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Banchi E, Manna V, Muggia L, Celussi M. Marine Fungal Diversity and Dynamics in the Gulf of Trieste (Northern Adriatic Sea). MICROBIAL ECOLOGY 2024; 87:78. [PMID: 38806848 PMCID: PMC11133070 DOI: 10.1007/s00248-024-02394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Fungi contribute to different important ecological processes, including decomposition of organic matter and nutrient cycling, but in the marine environment the main factors influencing their diversity and dynamics at the spatial and temporal levels are still largely unclear. In this study, we performed DNA metabarcoding on seawater sampled monthly over a year and a half in the Gulf of Trieste (northern Adriatic Sea), targeting the internal transcribed spacer (ITS) and the 18S rRNA gene regions. The fungal communities were diverse, very dynamic, and belonged predominantly to marine taxa. Samples could be clustered in two groups, mainly based on the high (> 30%) or low relative proportion of the ascomycetes Parengyodontium album, which emerged as a key taxon in this area. Dissolved and particulate organic C:N ratio played important roles in shaping the mycoplankton assemblages, suggesting that differently bioavailable organic matter pools may be utilized by different consortia. The proportion of fungal over total reads was 31% for ITS and 0.7% for 18S. ITS had the highest taxonomic resolution but low power to detect early divergent fungal lineages. Our results on composition, distribution, and environmental drivers extended our knowledge of the structure and function of the mycobiome of coastal waters.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy.
- NBFC, National Biodiversity Future Center, Palermo, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics (OGS), Trieste, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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2
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Stüer‐Patowsky K, Lilje O, Wurzbacher C. Quantification of the dark fungal taxon Cryptomycota using qPCR. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13257. [PMID: 38615691 PMCID: PMC11016352 DOI: 10.1111/1758-2229.13257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/20/2024] [Indexed: 04/16/2024]
Abstract
Fungi are present in a wide variety of natural environments, and in the last years, various studies have shown that they are quite abundant in aquatic ecosystems. In addition, a whole new highly diverse phylum, the Cryptomycota, was discovered. Nevertheless, research on aquatic fungi and a detailed evaluation of their functions and distribution are still sparse. One of the main reasons is a limitation in reliable identification and quantification methods. To bridge part of the research gap, this study aims to implement a quantitative PCR method to detect and quantify the newly discovered phylum. We developed and validated a Cryptomycota-specific qPCR primer pair targeting the 5.8S region that detects the majority of Cryptomycota, but Microsporidia. The resulting amplicon is 102 bp long. We used different environmental samples to evaluate the primer pair, various fungal sequences as negative control and positive control sequences. Obtained amplicons were sequenced using Illumina, and the obtained ASVs were all classified as Cryptomycota. The qPCR method works reliably and specifically for the quantification of Cryptomycota in environmental samples.
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Affiliation(s)
- Katrin Stüer‐Patowsky
- Chair of Urban Water Systems EngineeringTechnical University of MunichGarchingGermany
| | - Osu Lilje
- School of Life and Environmental SciencesThe University of SydneyCamperdownNew South WalesAustralia
| | - Christian Wurzbacher
- Chair of Urban Water Systems EngineeringTechnical University of MunichGarchingGermany
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3
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Perkins AK, Rose AL, Grossart HP, Schulz KG, Neubauer D, Tonge MP, Rosentreter JA, Eyre BD, Rojas-Jimenez K, Deschaseaux E, Oakes JM. Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166957. [PMID: 37704140 DOI: 10.1016/j.scitotenv.2023.166957] [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: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.
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Affiliation(s)
- Anita K Perkins
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia.
| | - Andrew L Rose
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Kai G Schulz
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Darshan Neubauer
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Matthew P Tonge
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Judith A Rosentreter
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Bradley D Eyre
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | | | - Elisabeth Deschaseaux
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Joanne M Oakes
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
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Chen X, Xu G, Xiong P, Peng J, Fang K, Wan S, Wang B, Gu F, Li J, Xiong H. Dry and wet seasonal variations of the sediment fungal community composition in the semi-arid region of the Dali River, Northwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:123694-123709. [PMID: 37993647 DOI: 10.1007/s11356-023-31042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there has been a lack of research on the seasonal variation of sediment microorganisms in the sediments of small river basins in typical semi-arid region. In this study, high-throughput DNA sequencing was used to investigate the fungal community and its influencing factors in the sediment of the Dali River in the dry and wet seasons. The results showed that there were obvious seasonal differences in fungal alpha diversity. The diversity and richness of fungi in the dry season were greater than that in the wet season, but the evenness of fungi in the dry season was lower than that in the wet season. In addition, Ascomycota and Basidiomycota were the most important phyla in the Dali River fungal community, but their distributions showed clear seasonal differences. In the dry season, the relative abundance of Ascomycota and Basidiomycota were 12.34-46.42% and 17.59-27.20%, respectively. In the wet season, the relative abundances of these two phyla were 24.33-36.56% and 5.75-12.26%, respectively. PICRUSt2 was used to predict the metabolic function of fungal community in the sediment, and it was found that at the first level, the proportion of biosynthesis in the dry season was higher than that in the wet season. The ecological network structure showed that the fungal community in the wet season was more complex and stable than that in the dry season. The characteristic fungi in the dry season sediment were chytrid fungi in the family Rhizophydiaceae and the order Rhizophydiales, whereas those in the wet season sediment were in the orders Eurotiales and Saccharomycetales. Canonical correspondence analysis (CCA) showed that the physicochemical properties of water and sediment together explained a greater proportion of the dry-season fungal community changes than of the wet-season changes. In the dry season, temperature and ammonia nitrogen in the water were the main factors affecting the change of fungal community, whereas in the wet season, total nitrogen concentration of the water, electrical conductivity, total organic carbon and available phosphorus of the sediment, pH, and temperature were the main factors affecting the changes in fungal community composition. The results of this study enhanced our understanding of microbial communities in semi-arid river ecosystems, and highlight the importance of the management and protection in river ecosystems.
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Affiliation(s)
- Xin Chen
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Guoce Xu
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China.
| | - Ping Xiong
- Shaanxi Forestry Survey and Planning Institute, Xi'an, 710082, Shaanxi, China
| | - Jianbo Peng
- Shaanxi Forestry Survey and Planning Institute, Xi'an, 710082, Shaanxi, China
| | - Kang Fang
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Shun Wan
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Bin Wang
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Fengyou Gu
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Jing Li
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Haijing Xiong
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
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Lane DM, Valentine DL, Peng X. Genomic analysis of the marine yeast Rhodotorula sphaerocarpa ETNP2018 reveals adaptation to the open ocean. BMC Genomics 2023; 24:695. [PMID: 37986036 PMCID: PMC10662464 DOI: 10.1186/s12864-023-09791-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Despite a rising interest in the diversity and ecology of fungi in marine environments, there are few published genomes of fungi isolated from the ocean. The basidiomycetous yeast (unicellular fungus) genus Rhodotorula are prevalent and abundant in the open ocean, and they have been isolated from a wide range of other environments. Many of these environments are nutrient poor, such as the Antarctica and the Atacama deserts, raising the question as to how Rhodotorula yeasts may have adapted their metabolic strategies to optimize survival under low nutrient conditions. In order to understand their adaptive strategies in the ocean, the genome of R. sphaerocarpa ETNP2018 was compared to that of fourteen representative Rhodotorula yeasts, isolated from a variety of environments. RESULTS Rhodotorula sphaerocarpa ETNP2018, a strain isolated from the oligotrophic part of the eastern tropical North Pacific (ETNP) oxygen minimum zone (OMZ), hosts the smallest of the fifteen genomes and yet the number of protein-coding genes it possesses is on par with the other strains. Its genome exhibits a distinct reduction in genes dedicated to Major Facilitator Superfamily transporters as well as biosynthetic enzymes. However, its core metabolic pathways are fully conserved. Our research indicates that the selective pressures of the ETNP OMZ favor a streamlined genome with reduced overall biosynthetic potential balanced by a stable set of core metabolisms and an expansion of mechanisms for nutrient acquisition. CONCLUSIONS In summary, this study offers insights into the adaptation of fungi to the oligotrophic ocean and provides valuable information for understanding the ecological roles of fungi in the ocean.
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Affiliation(s)
- Dylan M Lane
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA
| | - David L Valentine
- Marine Science Institute, University of California, Santa Barbara, CA, USA
- Department of Earth Science, University of California, Santa Barbara, CA, USA
| | - Xuefeng Peng
- School of Earth, Ocean, and Environment, University of South Carolina, Columbia, SC, USA.
- Marine Science Institute, University of California, Santa Barbara, CA, USA.
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6
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Mirabile G, Ferraro V, Mancuso FP, Pecoraro L, Cirlincione F. Biodiversity of Fungi in Freshwater Ecosystems of Italy. J Fungi (Basel) 2023; 9:993. [PMID: 37888249 PMCID: PMC10607542 DOI: 10.3390/jof9100993] [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: 09/04/2023] [Revised: 09/30/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Fungal biodiversity is still mostly unknown and their presence in particular ecosystems such as freshwater habitats is often underestimated. The ecological role that these fungi play in freshwater environments mainly concerns their activity as decomposers of litter and plant material. At present, it is estimated that 3870 species belong to the ecological group of freshwater fungi (13 phyla and 45 classes). In this survey, we provide an overview of the Italian freshwater fungal diversity on the basis of the field and literature data. In the literature, data on freshwater fungi are fragmentary and not updated, focusing mainly on northern Italy where the most important lakes and rivers are present, while data from central and southern Italy (including Sicily and Sardinia) are almost completely ineffective. In particular, Ascomycota are reported in only 14 publications, most of which concern the freshwater environments of Lombardia, Piemonte, and Veneto. Only one publication explores the biodiversity of freshwater Basidiomycota in the wetlands of the Cansiglio forest (Veneto). The field observation allowed for us to identify 38 species of Basidiomycota growing in riparian forest of Italy. However, the number of fungi in freshwater habitats of Italy is strongly underestimated and many species are still completely unknown.
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Affiliation(s)
- Giulia Mirabile
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg. 5, 90128 Palermo, Italy; (G.M.); (F.C.)
- NBFC, National Biodiversity Future Center, Piazza Marina 61 (c/o Palazzo Steri), 90133 Palermo, Italy
| | - Valeria Ferraro
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, University Campus “Ernesto Quagliariello”, Via E. Orabona 4, 70125 Bari, Italy
| | - Francesco Paolo Mancuso
- Department of Earth and Sea Sciences, University of Palermo, Viale delle Scienze, Bldg. 16, 90128 Palermo, Italy
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China;
| | - Fortunato Cirlincione
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg. 5, 90128 Palermo, Italy; (G.M.); (F.C.)
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McGuire PM, Butkevich N, Saksena AV, Walter MT, Shapleigh JP, Reid MC. Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors. Environ Microbiol 2023; 25:1696-1712. [PMID: 37105180 DOI: 10.1111/1462-2920.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 - removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.
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Affiliation(s)
- Philip M McGuire
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Natalie Butkevich
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Aryaman V Saksena
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Matthew C Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
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Drying Shapes Aquatic Fungal Community Assembly by Reducing Functional Diversity. DIVERSITY 2023. [DOI: 10.3390/d15020289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Aquatic fungi are highly diverse organisms that play a critical role in global biogeochemical cycles. Yet it remains unclear which assembly processes determine their co-occurrence and assembly patterns over gradients of drying intensity, which is a common stressor in fluvial networks. Although aquatic fungi possess drying-specific adaptations, little is known about how functional similarity influences co-occurrence probability and which functional traits are sorted by drying. Using field data from 15 streams, we investigated how co-occurrence patterns and assembly processes responded to drying intensity. To do so, we determined fungal co-occurrence patterns, functional traits that best explain species co-occurrence likelihood, and community assembly mechanisms explaining changes in functional diversity over the drying gradient. Our results identified 24 species pairs with positive co-occurrence probabilities and 16 species pairs with negative associations. The co-occurrence probability was correlated with species differences in conidia shape and fungal endophytic capacity. Functional diversity reduction over the drying gradient is generally associated with non-random abiotic filtering. However, the assembly processes changed over the drying gradient, with random assembly prevailing at low drying intensity and abiotic filtering gaining more importance as drying intensifies. Collectively, our results can help anticipate the impacts of global change on fungal communities and ecosystem functioning.
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9
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Arias-Real R, Menéndez M, Muñoz I, Pascoal C. Drying shapes the ecological niche of aquatic fungi with implications on ecosystem functioning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160374. [PMID: 36427710 DOI: 10.1016/j.scitotenv.2022.160374] [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: 07/21/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Fungi are among the most abundant and diverse organisms on Earth and play pivotal roles in global carbon processing, nutrient cycling and food webs. Despite their abundant and functional importance, little is known about the patterns and mechanisms governing their community composition in intermittent rivers and ephemeral streams, which are the most common fluvial ecosystems globally. Thus far, it is known that aquatic fungi have evolved various life-history strategies and functional adaptations to cope with drying. Nevertheless, some of these adaptations have a metabolic cost and trade-offs between growth, reproduction and dispersion that may affect ecosystem functioning. Thus, understanding their ecological strategies along a gradient of drying is crucial to assess how species will respond to global change and to identify meaningful taxa to maintain ecosystem functions. By combining in situ hydrological information with a niche-based approach, we analysed the role of drying in explaining the spatial segregation of fungal species, and we determined their specialization and affinity over a gradient of drying. In addition, we estimated whether species niches are good predictors of two key ecosystem processes: organic matter decomposition and fungal biomass accrual. Overall, we found that annual drying duration and frequency were the most influential variables upon species niche differentiation across the 15 studied streams. Our cluster analysis identified four drying niche-based groups with contrasting distributions and responses over the drying gradient: drying-sensitive, partly tolerant to drying, generalist, and drying-resistant specialist. In addition, we found that species belonging to the drying specialist group showed a weak contribution to both ecosystem processes, suggesting trade-offs between drying resistance strategies and the energy invested in growth. Taken together, our results suggest that increased water scarcity may jeopardise the capacity of aquatic fungi to guarantee ecosystem functioning and to maintain biogeochemical cycles despite their ability to cope with drying.
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Affiliation(s)
- Rebeca Arias-Real
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain.
| | - Margarita Menéndez
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Isabel Muñoz
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, Universitat de Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain
| | - Cláudia Pascoal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
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10
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Camelo FRB, Tonin AM, Salgueiro L, Sena G, Braga I, Medeiros AO, Gonçalves Júnior JF. Tropical stream microcosms of isolated fungal species suggest nutrient enrichment does not accelerate decomposition but might inhibit fungal biomass production. FEMS Microbiol Lett 2022; 369:6843576. [PMID: 36416839 DOI: 10.1093/femsle/fnac113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 10/06/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Terrestrial leaf litter is an essential energy source in forest streams and in many tropical streams, including Cerrado, litter undergoes biological decomposition mainly by fungi. However, there is a limited understanding of the contribution of isolated fungal species to in-stream litter decomposition in the tropics. Here we set a full factorial microcosms experiment using four fungal species (Aquanectria penicillioides, Lunulospora curvula, Pestalotiopsis submerses, and Pestalotiopsis sp.) incubated in isolation, two litter types (rapid and slow decomposing litter) and two nutrient levels (natural and enriched), all characteristics of Cerrado streams, to elucidate the role of isolated fungal species on litter decomposition. We found that all fungal species promoted litter mass loss but with contributions that varied from 1% to 8% of the initial mass. The fungal species decomposed 1.5 times more the slow decomposing litter and water nutrient enrichment had no effect on their contribution to mass loss. In contrast, fungal biomass was reduced by nutrient enrichment and was different among fungal species. We showed fungal contribution to decomposition depends on fungal identity and litter type, but not on water nutrients. These findings suggest that the identity of fungal species and litter types may have more important repercussions to in-stream decomposition than moderate nutrient enrichment in the tropics.
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Affiliation(s)
| | - Alan M Tonin
- Department of Ecology, Institute of Biological Sciences, University of Brasília (UnB) 70910-900, Brasília, Brazil
| | - Laís Salgueiro
- Department of Ecology, Institute of Biological Sciences, University of Brasília (UnB) 70910-900, Brasília, Brazil
| | - Guilherme Sena
- Department of Ecology, Institute of Biological Sciences, University of Brasília (UnB) 70910-900, Brasília, Brazil
| | - Isabela Braga
- Department of Ecology, Institute of Biological Sciences, University of Brasília (UnB) 70910-900, Brasília, Brazil
| | - Adriana Oliveira Medeiros
- Laboratório de Microbiologia Ambiental Instituto de Biologia, Universidade Federal da Bahia 40170-115, Campus Ondina, Salvador, Brazil
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11
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Shang Y, Wu X, Wang X, Dou H, Wei Q, Ma S, Sun G, Wang L, Sha W, Zhang H. Environmental factors and stochasticity affect the fungal community structures in the water and sediments of Hulun Lake, China. Ecol Evol 2022; 12:e9510. [PMID: 36415879 PMCID: PMC9674472 DOI: 10.1002/ece3.9510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/06/2022] [Accepted: 10/27/2022] [Indexed: 08/26/2023] Open
Abstract
Aquatic fungi form both morphologically and ecologically diverse communities. However, lake ecosystems are frequently overlooked as fungal habitats, despite the potentially important role of fungi in matter cycling and energy flow. Hulun Lake is a typical example of a seasonal glacial lake; however, previous studies have only focused on bacteria in this ecosystem. Therefore, in the current study, internal transcribed spacer ribosomal RNA (ITS rRNA) gene high-throughput sequencing was used to investigate the fungal communities in paired water and sediment samples from the Hulun Lake Basin in China. A significant difference was found between the fungal communities of the two sample types. Across all samples, we identified nine phyla, 30 classes, 78 orders, 177 families, and 307 genera. The dominant phyla in the lake were Ascomycota, Basidiomycota and Chytridiomycota. Our results show that both water and sediments have very high connectivity, are dominated by positive interactions, and have similar interaction patterns. The fungal community structures were found to be significantly affected by environmental factors (temperature, chemical oxygen demand, electrical conductivity, total phosphorus, and pH). In addition, the dispersal limitations of the fungi affected the structure of the fungal communities, and it was revealed that stochasticity is more important than deterministic mechanisms in influencing the structure and function of fungal communities. This study provides unique theoretical support for the study of seasonally frozen lake fungal communities and a scientific basis for the future management and protection of Hulun Lake.
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Affiliation(s)
| | - Xiaoyang Wu
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Xibao Wang
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid AreasHulunbuirChina
| | - Qinguo Wei
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Shengchao Ma
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Guolei Sun
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Lidong Wang
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life SciencesQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life SciencesQufu Normal UniversityQufuChina
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12
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Vass M, Eriksson K, Carlsson-Graner U, Wikner J, Andersson A. Co-occurrences enhance our understanding of aquatic fungal metacommunity assembly and reveal potential host-parasite interactions. FEMS Microbiol Ecol 2022; 98:fiac120. [PMID: 36202390 PMCID: PMC9621394 DOI: 10.1093/femsec/fiac120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023] Open
Abstract
Our knowledge of aquatic fungal communities, their assembly, distributions and ecological roles in marine ecosystems is scarce. Hence, we aimed to investigate fungal metacommunities of coastal habitats in a subarctic zone (northern Baltic Sea, Sweden). Using a novel joint species distribution model and network approach, we quantified the importance of biotic associations contributing to the assembly of mycoplankton, further, detected potential biotic interactions between fungi-algae pairs, respectively. Our long-read metabarcoding approach identified 493 fungal taxa, of which a dominant fraction (44.4%) was assigned as early-diverging fungi (i.e. Cryptomycota and Chytridiomycota). Alpha diversity of mycoplankton declined and community compositions changed along inlet-bay-offshore transects. The distributions of most fungi were rather influenced by environmental factors than by spatial drivers, and the influence of biotic associations was pronounced when environmental filtering was weak. We found great number of co-occurrences (120) among the dominant fungal groups, and the 25 associations between fungal and algal OTUs suggested potential host-parasite and/or saprotroph links, supporting a Cryptomycota-based mycoloop pathway. We emphasize that the contribution of biotic associations to mycoplankton assembly are important to consider in future studies as it helps to improve predictions of species distributions in aquatic ecosystems.
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Affiliation(s)
- Máté Vass
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Karolina Eriksson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Ulla Carlsson-Graner
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Johan Wikner
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
- Sweden Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
- Sweden Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
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13
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The Introduction of Two New Species of Aquatic Fungi from Anzali Lagoon, Northern Iran. DIVERSITY 2022. [DOI: 10.3390/d14100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
During a survey of aquatic fungi from Anzali Lagoon in Iran, several fungal specimens were isolated from freshwater habitats. Morphological evidence and comparing sequencing based on rDNA (ITS and LSU) and protein-coding genes (TEF1 and TUB2) showed that some isolates belong to undescribed fungal species. These isolates belong to Arthrobotrys and Sarocladium, two ascomycetes genera. Arthrobotrys hyrcanus, sp. nov., differs from closely related species such as A. dianchiensis by its larger conidia and septation of primary conidia. Sarocladium pseudokiliense, sp. nov., was similar to S. kiliense, but distinguished by its conidial shape and the absence of adelophialides and chlamydospores. Morphological descriptions, illustrations and multilocus phylogenetic analysis for both new species are provided.
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14
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Adam C, Magdalena Ś. Species Diversity of Mycoplankton on the Background of Selected Indicators of Water Quality in Stratified Mesotrophic Lakes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192013298. [PMID: 36293879 PMCID: PMC9602596 DOI: 10.3390/ijerph192013298] [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: 09/17/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 06/08/2023]
Abstract
The aim of the study was to determine mycoplankton species diversity in relation to the physico-chemical parameters of lake waters. The research was carried out in the summer months in 15 mesotrophic lakes and showed a high ecological significance index for Rhodotorula glutinis, Epicoccum nigrum, Fusarium sporotrichioides, and Trichophyton violaceum. Mycoplankton abundance and species diversity decreased with the depth of water, which coincided with a decrease in oxygen content and organic matter concentration. A high concentration of nitrogen compounds (total nitrogen-TN and dissolved nitrogen-DN) limited the development of mycobiota in the hypolimnion. In the metalimnion, the intensive development of organisms, especially bacteria, limited mycoplankton abundance despite perfect physical and chemical conditions for its development. Finally, mycoplankton functioned the best in slightly alkaline waters.
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Affiliation(s)
- Cudowski Adam
- Department of Water Ecology, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland
| | - Świsłocka Magdalena
- Department of Zoology and Genetics, Faculty of Biology, University of Bialystok, Ciolkowskiego 1J, 15-245 Bialystok, Poland
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15
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Li X, Wang T, Fu B, Mu X. Improvement of aquaculture water quality by mixed Bacillus and its effects on microbial community structure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69731-69742. [PMID: 35576039 DOI: 10.1007/s11356-022-20608-0] [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: 11/10/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Microbial remediation, especially the application of probiotics, has recently gained popularity in improving water quality and maintaining aquatic animal health. The efficacy and mechanism of mixed Bacillus for improvement of water quality and its effects on aquatic microbial community structure remain unknown. To elucidate these issues, we applied two groups of mixed Bacillus (Bacillus megaterium and Bacillus subtilis (A0 + BS) and Bacillus megaterium and Bacillus coagulans (A0 + BC)) to the aquaculture system of Crucian carp. Our results showed that the improvement effect of mixed Bacillus A0 + BS on water quality was better than that of A0 + BC, and the NH4+-N, NO2--N, NO3--N, and total phosphorus (TP) concentrations were reduced by 46.3%, 76.3%, 35.6%, and 80.3%, respectively. In addition, both groups of mixed Bacillus increased the diversity of the bacterial community and decreased the diversity of the fungal community. Microbial community analysis showed that mixed Bacillus A0 + BS increased the relative abundance of bacteria related with nitrogen and phosphorus removal, such as Proteobacteria, Actinobacteria, Comamonas, and Stenotrophomonas, but decreased the relative abundance of pathogenic bacteria (Acinetobacter and Pseudomonas) and fungi (Epicoccum and Fusarium). Redundancy analysis showed that NH4+-N, NO2--N, and TP were the primary environmental factors affecting the microbial community in aquaculture water. PICRUST analysis indicated that all functional pathways in the A0 + BS group were richer than those in other groups. These results indicated that mixed Bacillus A0 + BS addition produced good results in reducing nitrogenous and phosphorus compounds and shaped a favorable microbial community structure to further improve water quality.
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Affiliation(s)
- Xue Li
- School of Environmental Science, Liaoning University, Shenyang, 110036, People's Republic of China
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, 100141, People's Republic of China
| | - Tianjie Wang
- School of Environmental Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Baorong Fu
- School of Environmental Science, Liaoning University, Shenyang, 110036, People's Republic of China.
| | - Xiyan Mu
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, 100141, People's Republic of China
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16
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Yao Y, Zhao J, Miao L, Hou J. Effects of sediment physicochemical factors and heavy metals on the diversity, structure, and functions of bacterial and fungal communities from a eutrophic river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 303:119129. [PMID: 35283203 DOI: 10.1016/j.envpol.2022.119129] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Urbanization has destroyed river ecosystems, leading to eutrophication. Heavy metals are frequently observed in urban rivers, and the joint effects of eutrophication and heavy metals on microbial communities, especially on fungal communities, have not been adequately explored. In this study, we explored the effect of sediment physicochemical factors and heavy metals on the microbial diversity, community structure, and functions of bacterial and fungal communities from a black-odorous river in Wuhu, China. Twenty-four samples were collected, and the diversity and structure of fungal and bacterial communities were determined by high-throughput sequencing. Proteobacteria and Rozellomycota were the main phyla in the bacterial and fungal communities, respectively. The results showed different distribution patterns of bacterial and fungal communities along the river. Physicochemical factors and heavy metals exhibited different effects on microbial variation. Specifically, pH and Cr negatively affected bacterial α-diversity, whereas total phosphorus and Cr significantly affected fungal α-diversity. Variance partitioning analysis revealed that physicochemical factors explained more of the bacterial community structure than heavy metals (49.5% vs. 36.6%), with pH and total phosphorus being the dominant factors. Opposite patterns were observed for fungal community structure, with heavy metals contributing the most (48.0%). A similar influence pattern was observed for the predicted functions of the two communities. This study suggests that heavy metals in eutrophication rivers are essential factors that shift the microbial variation and should be considered in urban river evaluation and remediation.
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Affiliation(s)
- Yu Yao
- School of Environment, Nanjing Normal University, Nanjing, 210023, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China; Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing, 210023, China
| | - Jiaqi Zhao
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, People's Republic of China.
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17
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Orsi WD, Vuillemin A, Coskun ÖK, Rodriguez P, Oertel Y, Niggemann J, Mohrholz V, Gomez-Saez GV. Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis. THE ISME JOURNAL 2022; 16:1245-1261. [PMID: 34893690 PMCID: PMC9038920 DOI: 10.1038/s41396-021-01169-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
Fungi are ubiquitous in the ocean and hypothesized to be important members of marine ecosystems, but their roles in the marine carbon cycle are poorly understood. Here, we use 13C DNA stable isotope probing coupled with phylogenetic analyses to investigate carbon assimilation within diverse communities of planktonic and benthic fungi in the Benguela Upwelling System (Namibia). Across the redox stratified water column and in the underlying sediments, assimilation of 13C-labeled carbon from diatom extracellular polymeric substances (13C-dEPS) by fungi correlated with the expression of fungal genes encoding carbohydrate-active enzymes. Phylogenetic analysis of genes from 13C-labeled metagenomes revealed saprotrophic lineages related to the facultative yeast Malassezia were the main fungal foragers of pelagic dEPS. In contrast, fungi living in the underlying sulfidic sediments assimilated more 13C-labeled carbon from chemosynthetic bacteria compared to dEPS. This coincided with a unique seafloor fungal community and dissolved organic matter composition compared to the water column, and a 100-fold increased fungal abundance within the subseafloor sulfide-nitrate transition zone. The subseafloor fungi feeding on 13C-labeled chemolithoautotrophs under anoxic conditions were affiliated with Chytridiomycota and Mucoromycota that encode cellulolytic and proteolytic enzymes, revealing polysaccharide and protein-degrading fungi that can anaerobically decompose chemosynthetic necromass. These subseafloor fungi, therefore, appear to be specialized in organic matter that is produced in the sediments. Our findings reveal that the phylogenetic diversity of fungi across redox stratified marine ecosystems translates into functionally relevant mechanisms helping to structure carbon flow from primary producers in marine microbiomes from the surface ocean to the subseafloor.
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18
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Ilicic D, Grossart HP. Basal Parasitic Fungi in Marine Food Webs-A Mystery Yet to Unravel. J Fungi (Basel) 2022; 8:114. [PMID: 35205868 PMCID: PMC8874645 DOI: 10.3390/jof8020114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.
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Affiliation(s)
- Doris Ilicic
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany;
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany;
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
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19
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Wu JY, Hua ZL, Gu L, Li XQ, Gao C, Liu YY. Perfluorinated compounds (PFCs) in regional industrial rivers: Interactions between pollution flux and eukaryotic community phylosymbiosis. ENVIRONMENTAL RESEARCH 2022; 203:111876. [PMID: 34400162 DOI: 10.1016/j.envres.2021.111876] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/21/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Perfluorinated compounds (PFCs) pose serious threats to aquatic ecosystems, especially their microbial communities. However, little is known about the phylosymbiosis of aquatic fungal and viridiplantae communities in response to PFC accumulation. We quantified the distribution of 14 PFCs in rivers and found that PFBA was dominant in the transition from water to sediment. High through-put sequencing revealed that phyla Ascomycota, Basidiomycota, Anthophyta, and Chlorophyta were the predominant in eukaryotic community. The effects of PFCs on spatial community coalescence at taxonomic and phylogenetic levels (p < 0.05) were revealed. Fungal community coalescence triggered the spatial assembly of fungal and viridiplantae communities in riverine environments (p < 0.05). Null modeling indicated that PFBA, PFTrDA and PFOS, etc, mediated phylogenetic assembly (p < 0.05) and stochastic processes (86.67-100%) maintain phylogenetic turnover in the fungal community. Meanwhile, variable selection (27.78-54.44%) explained the viridiplantae community assemblage. Finally, we identified fungal genera Hannaella, Naganishia, Purpureocillium and Stachybotrys as indicators for PFC pollution (p < 0.001). These results help explain the effects of PFCs on riverine ecological remediation.
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Affiliation(s)
- Jian-Yi Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Zu-Lin Hua
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Li Gu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
| | - Xiao-Qing Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Chang Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Yuan-Yuan Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
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20
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Kluge M, Wauthy M, Clemmensen KE, Wurzbacher C, Hawkes JA, Einarsdottir K, Rautio M, Stenlid J, Peura S. Declining fungal diversity in Arctic freshwaters along a permafrost thaw gradient. GLOBAL CHANGE BIOLOGY 2021; 27:5889-5906. [PMID: 34462999 DOI: 10.1111/gcb.15852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Climate change-driven permafrost thaw has a strong influence on pan-Arctic regions, via, for example, the formation of thermokarst ponds. These ponds are hotspots of microbial carbon cycling and greenhouse gas production, and efforts have been put on disentangling the role of bacteria and archaea in recycling the increasing amounts of carbon arriving to the ponds from degrading watersheds. However, despite the well-established role of fungi in carbon cycling in the terrestrial environments, the interactions between permafrost thaw and fungal communities in Arctic freshwaters have remained unknown. We integrated data from 60 ponds in Arctic hydro-ecosystems, representing a gradient of permafrost integrity and spanning over five regions, namely Alaska, Greenland, Canada, Sweden, and Western Siberia. The results revealed that differences in pH and organic matter quality and availability were linked to distinct fungal community compositions and that a large fraction of the community represented unknown fungal phyla. Results display a 16%-19% decrease in fungal diversity, assessed by beta diversity, across ponds in landscapes with more degraded permafrost. At the same time, sites with similar carbon quality shared more species, aligning a shift in species composition with the quality and availability of terrestrial dissolved organic matter. We demonstrate that the degradation of permafrost has a strong negative impact on aquatic fungal diversity, likely via interactions with the carbon pool released from ancient deposits. This is expected to have implications for carbon cycling and climate feedback loops in the rapidly warming Arctic.
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Affiliation(s)
- Mariana Kluge
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maxime Wauthy
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
- Centre for Northern Studies (CEN), Université Laval, Québec, Québec, Canada
| | | | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | | | | | - Milla Rautio
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
- Centre for Northern Studies (CEN), Université Laval, Québec, Québec, Canada
- Group for Interuniversity Research in Limnology and Aquatic Environment (GRIL), Université de Montréal, Montréal, Québec, Canada
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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21
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Nam B, Lee DJ, Choi YJ. High-Temperature-Tolerant Fungus and Oomycetes in Korea, Including Saksenaea longicolla sp. nov. MYCOBIOLOGY 2021; 49:476-490. [PMID: 34803436 PMCID: PMC8583829 DOI: 10.1080/12298093.2021.1985698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Global temperatures are steadily increasing, leading to significant changes in microbial diversity and ecology. In the present study, we isolated high-temperature-growing fungi and fungi-like group (Oomycota) strains from freshwater environments of Korea and identified them based on cultural, morphological, and multilocus phylogenetic analyses. As a result, we introduce Saksenaea (Fungi) isolates as a new species, Saksenaea longicolla sp. nov. and record Phytophthora chlamydospora and P. lagoariana (Oomycota) new to Korea. In the growth experiments, they exhibited high-temperature tolerance, which can grow at 35-40 °C but become inactive at 4 °C and below. This study confirms the presence of high-temperature-tolerant fungi and oomycetes in Korea and suggests that the Korean climate conditions are changing in favor of these species. This indicates that climate warming is altering microbial distributions in freshwater environments.
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Affiliation(s)
- Bora Nam
- Department of Biology, College of Natural Sciences, Kunsan National University, Gunsan, Korea
| | - Dong-Jae Lee
- Department of Biology, College of Natural Sciences, Kunsan National University, Gunsan, Korea
| | - Young-Joon Choi
- Department of Biology, College of Natural Sciences, Kunsan National University, Gunsan, Korea
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22
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Baudy P, Zubrod JP, Konschak M, Röder N, Nguyen TH, Schreiner VC, Baschien C, Schulz R, Bundschuh M. Environmentally relevant fungicide levels modify fungal community composition and interactions but not functioning. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117234. [PMID: 33962304 DOI: 10.1016/j.envpol.2021.117234] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 05/25/2023]
Abstract
Aquatic hyphomycetes (AHs), a group of saprotrophic fungi adapted to submerged leaf litter, play key functional roles in stream ecosystems as decomposers and food source for higher trophic levels. Fungicides, controlling fungal pathogens, target evolutionary conserved molecular processes in fungi and contaminate streams via their use in agricultural and urban landscapes. Thus fungicides pose a risk to AHs and the functions they provide. To investigate the impacts of fungicide exposure on the composition and functioning of AH communities, we exposed four AH species in monocultures and mixed cultures to increasing fungicide concentrations (0, 5, 50, 500, and 2500 μg/L). We assessed the biomass of each species via quantitative real-time PCR. Moreover, leaf decomposition was investigated. In monocultures, none of the species was affected at environmentally relevant fungicide levels (5 and 50 μg/L). The two most tolerant species were able to colonize and decompose leaves even at very high fungicide levels (≥500 μg/L), although less efficiently. In mixed cultures, changes in leaf decomposition reflected the response pattern of the species most tolerant in monocultures. Accordingly, the decomposition process may be safeguarded by tolerant species in combination with functional redundancy. In all fungicide treatments, however, sensitive species were displaced and interactions between fungi changed from complementarity to competition. As AH community composition determines leaves' nutritional quality for consumers, the data suggest that fungicide exposures rather induce bottom-up effects in food webs than impairments in leaf decomposition.
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Affiliation(s)
- Patrick Baudy
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany
| | - Jochen P Zubrod
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany; Eußerthal Ecosystem Research Station, University of Koblenz-Landau, Birkenthalstraße 13, D-76857, Eußerthal, Germany
| | - Marco Konschak
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany
| | - Nina Röder
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany
| | - Thu Huyen Nguyen
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany
| | - Verena C Schreiner
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany
| | - Christiane Baschien
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, D-38124, Braunschweig, Germany
| | - Ralf Schulz
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany; Eußerthal Ecosystem Research Station, University of Koblenz-Landau, Birkenthalstraße 13, D-76857, Eußerthal, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, D-76829, Landau, Germany; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms Väg 9, SWE-75007, Uppsala, Sweden.
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23
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Baudy P, Zubrod JP, Konschak M, Kolbenschlag S, Pollitt A, Baschien C, Schulz R, Bundschuh M. Fungal-fungal and fungal-bacterial interactions in aquatic decomposer communities: bacteria promote fungal diversity. Ecology 2021; 102:e03471. [PMID: 34260739 DOI: 10.1002/ecy.3471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/19/2021] [Accepted: 03/15/2021] [Indexed: 11/07/2022]
Abstract
Fungi produce a variety of extracellular enzymes making recalcitrant substrates bioavailable. Thus, fungi are central for decomposition of dead organic matter such as leaf litter. Despite their ecological importance, our understanding of relationships between fungal species diversity and ecosystem functioning is limited, especially with regard to aquatic habitats. Moreover, fungal interactions with other groups of microorganisms such as bacteria are rarely investigated. This lack of information may be attributed to methodological limitations in tracking the biomass of individual fungal species in communities, impeding a detailed assessment of deviations from the overall performance expected from the sum of individual species' performances, so-called net diversity effects (NDEs). We used fungal species-specific biomolecular tools to target fungal-fungal and fungal-bacterial interactions on submerged leaves using four cosmopolitan aquatic fungal species and a stream microbial community dominated by bacteria. In microcosms, we experimentally manipulated fungal diversity and bacterial absence/presence and assessed functional performances and fungal community composition after 14 days of incubation. Fungal community data was used to evaluate NDEs on leaf colonization. The individual fungal species were functionally distinct and fungal cultures were on average more efficient than the bacterial culture. In absence of bacteria, NDEs correlated with growth rate (negatively) and genetic divergence (positively), but were predominantly negative, suggesting that higher fungal diversity led to a lower colonization success (niche overlap). In both absence and presence of bacteria, the overall functional performances of the communities were largely defined by their composition (i.e., no interactions at the functional level). In presence of bacteria, NDEs correlated with genetic divergence (positively) and were largely positive, suggesting higher fungal diversity stimulated colonization (niche complementarity). This stimulation may be driven by a bacteria-induced inhibition of fungal growth, alleviating competition among fungi. Resulting feedback loops eventually promote fungal coexistence and synergistic interactions. Nonetheless, overall functional performances are reduced compared to bacteria-free cultures. These findings highlight the necessity to conduct future studies, investigating biodiversity-ecosystem functioning relationships using artificial systems, without exclusion of key organisms naturally co-occurring in the compartment of interest. Otherwise, study outcomes might not reflect true ecological relationships and ultimately misguide conservation strategies.
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Affiliation(s)
- Patrick Baudy
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, D-76829, Germany
| | - Jochen P Zubrod
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, D-76829, Germany
- Eußerthal Ecosystem Research Station, University of Koblenz-Landau, Birkenthalstraße 13, Eußerthal, D-76857, Germany
| | - Marco Konschak
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, D-76829, Germany
| | - Sara Kolbenschlag
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, D-76829, Germany
| | - Annika Pollitt
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, D-76829, Germany
| | - Christiane Baschien
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, Braunschweig, D-38124, Germany
| | - Ralf Schulz
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, D-76829, Germany
- Eußerthal Ecosystem Research Station, University of Koblenz-Landau, Birkenthalstraße 13, Eußerthal, D-76857, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Koblenz-Landau, Fortstraße 7, Landau, D-76829, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Box 7050, Uppsala, SWE-75007, Sweden
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Varrella S, Barone G, Tangherlini M, Rastelli E, Dell’Anno A, Corinaldesi C. Diversity, Ecological Role and Biotechnological Potential of Antarctic Marine Fungi. J Fungi (Basel) 2021; 7:391. [PMID: 34067750 PMCID: PMC8157204 DOI: 10.3390/jof7050391] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/28/2022] Open
Abstract
The Antarctic Ocean is one of the most remote and inaccessible environments on our planet and hosts potentially high biodiversity, being largely unexplored and undescribed. Fungi have key functions and unique physiological and morphological adaptations even in extreme conditions, from shallow habitats to deep-sea sediments. Here, we summarized information on diversity, the ecological role, and biotechnological potential of marine fungi in the coldest biome on Earth. This review also discloses the importance of boosting research on Antarctic fungi as hidden treasures of biodiversity and bioactive molecules to better understand their role in marine ecosystem functioning and their applications in different biotechnological fields.
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Affiliation(s)
- Stefano Varrella
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Giulio Barone
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Largo Fiera della Pesca, 60125 Ancona, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Yang Y, Banos S, Gerdts G, Wichels A, Reich M. Mycoplankton Biome Structure and Assemblage Processes Differ Along a Transect From the Elbe River Down to the River Plume and the Adjacent Marine Waters. Front Microbiol 2021; 12:640469. [PMID: 33967979 PMCID: PMC8102988 DOI: 10.3389/fmicb.2021.640469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/12/2021] [Indexed: 11/25/2022] Open
Abstract
Rivers are transport systems and supply adjacent ecosystems with nutrients. They also serve human well-being, for example as a source of food. Microorganism biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that fungi are key players in freshwater nutrient cycling and food webs, data on planktonic fungi of streams with higher stream order are scarce. This study aims to fill this knowledge gap by a fungi-specific 18S ribosomal RNA (rRNA) gene tag sequencing approach, investigating mycoplankton diversity in the Elbe River along a transect from shallow freshwater, to the estuary and river plume down to the adjacent marine waters (sections of seventh stream order number). Using multivariate analyses and the quantitative process estimates (QPEs) method, questions (i) of how mycoplankton communities as part of the river continuum change along the transect, (ii) what factors, spatial and environmental, play a role, and (iii) what assembly processes, such as selection or dispersion, operate along the transect, were addressed. The partitioning of mycoplankton communities into three significant distant biomes was mainly driven by local environmental conditions that were partly under spatial control. The assembly processes underlying the biomes also differed significantly. Thus, variable selection dominated the upstream sections, while undominated processes like ecological drift dominated the sections close to the river mouth and beyond. Dispersal played a minor role. The results suggest that the ecological versatility of the mycoplankton communities changes along the transect as response, for example, to a drastic change from an autotrophic to a heterotrophic system caused by an abrupt increase in the river depth. Furthermore, a significant salinity-dependent occurrence of diverse basal fungal groups was observed, with no clade found exclusively in marine waters. These results provide an important framework to help understand patterns of riverine mycoplankton communities and serve as basis for a further in-depth work so that fungi, as an important ecological organism group, can be integrated into models of, e.g., usage-balance considerations of rivers.
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Affiliation(s)
- Yanyan Yang
- Molecular Ecology Group, University of Bremen, FB2, Bremen, Germany
| | - Stefanos Banos
- Molecular Ecology Group, University of Bremen, FB2, Bremen, Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Antje Wichels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Marlis Reich
- Molecular Ecology Group, University of Bremen, FB2, Bremen, Germany
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Carreira C, Lønborg C, Kühl M, Lillebø AI, Sandaa RA, Villanueva L, Cruz S. Fungi and viruses as important players in microbial mats. FEMS Microbiol Ecol 2021; 96:5910486. [PMID: 32966583 DOI: 10.1093/femsec/fiaa187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.
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Affiliation(s)
- Cátia Carreira
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Christian Lønborg
- Section for Applied Marine Ecology and Modelling, Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Ana I Lillebø
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Texel, The Netherlands
| | - Sónia Cruz
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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Ani E, Adekunle AA, Kadiri AB, Njoku KL. Rhizoremediation of hydrocarbon contaminated soil using Luffa aegyptiaca (Mill) and associated fungi. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 23:1444-1456. [PMID: 33765399 DOI: 10.1080/15226514.2021.1901852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The potentials of Luffa aegyptiaca and its rhizospheric, non-mycorrhizal fungi in biodegrading and bio-remediating hydrocarbon contaminated soil were investigated in-vitro and in-situ. Biodegradation study was done in two stages: preliminary study using hydrocarbon treated filter paper and in-vitro with Mineral Salt Media (MSM) read on Spectrophotometer at two photo synthetically active wavelengths (530 nm and 620 nm) while rhizoremediation study was done in-situ in contaminated plot of land. Hydrocarbon utilization ability of the fungi and plant were confirmed using total petroleum hydrocarbon (TPH) analysis and gas chromatography mass spectroscopy (GC-MS). Results show differing rates of hydrocarbon utilization by isolated fungi. In-vitro biodegradation study showed that Aspergillus niger, Fusarium solani, Curvularia lunata and Trichoderma harzianum were best in degrading kerosene (78%), diesel (70%), spent engine oil (83%) and crude oil (77%) respectively. Rhizoremediation study using L. aegyptiaca and C. lunata show that remediation was enhanced to 72.15% as against 32.32% and 14% when only the plant or fungus is used respectively. Hydrocarbon accumulation by L. aegyptiaca also decreased in the presence of the fungus. Curvularia lunata is shown in this study to enhance the germination, survival, growth and bioremediation efficiency of L. aegyptiaca in polluted environment.Novelty statement The potentials of Curvularia lunata, a non-mycorrhizal fungi associated with L. aegyptiaca in survival, growth and phytoremediation of petroleum hydrocarbon polluted soil by L. aegyptiaca is highlighted in this study. Luffa aegyptiaca and its associated fungi is shown to bio-remediate petroleum hydrocarbon through phyto-accumulation and rhizosphere effect.
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Affiliation(s)
- Emmanuel Ani
- Environmental Biology Unit, Department of Biological Sciences, Yaba College of Technology, Lagos, Nigeria
| | | | - Akeem B Kadiri
- Department of Botany, University of Lagos, Lagos, Nigeria
| | - Kelechi L Njoku
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
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The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México. J Fungi (Basel) 2021; 7:jof7030210. [PMID: 33809206 PMCID: PMC7999539 DOI: 10.3390/jof7030210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/15/2023] Open
Abstract
The abundance and diversity of fungi were evaluated in a hypersaline microbial mat from Guerrero Negro, México, using a combination of quantitative polymerase chain reaction (qPCR) amplification of domain-specific primers, and metagenomic sequencing. Seven different layers were analyzed in the mat (Layers 1–7) at single millimeter resolution (from the surface to 7 mm in depth). The number of copies of the 18S rRNA gene of fungi ranged between 106 and 107 copies per g mat, being two logarithmic units lower than of the 16S rRNA gene of bacteria. The abundance of 18S rRNA genes of fungi varied significantly among the layers with layers 2–5 mm from surface contained the highest numbers of copies. Fifty-six fungal taxa were identified by metagenomic sequencing, classified into three different phyla: Ascomycota, Basidiomycota and Microsporidia. The prevalent genera of fungi were Thermothelomyces, Pyricularia, Fusarium, Colletotrichum, Aspergillus, Botrytis, Candida and Neurospora. Genera of fungi identified in the mat were closely related to genera known to have saprotrophic and parasitic lifestyles, as well as genera related to human and plant pathogens and fungi able to perform denitrification. This research suggests that fungi in the mat may participate in nutrient recycling, modification of community composition through parasitic activities, and denitrification.
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29
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Álvarez-Barragán J, Cravo-Laureau C, Wick LY, Duran R. Fungi in PAH-contaminated marine sediments: Cultivable diversity and tolerance capacity towards PAH. MARINE POLLUTION BULLETIN 2021; 164:112082. [PMID: 33524832 DOI: 10.1016/j.marpolbul.2021.112082] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
The cultivable fungal diversity from PAH-contaminated sediments was examined for the tolerance to polycyclic aromatic hydrocarbon (PAH). The 85 fungal strains, isolated in non-selective media, revealed a large diversity by ribosomal internal transcribed spacer (ITS) sequencing, even including possible new species. Most strains (64%) exhibited PAH-tolerance, indicating that sediments retain diverse cultivable PAH-tolerant fungi. The PAH-tolerance was linked neither to a specific taxon nor to the peroxidase genes (LiP, MnP and Lac). Examining the PAH-removal (degradation and/or sorption), Alternaria destruens F10.81 showed the best capacity with above 80% removal for phenanthrene, pyrene and fluoranthene, and around 65% for benzo[a]pyrene. A. destruens F10.81 internalized pyrene homogenously into the hyphae that contrasted with Fusarium pseudoygamai F5.76 in which PAH-vacuoles were observed but PAH removal was below 20%. Thus, our study paves the way for the exploitation of fungi in remediation strategies to mitigate the effect of PAH in coastal marine sediments.
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Affiliation(s)
- Joyce Álvarez-Barragán
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - Cristiana Cravo-Laureau
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Leipzig, 04318, Germany
| | - Robert Duran
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM UMR CNRS 5254, Bat. IBEAS, Pau, France.
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Zhang Z, Deng Q, Cao X, Zhou Y, Song C. Patterns of Sediment Fungal Community Dependent on Farming Practices in Aquaculture Ponds. Front Microbiol 2021; 12:542064. [PMID: 33679624 PMCID: PMC7933557 DOI: 10.3389/fmicb.2021.542064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 01/26/2021] [Indexed: 01/01/2023] Open
Abstract
Despite fungi playing an important role in nutrient decomposition in aquatic ecosystems and being considered as vital actors in the ecological processes, they received limited attention regarding the community in aquaculture pond sediments which are extremely important and typically disturbed habitats. Using an ITS1 region of fungal rDNA, this study aimed to investigate sediment fungal communities in fish, crab, and crayfish ponds for decades of farming practices at representative aquaculture regions in the middle Yangtze River basin, China. We then aimed to explore the community patterns associated with species-based farming practices in the ponds at 18 farms. The results showed that the pond sediments harbored more than 9,000 operational taxonomic units. The sediments had significantly higher alpha diversity in crab ponds compared to that in fish and crayfish ponds. The fungal phyla largely belonged to Ascomycota and Chytridiomycota, and the dominance of Rozellomycota over Basidiomycota and Aphelidiomycota was observed. The majority of sediment fungal members were ascribed to unclassified fungi, with higher proportions in fish ponds than crab and crayfish ponds. Further, the fungal communities were markedly distinct among the three types of ponds, suggesting divergent patterns of fungal community assemblages caused by farming practices in aquaculture ponds. The community diversity and structure were closely correlated to sediment properties, especially sediment carbon content and pH. Thus, the distribution and pattern of fungal communities in the sediments appear to primarily depend on species-based farming practices responsible for the resulting sediment carbon content and pH in aquaculture ponds. This study provides a detailed snapshot and extension of understanding fungal community structure and variability in pond ecosystems, highlighting the impacts of farming practices on the assembly and succession of sediment fungal communities in aquaculture ponds.
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Affiliation(s)
- Zhimin Zhang
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qinghui Deng
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiuyun Cao
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yiyong Zhou
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunlei Song
- Key Laboratory of Algal Biology, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Farthing HN, Jiang J, Henwood AJ, Fenton A, Garner TWJ, Daversa DR, Fisher MC, Montagnes DJS. Microbial Grazers May Aid in Controlling Infections Caused by the Aquatic Zoosporic Fungus Batrachochytrium dendrobatidis. Front Microbiol 2021; 11:592286. [PMID: 33552011 PMCID: PMC7858660 DOI: 10.3389/fmicb.2020.592286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Free-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytrid Batrachochytrium dendrobatidis (Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 μm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliate Tetrahymena pyriformis, which likely co-occurs with Bd, grew at near its maximum rate (r = 1.7 d-1). A functional response (ingestion vs. prey abundance) for T. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (I max ) of 1.63 × 103 zoospores d-1, with a half saturation constant (k) of 5.75 × 103 zoospores ml-1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could control Bd and potentially prevent chytridiomycosis (defined as 104 sporangia host-1). However, simulated inferior micrograzers (0.7 × I max and 1.5 × k) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modeling disease dynamics for Bd and other zoosporic fungi.
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Affiliation(s)
- Hazel N. Farthing
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
- Department of Evolution, Ecology and Behaviour, Biosciences Building, University of Liverpool, Liverpool, United Kingdom
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Alexandra J. Henwood
- Department of Evolution, Ecology and Behaviour, Biosciences Building, University of Liverpool, Liverpool, United Kingdom
| | - Andy Fenton
- Department of Evolution, Ecology and Behaviour, Biosciences Building, University of Liverpool, Liverpool, United Kingdom
| | - Trent W. J. Garner
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - David R. Daversa
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Matthew C. Fisher
- Department of Evolution, Ecology and Behaviour, Biosciences Building, University of Liverpool, Liverpool, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - David J. S. Montagnes
- Department of Evolution, Ecology and Behaviour, Biosciences Building, University of Liverpool, Liverpool, United Kingdom
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Li J, Wang P, Salam N, Li X, Ahmad M, Tian Y, Duan L, Huang L, Xiao M, Mou X, Li W. Unraveling bacteria-mediated degradation of lignin-derived aromatic compounds in a freshwater environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141236. [PMID: 32846344 DOI: 10.1016/j.scitotenv.2020.141236] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Terrestrial organic carbon-lignin plays a crucial role in the global carbon balance. However, limited studies presented the functional and ecological traits of lignin decomposers population in natural aquatic ecosystem. In this study, we performed a multi-omics analysis by deploying amplicon, metagenomic, and metatranscriptomic approaches to identify the key potential degraders and pathways involved lignin-derived aromatic compounds in the later stage of lignin degradation. By establishing microcosms with model lignin-derived aromatic compound (vanillic acid, VAN), based on the estimated absolute abundance (EAA) and the metagenome-assembled genomes (MAGs), novel potential lignin-derived aromatic compounds degraders were identified in the aquatic ecosystem. Furthermore, members of the phyla Proteobacteria and Actinobacteria were the potential major lignin-derived aromatic compounds degraders in the studied ecosystem. Our study demonstrated that genomes of the class Betaproteobacteria (Proteobacteria) possess a complete enzymatic system for the degradation of diarylpropanes, vanillate and protocatechuate, besides having the capacity to degrade other lignin-derived aromatic compounds. This study provides strong evidence for the ability of aquatic bacteria to degrade lignin-derived aromatic compounds and suggest that different microbes might occupy different niches in the later stage of lignin degradation.
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Affiliation(s)
- Jialing Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Pandeng Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Nimaichand Salam
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Xin Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Manzoor Ahmad
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Ye Tian
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Li Duan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Linan Huang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Min Xiao
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, Kent, 44242, OH, USA.
| | - Wenjun Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong, China.
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Mammo FK, Amoah ID, Gani KM, Pillay L, Ratha SK, Bux F, Kumari S. Microplastics in the environment: Interactions with microbes and chemical contaminants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140518. [PMID: 32653705 DOI: 10.1016/j.scitotenv.2020.140518] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 05/02/2023]
Abstract
Microplastics (MPs) are contaminants of emerging concern that have gained considerable attention during the last few decades due to their adverse impact on living organisms and the environment. Recent studies have shown their ubiquitous presence in the environment including the atmosphere, soil, and water. Though several reviews have focused on the occurrence of microplastics in different habitats, little attention has been paid to their interaction with biological and chemical pollutants in the environment. This review therefore presents the state of knowledge on the interaction of MPs with chemicals and microbes in different environments. The distribution of MPs, the association of toxic chemicals with MPs, microbial association with MPs and the microbial-induced fate of MPs in the environment are discussed. The biodegradation and bioaccumulation of MPs by and in microbes and its potential impact on the food chain are also reviewed. The mechanisms driving these interactions and how these, in turn, affect living organisms however are not yet fully understood and require further attention.
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Affiliation(s)
- F K Mammo
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - I D Amoah
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - K M Gani
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - L Pillay
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - S K Ratha
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - F Bux
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - S Kumari
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
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Rojas-Jimenez K, Grossart HP, Cordes E, Cortés J. Fungal Communities in Sediments Along a Depth Gradient in the Eastern Tropical Pacific. Front Microbiol 2020; 11:575207. [PMID: 33240232 PMCID: PMC7681244 DOI: 10.3389/fmicb.2020.575207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/21/2020] [Indexed: 01/04/2023] Open
Abstract
Deep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3,474 m) in two transects of about 1,500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63% of all fungal sequences: the yeast Metschnikowia (49.4%), Rhizophydium (6.9%), and Cladosporium (6.7%). We distinguished a cluster composed mainly by yeasts, and a second cluster by filamentous fungi, but we were unable to detect a strong effect of depth and the overlying water temperature, salinity, dissolved oxygen (DO), and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.
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Affiliation(s)
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Erik Cordes
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Jorge Cortés
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Ciencias del Mar y Limnología, Universidad de Costa Rica, San José, Costa Rica
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Li Q, Liu J, Gadd GM. Fungal bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals. Appl Microbiol Biotechnol 2020; 104:8999-9008. [PMID: 32940735 PMCID: PMC7567682 DOI: 10.1007/s00253-020-10854-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/11/2020] [Accepted: 08/23/2020] [Indexed: 11/27/2022]
Abstract
Abstract Much research has been carried out on the bacterial bioremediation of soil contaminated with petroleum hydrocarbons and toxic metals but much less is known about the potential of fungi in sites that are co-contaminated with both classes of pollutants. This article documents the roles of fungi in soil polluted with both petroleum hydrocarbons and toxic metals as well as the mechanisms involved in the biotransformation of such substances. Soil characteristics (e.g., structural components, pH, and temperature) and intracellular or excreted extracellular enzymes and metabolites are crucial factors which affect the efficiency of combined pollutant transformations. At present, bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals is mostly focused on the removal, detoxification, or degradation efficiency of single or composite pollutants of each type. Little research has been carried out on the metabolism of fungi in response to complex pollutant stress. To overcome current bottlenecks in understanding fungal bioremediation, the potential of new approaches, e.g., gradient diffusion film technology (DGT) and metabolomics, is also discussed. Key points • Fungi play important roles in soil co-contaminated with TPH and toxic metals. • Soil characteristics, enzymes, and metabolites are major factors in bioremediation. • DGT and metabolomics can be applied to overcome current bottlenecks.
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Affiliation(s)
- Qianwei Li
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China.
| | - Jicheng Liu
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
| | - Geoffrey Michael Gadd
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China.
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK.
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Sudová R, Kohout P, Rydlová J, Čtvrtlíková M, Suda J, Voříšková J, Kolaříková Z. Diverse fungal communities associated with the roots of isoetid plants are structured by host plant identity. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Jeong SY, Choi JY, Kim TG. Coordinated Metacommunity Assembly and Spatial Distribution of Multiple Microbial Kingdoms within a Lake. MICROBIAL ECOLOGY 2020; 79:801-814. [PMID: 31705158 DOI: 10.1007/s00248-019-01453-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Freshwater planktonic communities comprise a tremendous diversity of microorganisms. This study investigated the distribution patterns of microbial kingdoms (bacteria, fungi, protists, and microbial metazoans) within a lake ecosystem. Water samples were collected from 50 sites along the shoreline in a lake during an early eutrophication period, and MiSeq sequencing was performed with different marker genes. Metacommunity analyses revealed a bimodal occupancy-frequency distribution and a Clementsian gradient persisting throughout all microbial kingdoms, suggesting similar regional processes in all kingdoms. Variation partitioning revealed that environmental characteristics, macrophyte/macroinvertebrate composition, space coordinates, and distance-based Moran's eigenvector maps (dbMEM) together could explain up to 29% of the community variances in microbial kingdoms. Kingdom synchrony results showed strong couplings between kingdoms (R2 ≥ 0.31), except between Fungi and Metazoa (R2 = 0.09). Another variation partitioning revealed that microbial kingdoms could well explain their community variances up to 73%. Interestingly, the kingdom Protista was best synchronized with the other kingdoms. A correlation network showed that positive associations between kingdoms outnumbered the negative ones and that the kingdom Protista acted as a hub among kingdoms. Module analysis showed that network modules included multi-kingdom associations that were prevalent. Our findings suggest that protists coordinate community assembly and distribution of other kingdoms, and inter-kingdom interactions are a key determinant in shaping their community structures in a freshwater lake.
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Affiliation(s)
- So-Yeon Jeong
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea
| | - Jong-Yun Choi
- Division of Ecological Assessment, National Institute of Ecology, Seocheon, Choongnam, 33657, South Korea
| | - Tae Gwan Kim
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea.
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Composition and Diversity of Fungal Decomposers of Submerged Wood in Two Lakes in the Brazilian Amazon State of Pará. Int J Microbiol 2020. [DOI: 10.1155/2020/6582514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aquatic ecosystems in tropical forests have a high diversity of microorganisms, including fungi, which are important decomposers of submerged wood. Despite the importance of their role in decomposition, research concerning the diversity of freshwater fungi from Brazilian Amazonian environments is scarce. The aim of this work was to describe the composition and diversity of fungi present on submerged wood in two lakes of the Brazilian Amazon (State of Pará). Fragments of decaying wood (30 samples per lake) were collected from the Lakes Juá and Maicá. The wood samples were inspected for 6 months in the presence of fungal reproductive structures. Fungi observed in the wood were identified morphologically. Twenty-three taxa were identified in the Lake Juá (10 sexual and 13 asexual) and 26 taxa in the Lake Maicá (17 sexual, 9 asexual). ITS sequences were obtained for 14 taxa to aid in identification. In the Lakes Juá and Maicá, the diversity indices were H': 2.6514 and H': 2.8174, respectively. The Sørensen index of the fungal communities in the studied lakes was 0.3673. This study is the first to describe the fungal biodiversity of two important aquatic environments in Pará, Brazil.
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Góralska K, Błaszkowska J, Dzikowiec M. The occurrence of potentially pathogenic filamentous fungi in recreational surface water as a public health risk. JOURNAL OF WATER AND HEALTH 2020; 18:127-144. [PMID: 32300087 DOI: 10.2166/wh.2020.096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microfungi occurring in surface water may represent an important health risk. Recreational water reservoirs are a potential reservoir of pathogenic fungi. The aim of the study was to assess the diversity of mycobiota in selected artificial bathing reservoirs with regard to its biosafety for the human population. The studies were conducted during the summer of 2016 in three research seasons (June (I), July and August (II), and September (III)), taking into account the various periods of recreational activities. Filamentous fungi were isolated from water samples collected at five different ponds utilized for recreation. From 162 water samples, 149 fungal taxa of filamentous fungi were identified: 140 were classified to species level and only nine to genus level. Aspergillus fumigatus was the dominant species. The highest species richness (S) was noted in June, with 93 fungal taxa (Menhinick's index from 2.65 to 4.49). Additionally, in season I, the highest diversity of fungal species was revealed (Simpson's diversity index from 0.83 to 0.99). The average number of CFU/1 mL sample ranged between 0.4 and 4.6 depending on the time of sampling and ponds. Of all the isolated species, 128 were clinically relevant (11 from RG-2 and 117 from RG-1), highlighting the need to introduce seasonal mycological monitoring of such reservoirs.
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Affiliation(s)
- Katarzyna Góralska
- Department of Biology and Parasitology Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland E-mail:
| | - Joanna Błaszkowska
- Department of Biology and Parasitology Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland E-mail:
| | - Magdalena Dzikowiec
- Department of Biomedicine and Genetics Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
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Abstract
Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.
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Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Taube R, Fabian J, Van den Wyngaert S, Agha R, Baschien C, Gerphagnon M, Kagami M, Krüger A, Premke K. Potentials and limitations of quantification of fungi in freshwater environments based on PLFA profiles. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lin Y, Chen A, Luo S, Kuang X, Li R, Lepo JE, Gu JD, Zeng Q, Shao J. Cyanobacterial bloom mitigation by sanguinarine and its effects on aquatic microbial community structure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 253:497-506. [PMID: 31330342 DOI: 10.1016/j.envpol.2019.07.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/28/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Sanguinarine has strong inhibitory effects against the cyanobacterium Microcystis aeruginosa. However, previous studies were mainly limited to laboratory tests. The efficacy of sanguinarine for mitigation of cyanobacterial blooms under field conditions, and its effects on aquatic microbial community structure remain unknown. To elucidate these issues, we carried out in situ cyanobacterial bloom mitigation tests. Our results showed that sanguinarine decreased population densities of the harmful cyanobacteria Microcystis and Anabaena. The inhibitory effects of sanguinarine on these cyanobacteria lasted 17 days, after which the harmful cyanobacteria recovered and again became the dominant species. Concentrations of microcystins in the sanguinarine treatments were lower than those of the untreated control except during the early stage of the field test. The results of community DNA pyrosequencing showed that sanguinarine decreased the relative abundance of the prokaryotic microorganisms Cyanobacteria, Actinobacteria, Planctomycetes and eukaryotic microorganisms of Cryptophyta, but increased the abundance of the prokaryotic phylum Proteobacteria and eukaryotic microorganisms within Ciliophora and Choanozoa. The shifting of prokaryotic microbial community in water column was directly related to the toxicity of sanguinarine, whereas eukaryotic microbial community structure was influenced by factors other than direct toxicity. Harmful cyanobacteria mitigation efficacy and microbial ecological effects of sanguinarine presented in this study will inform the broad application of sanguinarine in cyanobacteria mitigation.
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Affiliation(s)
- Yiqing Lin
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China; Hunan Engineering & Technology Research Center for Irrigation Water Purification, Hunan Agricultural University, Changsha, 410128, PR China
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Si Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Xiaolin Kuang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Renhui Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Joe Eugene Lepo
- Department of Biology, Center for Environmental Diagnostics and Bioremediation, University of West Florida, Florida, 32514, USA
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, PR China
| | - Qingru Zeng
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Jihai Shao
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China; Hunan Engineering & Technology Research Center for Irrigation Water Purification, Hunan Agricultural University, Changsha, 410128, PR China.
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Inkinen J, Jayaprakash B, Siponen S, Hokajärvi AM, Pursiainen A, Ikonen J, Ryzhikov I, Täubel M, Kauppinen A, Paananen J, Miettinen IT, Torvinen E, Kolehmainen M, Pitkänen T. Active eukaryotes in drinking water distribution systems of ground and surface waterworks. MICROBIOME 2019; 7:99. [PMID: 31269979 PMCID: PMC6610866 DOI: 10.1186/s40168-019-0715-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/20/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Eukaryotes are ubiquitous in natural environments such as soil and freshwater. Little is known of their presence in drinking water distribution systems (DWDSs) or of the environmental conditions that affect their activity and survival. METHODS Eukaryotes were characterized by Illumina high-throughput sequencing targeting 18S rRNA gene (DNA) that estimates the total community and the 18S rRNA gene transcript (RNA) that is more representative of the active part of the community. DWDS cold water (N = 124), hot water (N = 40), and biofilm (N = 16) samples were collected from four cities in Finland. The sampled DWDSs were from two waterworks A-B with non-disinfected, recharged groundwater as source water and from three waterworks utilizing chlorinated water (two DWDSs of surface waterworks C-D and one of ground waterworks E). In each DWDS, samples were collected from three locations during four seasons of 1 year. RESULTS A beta-diversity analysis revealed that the main driver shaping the eukaryotic communities was the DWDS (A-E) (R = 0.73, P < 0.001, ANOSIM). The kingdoms Chloroplastida (green plants and algae), Metazoa (animals: rotifers, nematodes), Fungi (e.g., Cryptomycota), Alveolata (ciliates, dinoflagellates), and Stramenopiles (algae Ochrophyta) were well represented and active-judging based on the rRNA gene transcripts-depending on the surrounding conditions. The unchlorinated cold water of systems (A-B) contained a higher estimated total number of taxa (Chao1, average 380-480) than chlorinated cold water in systems C-E (Chao1 ≤ 210). Within each DWDS, unique eukaryotic communities were identified at different locations as was the case also for cold water, hot water, and biofilms. A season did not have a consistent impact on the eukaryotic community among DWDSs. CONCLUSIONS This study comprehensively characterized the eukaryotic community members within the DWDS of well-maintained ground and surface waterworks providing good quality water. The study gives an indication that each DWDS houses a unique eukaryotic community, mainly dependent on the raw water source and water treatment processes in place at the corresponding waterworks. In particular, disinfection as well as hot water temperature seemed to represent a strong selection pressure that controlled the number of active eukaryotic species.
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Affiliation(s)
- Jenni Inkinen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | | | - Sallamaari Siponen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Anna-Maria Hokajärvi
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Anna Pursiainen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Jenni Ikonen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Ivan Ryzhikov
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Martin Täubel
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Ari Kauppinen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Ilkka T. Miettinen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Eila Torvinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Mikko Kolehmainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Tarja Pitkänen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
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Rojas-Jimenez K, Rieck A, Wurzbacher C, Jürgens K, Labrenz M, Grossart HP. A Salinity Threshold Separating Fungal Communities in the Baltic Sea. Front Microbiol 2019; 10:680. [PMID: 30984159 PMCID: PMC6449873 DOI: 10.3389/fmicb.2019.00680] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/18/2019] [Indexed: 02/02/2023] Open
Abstract
Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world's largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm.
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Affiliation(s)
- Keilor Rojas-Jimenez
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Angelika Rieck
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Christian Wurzbacher
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Chair of Urban Water Systems Engineering, Technical University of Munich, Munich, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | | | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Lepère C, Domaizon I, Humbert JF, Jardillier L, Hugoni M, Debroas D. Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ 2019; 7:e6247. [PMID: 30809429 PMCID: PMC6387782 DOI: 10.7717/peerj.6247] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.
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Affiliation(s)
- Cécile Lepère
- Laboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Isabelle Domaizon
- CARRTEL, Université Savoie Mont Blanc, INRA, Thonon Les Bains, France
| | | | - Ludwig Jardillier
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Mylène Hugoni
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, Villeurbanne Cedex, France
| | - Didier Debroas
- Laboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
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Ortega-Arbulú AS, Pichler M, Vuillemin A, Orsi WD. Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon. Environ Microbiol 2018; 21:374-388. [PMID: 30411473 PMCID: PMC7379666 DOI: 10.1111/1462-2920.14469] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 11/30/2022]
Abstract
Fungi living in sediments (‘mycobenthos’) are hypothesized to play a role in the degradation of organic matter deposited at the land‐sea interface, but the environmental factors influencing the mycobenthos are poorly understood. We used mock community calibrated Illumina sequencing to show that the mycobenthos community structure in a coastal lagoon was significantly changed after exposure to a lignocellulose extract and subsequent development of benthic anoxia over a relatively short (10 h) incubation. Saprotrophic taxa dominated and were selected for under benthic anoxia, specifically Aquamyces (Chytridiomycota) and Orbilia (Ascomycota), implicating these genera as important benthic saprotrophs. Protein encoding genes involved in energy and biomass production from Fungi and the fungal‐analogue group Labyrinthulomycetes had the highest increase in expression with the added organic matter compared with all other groups, indicating that lignocellulose stimulates metabolic activity in the mycobenthos. Flavobacteria dominated the active bacterial community that grew rapidly with the lignocellulose extract and crashed sharply upon O2 depletion. Our findings indicate that the diversity, activity and trophic potential of the mycobenthos changes rapidly in response to organic matter and decreasing O2 concentrations, which together with heterotrophic Flavobacteria, undergo ‘boom and bust’ dynamics during lignocellulose degradation in estuarine ecosystems.
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Affiliation(s)
- Ana-Sofia Ortega-Arbulú
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Monica Pichler
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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48
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Nawaz A, Purahong W, Lehmann R, Herrmann M, Totsche KU, Küsel K, Wubet T, Buscot F. First insights into the living groundwater mycobiome of the terrestrial biogeosphere. WATER RESEARCH 2018; 145:50-61. [PMID: 30118976 DOI: 10.1016/j.watres.2018.07.067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/02/2018] [Accepted: 07/27/2018] [Indexed: 05/15/2023]
Abstract
Although fungi play important roles in biogeochemical cycling in aquatic ecosystems and have received a great deal of attention, much remains unknown about the living fractions of fungal communities in aquifers of the terrestrial subsurface in terms of diversity, community dynamics, functional roles, the impact of environmental factors and presence of fungal pathogens. Here we address this gap in knowledge by using RNA-based high throughput pair-end illumina sequencing analysis of fungal internal transcribed spacer (ITS) gene markers, to target the living fractions of groundwater fungal communities from fractured alternating carbonate-/siliciclastic-rock aquifers of the Hainich Critical Zone Exploratory. The probed levels of the hillslope multi-storey aquifer system differ primarily in their oxygen and nitrogen content due to their different connections to the surface. We discovered highly diverse living fungal communities (384 Operational Taxonomic Units, OTUs) with different taxonomic affiliations and ecological functions. The observed fungal communities primarily belonged to three phyla: Ascomycota, Basidiomycota and Chytridiomycota. Perceived dynamics in the composition of living fungal communities were significantly shaped by the concentration of ammonium in the moderately agriculturally impacted aquifer system. Apart from fungal saprotrophs, we also detected living plant and animal pathogens for the first time in this aquifer system. This work also demonstrates that the RNA-based high throughput pair-end illumina sequencing method can be used in future for water quality monitoring in terms of living fungal load and subsequent risk assessments. In general, this study contributes towards the growing knowledge of aquatic fungi in terrestrial subsurface biogeosphere.
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Affiliation(s)
- Ali Nawaz
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology, Halle (Saale), Germany; Helmholtz Centre for Environmental Research - UFZ, Department of Community Ecology, Halle (Saale), Germany; Department of Biology, University of Leipzig, Leipzig, Germany.
| | - Witoon Purahong
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology, Halle (Saale), Germany
| | - Robert Lehmann
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Martina Herrmann
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Kai Uwe Totsche
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Tesfaye Wubet
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology, Halle (Saale), Germany; Helmholtz Centre for Environmental Research - UFZ, Department of Community Ecology, Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - François Buscot
- Helmholtz Centre for Environmental Research - UFZ, Department of Soil Ecology, Halle (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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49
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Kirstein IV, Wichels A, Krohne G, Gerdts G. Mature biofilm communities on synthetic polymers in seawater - Specific or general? MARINE ENVIRONMENTAL RESEARCH 2018; 142:147-154. [PMID: 30337052 DOI: 10.1016/j.marenvres.2018.09.028] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/28/2018] [Accepted: 09/30/2018] [Indexed: 05/19/2023]
Abstract
To understand the ecological impacts of the "Plastisphere", those microbes need to be identified that preferentially colonize and interact with synthetic polymer surfaces, as opposed to general surface colonizers. It was hypothesized that the microbial biofilm composition varies distinctly between different substrates. A long-term incubation experiment was conducted (15month) with nine different synthetic polymer films as substrate as well as glass using a natural seawater flow-through system. To identify colonizing microorganisms, 16S and 18SrRNA gene tag sequencing was performed. The microbial biofilms of these diverse artificial surfaces were visualized via scanning electron microscopy. Biofilm communities attached to synthetic polymers are distinct from glass associated biofilms; apparently a more general marine biofilm core community serves as shared core among all synthetic polymers rather than a specific synthetic polymer community. Nevertheless, characteristic and discriminatory taxa of significantly different biofilm communities were identified, indicating their specificity to a given substrate.
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Affiliation(s)
- Inga V Kirstein
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany.
| | - Antje Wichels
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Georg Krohne
- University of Würzburg, Biocenter, Imaging Core Facility, Würzburg, Germany
| | - Gunnar Gerdts
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany
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50
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Kolmakova OV, Gladyshev MI, Fonvielle JA, Ganzert L, Hornick T, Grossart HP. Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling. Environ Microbiol 2018; 21:34-49. [PMID: 30246449 DOI: 10.1111/1462-2920.14418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 11/27/2022]
Abstract
Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh 13 C-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.
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Affiliation(s)
- Olesya V Kolmakova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia.,Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michail I Gladyshev
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Jérémy André Fonvielle
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Lars Ganzert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,GFZ German Research Centre for Geosciencess, Section 5.3 Geomicrobiology, Potsdam, Germany.,Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, Germany
| | - Thomas Hornick
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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