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Rabbachin L, Nir I, Waldherr M, Vassallo Y, Piñar G, Graf A, Kushmaro A, Sterflinger K. Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1400380. [PMID: 39035870 PMCID: PMC11257853 DOI: 10.3389/ffunb.2024.1400380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/14/2024] [Indexed: 07/23/2024]
Abstract
The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO3 and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph's deterioration.
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Affiliation(s)
- Laura Rabbachin
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Irit Nir
- Environmental Biotechnology Laboratory, Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Monika Waldherr
- Department of Bioinformatics, University of Applied Sciences, Vienna, Austria
| | - Ylenia Vassallo
- Laboratory of Plant Pathology, Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Guadalupe Piñar
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Alexandra Graf
- Department of Bioinformatics, University of Applied Sciences, Vienna, Austria
| | - Ariel Kushmaro
- Environmental Biotechnology Laboratory, Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Katja Sterflinger
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
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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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Islam W, Zeng F, Ahmed Dar A, Sohail Yousaf M. Dynamics of soil biota and nutrients at varied depths in a Tamarix ramosissima-dominated natural desert ecosystem: Implications for nutrient cycling and desertification management. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120217. [PMID: 38340666 DOI: 10.1016/j.jenvman.2024.120217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
The underground community of soil organisms, known as soil biota, plays a critical role in terrestrial ecosystems. Different ecosystems exhibit varied responses of soil organisms to soil physical and chemical properties (SPCPs). However, our understanding of how soil biota react to different soil depths in naturally established population of salinity tolerant Tamarix ramosissima in desert ecosystems, remains limited. To address this, we employed High-Throughput Illumina HiSeq Sequencing to examine the population dynamics of soil bacteria, fungi, archaea, protists, and metazoa at six different soil depths (0-100 cm) in the naturally occurring T. ramosissima dominant zone within the Taklimakan desert of China. Our observations reveal that the alpha diversity of bacteria, fungi, metazoa, and protists displayed a linear decrease with the increase of soil depth, whereas archaea exhibited an inverse pattern. The beta diversity of soil biota, particularly metazoa, bacteria, and protists, demonstrated noteworthy associations with soil depths through Non-Metric Dimensional Scaling analysis. Among the most abundant classes of soil organisms, we observed Actinobacteria, Sordariomycetes, Halobacteria, Spirotrichea, and Nematoda for bacteria, fungi, archaea, protists, and metazoa, respectively. Additionally, we identified associations between the vertical distribution of dominant biotic communities and SPCPs. Bacterial changes were mainly influenced by total potassium, available phosphorus (AP), and soil water content (SWC), while fungi were impacted by nitrate (NO3-) and available potassium (AK). Archaea showed correlations with total carbon (TC) and AK thus suggesting their role in methanogenesis and methane oxidation, protists with AP and SWC, and metazoa with AP and pH. These correlations underscore potential connections to nutrient cycling and the production and consumption of greenhouse gases (GhGs). This insight establishes a solid foundation for devising strategies to mitigate nutrient cycling and GHG emissions in desert soils, thereby playing a pivotal role in the advancement of comprehensive approaches to sustainable desert ecosystem management.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Afzal Ahmed Dar
- Department of Building, Civil and Environmental Engineering, Concordia University, 1455 de Maisonneuve Blvd. W. Montreal, Quebec H3G1M8, Canada
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Islam W, Ullah A, Zeng F. Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166027. [PMID: 37541502 DOI: 10.1016/j.scitotenv.2023.166027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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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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Chen X, Wang Y, Wang Y, Zhang Y, Shen Y, He X, Xiao C. A Natural Moisture Gradient Affects Soil Fungal Communities on the South Shore of Hulun Lake, Inner Mongolia, China. J Fungi (Basel) 2023; 9:jof9050549. [PMID: 37233260 DOI: 10.3390/jof9050549] [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: 02/20/2023] [Revised: 03/14/2023] [Accepted: 04/30/2023] [Indexed: 05/27/2023] Open
Abstract
Soil moisture content (SWC) can change the diversity and composition of soil fungal communities by affecting soil texture and soil nutrients. To explore the response of soil fungal communities to moisture in the grassland ecosystem on the south shore of Hulun Lake, we set up a natural moisture gradient that was subdivided into high (HW), medium (MW), and low (LW) water contents. Vegetation was investigated by quadrat method, and aboveground biomass was collected by the mowing method. Soil physicochemical properties were obtained by internal experiments. The composition of the soil fungal community was determined using high-throughput sequencing technology. The results showed significant differences in soil texture, nutrients, and fungal species diversity under the moisture gradients. Although there was significant clustering of fungal communities in different treatments, the fungal community composition was not significantly different. According to the phylogenetic tree, the Ascomycota and Basidiomycota were the most important branches. The fungal species diversity was smaller when SWC was higher, and in this environment (HW), the fungal-dominant species were significantly related to SWC and soil nutrients. At this time, soil clay formed a protective barrier for the survival of the dominant classes Sordariomycetes and Dothideomycetes and increased their relative abundance. In summary, the fungal community responded significantly to SWC on the southern shore of the Hulun Lake ecosystem in Inner Mongolia, China, and the fungal community composition of the HW group was stable and easier to survive.
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Affiliation(s)
- Xin Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yujue Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yao Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yushu Zhang
- Beijing Key Laboratory of Ecological Function Assessment and Regulation Technology of Green Space, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yuting Shen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xiaojia He
- The Administrative Center for China's Agenda 21, Beijing 100038, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert. Fungal Biol 2023; 127:997-1003. [PMID: 37024159 DOI: 10.1016/j.funbio.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.
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Wang M, Wang C, Yu Z, Wang H, Wu C, Masoudi A, Liu J. Fungal diversities and community assembly processes show different biogeographical patterns in forest and grassland soil ecosystems. Front Microbiol 2023; 14:1036905. [PMID: 36819045 PMCID: PMC9928764 DOI: 10.3389/fmicb.2023.1036905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Soil fungal community has been largely explored by comparing their natural diversity. However, there is a relatively small body of literature concerned with fungal community assembly processes and their co-occurrence network correlations carried out across large spatial-temporal scales with complex environmental gradients in natural ecosystems and different habitats in China. Thus, soil fungal community assembly processes were assessed to predict changes in soil function in 98 different forest and grassland sites from the Sichuan, Hubei, and Hebei Provinces of China using high-throughput sequencing of nuclear ribosomal internal transcribed spacer 2 (ITS-2). The 10 most abundant fungal phyla results showed that Ascomycota was the most abundant phylum in forests from Sichuan province (64.42%) and grassland habitats from Hebei province (53.46%). Moreover, core fungal taxa (487 OTUs) represented 0.35% of total fungal OTUs. We observed higher fungal Shannon diversity and richness (the Chao1 index) from diverse mixed forests of the Sichuan and Hubei Provinces than the mono-cultured forest and grassland habitats in Hebei Province. Although fungal alpha and beta diversities exhibited different biogeographical patterns, the fungal assembly pattern was mostly driven by dispersal limitation than selection in different habitats. Fungal co-occurrence analyses showed that the network was more intense at Saihanba National Forest Park (SNFP, Hebei). In contrast, the co-occurrence network was more complex at boundaries between forests and grasslands at SNFP. Additionally, the highest number of positive (co-presence or co-operative) correlations of fungal genera were inferred from grassland habitat, which led fungal communities to form commensalism relationships compared to forest areas with having higher negative correlations (mutual exclusion or competitive). The generalized additive model (GAM) analysis showed that the association of fungal Shannon diversity and richness indices with geographical coordinates did not follow a general pattern; instead, the fluctuation of these indices was restricted to local geographical coordinates at each sampling location. These results indicated the existence of a site effect on the diversity of fungal communities across our sampling sites. Our observation suggested that higher fungal diversity and richness of fungal taxa in a particular habitat are not necessarily associated with more complex networks.
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Novak Babič M, Gunde-Cimerman N, Breskvar M, Džeroski S, Brandão J. Occurrence, Diversity and Anti-Fungal Resistance of Fungi in Sand of an Urban Beach in Slovenia—Environmental Monitoring with Possible Health Risk Implications. J Fungi (Basel) 2022; 8:jof8080860. [PMID: 36012848 PMCID: PMC9410438 DOI: 10.3390/jof8080860] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Beach safety regulation is based on faecal indicators in water, leaving out sand and fungi, whose presence in both matrices has often been reported. To study the abundance, diversity and possible fluctuations of mycobiota, fungi from sand and seawater were isolated from the Portorož beach (Slovenia) during a 1-year period. Sand analyses yielded 64 species of 43 genera, whereas seawater samples yielded 29 species of 18 genera. Environmental and taxonomical data of fungal communities were analysed using machine learning approaches. Changes in the air and water temperature, sunshine hours, humidity and precipitation, air pressure and wind speed appeared to affect mycobiota. The core genera Aphanoascus, Aspergillus, Fusarium, Bisifusarium, Penicillium, Talaromyces, and Rhizopus were found to compose a stable community within sand, although their presence and abundance fluctuated along with weather changes. Aspergillus spp. were the most abundant and thus tested against nine antimycotics using Sensititre Yeast One kit. Aspergillus niger and A. welwitschiae isolates were found to be resistant to amphotericin B. Additionally, four possible human pollution indicators were isolated during the bathing season, including Meyerozyma, which can be used in beach microbial regulation. Our findings provide the foundations for additional research on sand and seawater mycobiota and show the potential effect of global warming and extreme weather events on fungi in sand and sea.
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Affiliation(s)
- Monika Novak Babič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
- Correspondence: (M.N.B.); (J.B.)
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Martin Breskvar
- Department of Knowledge Technologies, Jožef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
| | - Sašo Džeroski
- Department of Knowledge Technologies, Jožef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova Cesta 39, 1000 Ljubljana, Slovenia
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1600-609 Lisbon, Portugal
- Centre for Environmental and Marine Studies (CESAM)—Department of Animal Biology, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal
- Correspondence: (M.N.B.); (J.B.)
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Samarakoon BC, Wanasinghe DN, Bhat J, Chomnunti P. Taxonomy and phylogeny of Smaragdinisetamusae sp. nov. and Albifimbriaverrucaria (Hypocreales, Stachybotryaceae) on Musa from Thailand. Biodivers Data J 2022; 10:e89360. [PMID: 36761612 PMCID: PMC9848465 DOI: 10.3897/bdj.10.e89360] [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: 06/21/2022] [Accepted: 07/22/2022] [Indexed: 11/12/2022] Open
Abstract
Background Smaragdinisetamusae is introduced as a leaf-based novel saprobic species from Musa. Multi-gene phylogenetic analyses of internal transcribed spacer (ITS), RNA polymerase II second largest subunit (rpb2) and β-tubulin (tub2) data support the taxonomic placement of the new collection in Smaragdiniseta (Hypocreales, Stachybotryaceae). The novel species is characterised by cup-shaped sporodochia covered by numerous peripheral setae and simple hyaline, guttulate conidia produced by the ultimate branches (phialides) of conidiophores. New information This is the first report of Smaragdiniseta from Thailand and on Musaceae. In addition, we report Albifimbriaverrucaria for the first time from Thailand, based on morpho-molecular evidence.
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Affiliation(s)
- Binu C. Samarakoon
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, ThailandCenter of Excellence in Fungal Research, Mae Fah Luang UniversityChiang Rai, 57100Thailand,School of Science, Mae Fah Luang University, Chiang Rai, 57100, ThailandSchool of Science, Mae Fah Luang UniversityChiang Rai, 57100Thailand
| | - Dhanushka N. Wanasinghe
- CIFOR-ICRAF China Program, World Agroforestry (ICRAF), Kunming 650201, ChinaCIFOR-ICRAF China Program, World Agroforestry (ICRAF)Kunming 650201China,Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, Yunnan, ChinaCentre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of SciencesHonghe 654400, YunnanChina
| | - Jayarama Bhat
- Department of Botany, Goa University, Goa, IndiaDepartment of Botany, Goa UniversityGoaIndia
| | - Putarak Chomnunti
- School of Science, Mae Fah Luang University, Chiang Rai 57100, ThailandSchool of Science, Mae Fah Luang UniversityChiang Rai 57100Thailand
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11
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Hernández-Guzmán M, Pérez-Hernández V, Gómez-Acata S, Jiménez-Bueno N, Verhulst N, Muñoz-Arenas LC, Navarro-Noya YE, Luna-Guido ML, Dendooven L. Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study. Arch Microbiol 2022; 204:458. [PMID: 35788780 DOI: 10.1007/s00203-022-03060-z] [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: 09/21/2021] [Revised: 05/01/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022]
Abstract
To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.
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Affiliation(s)
| | | | - Selene Gómez-Acata
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | | | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, Mexico
| | | | | | - Marco L Luna-Guido
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico.
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12
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Maldonado JE, Gaete A, Mandakovic D, Aguado-Norese C, Aguilar M, Gutiérrez RA, González M. Partners to survive: Hoffmannseggia doellii root-associated microbiome at the Atacama Desert. THE NEW PHYTOLOGIST 2022; 234:2126-2139. [PMID: 35274744 DOI: 10.1111/nph.18080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The discovery and characterization of plant species adapted to extreme environmental conditions have become increasingly important. Hoffmannseggia doellii is a perennial herb endemic to the Chilean Atacama Desert that grows in the western Andes between 2800 and 3600 m above sea level. Its growing habitat is characterized by high radiation and low water and nutrient availability. Under these conditions, H. doellii can grow, reproduce, and develop an edible tuberous root. We characterized the H. doellii soil-associated microbiomes to understand the biotic factors that could influence their surprising ability to survive. We found an increased number of observed species and higher phylogenetic diversity of bacteria and fungi on H. doellii root soils compared with bare soil (BS) along different sites and to soil microbiomes of other plant species. Also, the H. doellii-associated microbiome had a higher incidence of overall positive interactions and fungal within-kingdom interactions than their corresponding BS network. These findings suggest a microbial diversity soil modulation mechanism that may be a characteristic of highly tolerant plants to diverse and extreme environments. Furthermore, since H. doellii is related to important cultivated crops, our results create an opportunity for future studies on climate change adaptation of crop plants.
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Affiliation(s)
- Jonathan E Maldonado
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
- Laboratorio de Multiómica Vegetal y Bioinformática, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile
| | - Alexis Gaete
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, 8580745, Chile
| | - Constanza Aguado-Norese
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
| | - Melissa Aguilar
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Departamento de Genética Molecular y Microbiología, ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 7500565, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, 8370415, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, 7830490, Chile
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13
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Thermotolerance and Adaptation to Climate Change. Fungal Biol 2022. [DOI: 10.1007/978-3-030-89664-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Samarasinghe H, Lu Y, Aljohani R, Al-Amad A, Yoell H, Xu J. Global patterns in culturable soil yeast diversity. iScience 2021; 24:103098. [PMID: 34622153 PMCID: PMC8479693 DOI: 10.1016/j.isci.2021.103098] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Yeasts, broadly defined as unicellular fungi, fulfill essential roles in soil ecosystems as decomposers and nutrition sources for fellow soil-dwellers. Broad-scale investigations of soil yeasts pose a methodological challenge as metagenomics are of limited use for identifying this group of fungi. Here we characterize global soil yeast diversity using fungal DNA barcoding on 1473 yeasts cultured from 3826 soil samples obtained from nine countries in six continents. We identify mean annual precipitation and international air travel as two significant correlates with soil yeast community structure and composition worldwide. Evidence for anthropogenic influences on soil yeast communities, directly via travel and indirectly via altered rainfall patterns resulting from climate change, is concerning as we found common infectious yeasts frequently distributed in soil in several countries. Our discovery of 41 putative novel species highlights the continued need for culture-based studies to advance our knowledge of environmental yeast diversity. Mean annual rainfall is a positive predictor of global soil yeast diversity International travel predicts number of shared yeast species between countries 41 novel yeast species were discovered from soils in eight countries Continued culture-based studies are needed to investigate soil yeast populations
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Affiliation(s)
| | - Yi Lu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Renad Aljohani
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Department of Infectious Diseases, South Kensington Campus, Imperial College London, London, UK
| | - Ahmad Al-Amad
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Heather Yoell
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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15
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Ijoma GN, Heri SM, Matambo TS, Tekere M. Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. J Fungi (Basel) 2021; 7:700. [PMID: 34575737 PMCID: PMC8464691 DOI: 10.3390/jof7090700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.
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Affiliation(s)
- Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Sylvie M. Heri
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Tonderayi S. Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Memory Tekere
- Department of Environmental Science, College of Agricultural and Environmental Science, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa;
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16
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Decay Process Characteristics and Fungal Community Composition of Salix psammophila Sand Barriers in an Arid Area, Northern China. SUSTAINABILITY 2021. [DOI: 10.3390/su13147590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
With the increase in setting years in deserts, Salix psammophila sand barriers with different degrees of lodging damage caused by decay are losing wind-prevention and sand-fixation properties. In this study, we focus on the change in chemical properties of soils, and physical and mechanical properties of plants along different setting years; meanwhile, the change in fungal communities has been analyzed using high-throughput sequencing technology. The results show that a change in physical and mechanical properties and the loss of primary chemical components led to the degradation of the protective properties of the barrier to different degrees. After five years of setting, the physical parameters of basic density and shrinkage rate decreased by 44.04% and 28.68%, respectively, and the loss of the modulus of rupture mechanical index declined by 62.72%. After seven years of setting, the mechanical indexes of the modulus of rupture decreased by 76.95%. Five and seven years represented important inflection points in the decay process. Sordariomycetes (53.75%) and Eurotiomycetes (19.78%) were the main fungal groups present during the decay of the sand barrier. The basic density, moisture content, cellulose, and lignin of the sand barrier were the main driving factors affecting the distribution of fungal communities. The mechanism on fungal community to the decay of sand barriers still needs further studies to keep the function of sand barriers in fragile desert ecosystems.
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17
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Abdel-Azeem AM, Abu-Elsaoud AM, Abo Nahas HH, Abdel-Azeem MA, Balbool BA, Mousa MK, Ali NH, Darwish AMG. Biodiversity and Industrial Applications of Genus Chaetomium. Fungal Biol 2021. [DOI: 10.1007/978-3-030-67561-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Abed RM. Exploring Fungal Biodiversity of Genus Epicoccum and Their Biotechnological Potential. Fungal Biol 2021. [DOI: 10.1007/978-3-030-67561-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Osborne P, Hall LJ, Kronfeld-Schor N, Thybert D, Haerty W. A rather dry subject; investigating the study of arid-associated microbial communities. ENVIRONMENTAL MICROBIOME 2020; 15:20. [PMID: 33902728 PMCID: PMC8067391 DOI: 10.1186/s40793-020-00367-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/12/2020] [Indexed: 05/08/2023]
Abstract
Almost one third of Earth's land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.
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Affiliation(s)
- Peter Osborne
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK.
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
| | | | - David Thybert
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK
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20
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Microbial Diversity of Some Sabkha and Desert Sites in Saudi Arabia. Saudi J Biol Sci 2020; 27:2778-2789. [PMID: 32994737 PMCID: PMC7499299 DOI: 10.1016/j.sjbs.2020.06.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Several studies isolated fungal and bacterial species from extreme environments, such as Sabkha and hot deserts, as their natural habitat, some of which are of medicinal importance. Current research aimed investigating the microbial (fungi and bacteria) diversity and abundance in Sabkha and desert areas in Saudi Arabia. Soil samples from nine different geographical areas (Al-Aushazia lake, AlQasab, AlKasar, Tabuk, Al-Kharj, Al-Madina, Jubail, Taif and Abqaiq) were collected and cultured for microbial isolation. Isolated fungi and bacteria were identified by molecular techniques (PCR and sequencing). Based on 18S rDNA sequencing, 203 fungal species belonging to 33 genera were identified. The most common fungal genera were Fusarium, Alternaria, Chaetomium, Aspergillus Cochliobolus and Pencillium, while the most common species were Chaetomium globosum and Fusarium oxysporum. By 16S rDNA sequencing 22 bacterial species belonging to only two genera, Bacillus and Lactobacillus, were identified. The most commonly isolated bacterial species were Bacillus subtilis and Lactobacillus murinus. Some fungal species were confined to specific locations, such as Actinomyces elegans, Fusarium proliferatum, Gymnoascus reesii and Myzostoma spp. that were only isolated from Al-Aushazia soil. AlQasab soil had the highest microbial diversity among other areas with abundances of 23.5% and 4.4% of total fungi, and bacteria, respectively. Findings of this study show a higher degree of fungal diversity than that of bacteria in all studied areas. Further studies needed to investigate the connection between some isolated species and their habitat ecology, as well as to identify those of medicinal importance.
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21
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Mapook A, Hyde KD, McKenzie EHC, Jones EBG, Bhat DJ, Jeewon R, Stadler M, Samarakoon MC, Malaithong M, Tanunchai B, Buscot F, Wubet T, Purahong W. Taxonomic and phylogenetic contributions to fungi associated with the invasive weed Chromolaena odorata (Siam weed). FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00444-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Masetti R, Prodi A, Liberatore A, Carfagnini F, Cappelletti E, Leardini D, Pession A, De Carolis E, Cricca M. Occurrence of Albifimbria verrucaria in the Blood of a Female Child With Neuroblastoma. Front Med (Lausanne) 2020; 7:13. [PMID: 32118003 PMCID: PMC7033736 DOI: 10.3389/fmed.2020.00013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/13/2020] [Indexed: 11/13/2022] Open
Abstract
We report for the first time the occurrence of a filamentous fungus, Albifimbria verrucaria, in the blood of a pediatric neuroblastoma patient. The Albifimbria genus comprises common soil-inhabiting and saprophytic fungi and has been isolated as a plant pathogen in Northern and Southern Italy. As a human pathogen, A. verrucaria has been implicated in keratitis and can produce trichothecene toxins, which are weakly cytotoxic for mammalian cell lines. A. verrucaria was isolated from blood during the follow-up of a previous coagulase-negative Staphylococcus catheter-related infection. Lung nodules, compatible with fungal infection, had been observed on a CT scan 6 months earlier; they still persist. Possible routes of transmission were considered to be airborne, catheter related, or transfusion dependent, as the patient had undergone platelet and red blood cell transfusions during rescue chemotherapy. No filamentous fungi were isolated from sputum or CVCs. In conclusion, we describe an unprecedented fungemia caused by A. verrucaria and show how an unexpected pathogen may be acquired from the environment by patients at high risk due to immunosuppression. The route of transmission remains unknown.
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Affiliation(s)
- Riccardo Masetti
- "Lalla Seràgnoli", Hematology-Oncology Unit, Department of Pediatrics, University of Bologna, Bologna, Italy
| | - Antonio Prodi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Andrea Liberatore
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | | | - Eleonora Cappelletti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Davide Leardini
- "Lalla Seràgnoli", Hematology-Oncology Unit, Department of Pediatrics, University of Bologna, Bologna, Italy
| | - Andrea Pession
- "Lalla Seràgnoli", Hematology-Oncology Unit, Department of Pediatrics, University of Bologna, Bologna, Italy
| | - Elena De Carolis
- Institute of Microbiology, IRCCS, Catholic University of the Sacred Heart, Polyclinic University Foundation Agostino Gemelli, Rome, Italy
| | - Monica Cricca
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
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23
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Fuentes A, Herrera H, Charles TC, Arriagada C. Fungal and Bacterial Microbiome Associated with the Rhizosphere of Native Plants from the Atacama Desert. Microorganisms 2020; 8:microorganisms8020209. [PMID: 32033093 PMCID: PMC7074712 DOI: 10.3390/microorganisms8020209] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/19/2020] [Accepted: 01/30/2020] [Indexed: 11/16/2022] Open
Abstract
The rhizosphere microbiome is key in survival, development, and stress tolerance in plants. Salinity, drought, and extreme temperatures are frequent events in the Atacama Desert, considered the driest in the world. However, little information of the rhizosphere microbiome and its possible contribution to the adaptation and tolerance of plants that inhabit the desert is available. We used a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the rhizosphere of Baccharis scandens and Solanum chilense native plants from the Atacama Desert. Our results showed that the fungal phyla Ascomycota and Basidiomycota and the bacterial phyla Actinobacteria and Proteobacteria were the dominant taxa in the rhizosphere of both plants. The linear discriminant analysis (LDA) effect size (LefSe) of the rhizosphere communities associated with B. scandens showed the genera Penicillium and Arthrobacter were the preferential taxa, whereas the genera Oidiodendron and Nitrospirae was the preferential taxa in S. chilense. Both plant showed similar diversity, richness, and abundance according to Shannon index, observed OTUs, and evenness. Our results indicate that there are no significant differences (p = 0.1) between the fungal and bacterial communities of both plants, however through LefSe, we find taxa associated with each plant species and the PCoA shows a separation between the samples of each species. This study provides knowledge to relate the assembly of the microbiome to the adaptability to drought stress in desert plants.
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Affiliation(s)
- Alejandra Fuentes
- Laboratorio Biorremediación, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Francisco Salazar, Temuco 01145, Chile; (A.F.); (H.H.)
| | - Héctor Herrera
- Laboratorio Biorremediación, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Francisco Salazar, Temuco 01145, Chile; (A.F.); (H.H.)
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, University Avenue West, Waterloo, ON N2L 3G1; Canada;
| | - Cesar Arriagada
- Laboratorio Biorremediación, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Francisco Salazar, Temuco 01145, Chile; (A.F.); (H.H.)
- Correspondence: ; Tel.: +56-045-2325662; Fax: +56-045-2341467
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25
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Sayed AM, Hassan MHA, Alhadrami HA, Hassan HM, Goodfellow M, Rateb ME. Extreme environments: microbiology leading to specialized metabolites. J Appl Microbiol 2019; 128:630-657. [PMID: 31310419 DOI: 10.1111/jam.14386] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.
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Affiliation(s)
- A M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - M H A Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - H A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - H M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
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Suleiman MK, Dixon K, Commander L, Nevill P, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Assessment of the Diversity of Fungal Community Composition Associated With Vachellia pachyceras and Its Rhizosphere Soil From Kuwait Desert. Front Microbiol 2019; 10:63. [PMID: 30766519 PMCID: PMC6365840 DOI: 10.3389/fmicb.2019.00063] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
This research examined the general soil fungi and AM fungal communities associated with a Lonely Tree species (Vachellia pachyceras) existing in the Sabah Al-Ahmad Natural Reserve located at the Kuwait desert. The goals of the study were to describe the general fungal and AM fungal communities present in the rhizospheric, non-rhizospheric soils and roots of V. pachyceras, respectively, as well as local and non-local V. pachyceras seedlings when grown under standard nursery growing environments. Soil and root samples were analyzed for an array of characteristics including soil physicochemical composition, and culture-independent method termed PCR-cloning, intermediate variable region of rDNA, the large subunit (LSU) and internal transcribed spacer (ITS) region sequence identifications. The results reveal that the fungal phylotypes were classified in four major fungal phyla namely Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblage of fungal analyses showed communities dominated by members of the phylum Ascomycota. The assays also revealed a wealth of incertae sedis fungi, mostly affiliated to uncultured fungi from diverse environmental conditions. Striking difference between rhizosphere and bulk soils communities, with more fungal diversities and Operational Taxonomic Units (OTUs) richness associated with both the field and nursery rhizosphere soils. In contrast, a less diverse fungal community was found in the bulk soil samples. The characterization of AM fungi from the root system demonstrated that the most abundant and diversified group belongs to the family Glomeraceae, with the common genus Rhizophagus (5 phylotypes) and another unclassified taxonomic group (5 phylotypes). Despite the harsh climate that prevails in the Kuwait desert, studied roots displayed the existence of considerable number of AM fungal biota. The present work thus provides a baseline of the fungal and mycorrhizal community associated with rhizosphere and non-rhizosphere soils and roots of only surviving V. pachyceras tree from the Kuwaiti desert and seedlings under nursery growing environments.
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Affiliation(s)
- Majda K. Suleiman
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Kingsley Dixon
- ARC Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Lucy Commander
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Ali M. Quoreshi
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Narayana R. Bhat
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Anitha J. Manuvel
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - Mini T. Sivadasan
- Environment and Life Sciences Research Center, Desert Agriculture and Ecosystems Program, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
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Murgia M, Fiamma M, Barac A, Deligios M, Mazzarello V, Paglietti B, Cappuccinelli P, Al‐Qahtani A, Squartini A, Rubino S, Al‐Ahdal MN. Biodiversity of fungi in hot desert sands. Microbiologyopen 2019; 8:e00595. [PMID: 29504263 PMCID: PMC6341031 DOI: 10.1002/mbo3.595] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/08/2018] [Indexed: 11/09/2022] Open
Abstract
The fungal community of six sand samples from Saudi Arabia and Jordan deserts was characterized by culture-independent analysis via next generation sequencing of the 18S rRNA genes and by culture-dependent methods followed by sequencing of internal transcribed spacer (ITS) region. By 18S sequencing were identified from 163 to 507 OTUs per sample, with a percentage of fungi ranging from 3.5% to 82.7%. The identified fungal Phyla were Ascomycota, Basal fungi, and Basidiomycota and the most abundant detected classes were Dothideomycetes, Pezizomycetes, and Sordariomycetes. A total of 11 colonies of filamentous fungi were isolated and cultured from six samples, and the ITS sequencing pointed toward five different species of the class Sordariomycetes, belonging to genera Fusarium (F. redolens, F. solani, F. equiseti), Chaetomium (C. madrasense), and Albifimbria (A. terrestris). The results of this study show an unexpectedly large fungal biodiversity in the Middle East desert sand and their possible role and implications on human health.
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Affiliation(s)
- Manuela Murgia
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maura Fiamma
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Aleksandra Barac
- Clinic for Infectious and Tropical DiseasesClinical Centre of SerbiaFaculty of MedicineUniversity of BelgradeBelgradeSerbia
| | - Massimo Deligios
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | | | - Bianca Paglietti
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | | | - Ahmed Al‐Qahtani
- Department of Infection and ImmunityKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Andrea Squartini
- Department of Agronomy Animals, Food, Natural Resources and EnvironmentDAFNAEUniversity of PadovaPadovaItaly
| | - Salvatore Rubino
- Department of Biomedical SciencesUniversity of SassariSassariItaly
- Department of Infection and ImmunityKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Mohammed N. Al‐Ahdal
- Department of Infection and ImmunityKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
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