biocides, opening the perspective of its use as reference organisms in material testing procedures.
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