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Bolhuis H, Grego M. Cryopreservation and recovery of a complex hypersaline microbial mat community. Cryobiology 2024; 114:104859. [PMID: 38336089 DOI: 10.1016/j.cryobiol.2024.104859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/15/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Cryopreservation of microorganisms is an essential tool in industrial- and food applications where conservation of microbial activity and critical beneficial traits need to be guaranteed to provide a consistent product or production process. This often refers to simple, single species or low diversity assemblages in liquid cultures that can easily be revived and regrown to perform the desired process. Cryopreservation is also of essence for scientific experimentation where many environmental samples are taken in remote sampling sites and at high costs. Biobanking, or the long term preservation and potential revival of complex, structured samples come with an additional challenge related to maintaining the structure upon revival. Here we look at cryopreserving and reviving a complex photosynthesis driven microbial mat from a hypersaline ecosystem. Amplicon sequencing of the 16S and 18S ribosomal RNA gene was used to determine the community composition of bacteria and eukaryotes respectively. The tests included the use of different cryopreservative agents and different times of cryopreservation at -150 °C. Upon revival, the cryopreservatives cannot be separated from the preserved samples without disturbing the community structure, while carryover of these compounds may influence reconstitution of the communities. Indeed, although both glycerol and Me2SO are good cryopreservatives of microbial assemblages, carryover of these compounds had a profound negative effect on the reestablishment of a functional microbial mat. Best cryopreservation and reconstitution results were obtained in the absence of a cryopreservative agent or when methanol was used.
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Affiliation(s)
- Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Hoorn, the Netherlands.
| | - Michele Grego
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Den Hoorn, the Netherlands.
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Yang Y, Rivera Pérez CA, Richter-Heitmann T, Nimzyk R, Friedrich MW, Reich M. Effects of oxygen availability on mycobenthic communities of marine coastal sediments. Sci Rep 2023; 13:15218. [PMID: 37709848 PMCID: PMC10502103 DOI: 10.1038/s41598-023-42329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023] Open
Abstract
In coastal marine sediments, oxygen availability varies greatly, and anoxic conditions can develop quickly over low spatial resolution. Although benthic fungi are important players in the marine carbon cycle, little is known about their adaptation to fluctuating availability of oxygen as terminal electron acceptor. Here, we study which part of a mycobenthic community from oxic coastal sediments can thrive under temporarily anoxic conditions. We test whether phylogeny or certain fungal traits promote plasticity in respect to changes in oxygen availability. Therefore, we incubated mycobenthos under oxic and anoxic conditions, performed ITS2 Illumina tag-sequencing and an additional meta-analysis on a literature survey. Half of all OTUs showed a plasticity towards changing oxygen availability and exhibited different strategies towards anoxic conditions, with rapid response within hours or a delayed one after several days. The strategy of dimorphism and facultative yeasts were significantly linked to OTU occurrence in anoxic conditions, while phylogeny and other traits had less effect. Our results suggest that different fungal niches are formed over the duration of prolonged anoxic conditions. The taxon-specific proliferation seems to be regulated by the fine-tuning of various traits and factors. It is essential to take these results into account when conducting conceptual work on the functionality of the marine benthos.
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Affiliation(s)
- Yanyan Yang
- Molecular Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Carmen Alicia Rivera Pérez
- Molecular Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
- Biodiversity and Evolution of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- Microbial Ecophysiology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marlis Reich
- Molecular Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany.
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Hoque E, Fritscher J. Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment? Crit Rev Microbiol 2023:1-24. [PMID: 37452612 DOI: 10.1080/1040841x.2023.2224425] [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: 12/31/2021] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 07/18/2023]
Abstract
Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.
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Affiliation(s)
- Enamul Hoque
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Fritscher
- Department of Biotechnology, University of Science and Technology, Foy's Lake, Chittagong, Bangladesh
- International Virtual Institute for Advanced Science and Technology (IVAST), Section Microbial Technology, Munich, Germany
- Department of Environmental Science, Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Neuherberg, Germany
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Jiang JP, Liu X, Liao YF, Shan J, Zhu YP, Liu CH. Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments. Front Microbiol 2023; 14:1216714. [PMID: 37455735 PMCID: PMC10339353 DOI: 10.3389/fmicb.2023.1216714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Aspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited. Methods Here, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform. Results and Discussion The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years.
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Affiliation(s)
- Jun-Peng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Yi-Fan Liao
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yu-Ping Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
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Rodrigues-Filho JL, Macêdo RL, Sarmento H, Pimenta VRA, Alonso C, Teixeira CR, Pagliosa PR, Netto SA, Santos NCL, Daura-Jorge FG, Rocha O, Horta P, Branco JO, Sartor R, Muller J, Cionek VM. From ecological functions to ecosystem services: linking coastal lagoons biodiversity with human well-being. HYDROBIOLOGIA 2023; 850:2611-2653. [PMID: 37323646 PMCID: PMC10000397 DOI: 10.1007/s10750-023-05171-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 06/17/2023]
Abstract
In this review we highlight the relevance of biodiversity that inhabit coastal lagoons, emphasizing how species functions foster processes and services associated with this ecosystem. We identified 26 ecosystem services underpinned by ecological functions performed by bacteria and other microbial organisms, zooplankton, polychaetae worms, mollusks, macro-crustaceans, fishes, birds, and aquatic mammals. These groups present high functional redundancy but perform complementary functions that result in distinct ecosystem processes. Because coastal lagoons are located in the interface between freshwater, marine and terrestrial ecosystems, the ecosystem services provided by the biodiversity surpass the lagoon itself and benefit society in a wider spatial and historical context. The species loss in coastal lagoons due to multiple human-driven impacts affects the ecosystem functioning, influencing negatively the provision of all categories of services (i.e., supporting, regulating, provisioning and cultural). Because animals' assemblages have unequal spatial and temporal distribution in coastal lagoons, it is necessary to adopt ecosystem-level management plans to protect habitat heterogeneity and its biodiversity, ensuring the provision of services for human well-being to multi-actors in the coastal zone.
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Affiliation(s)
- Jorge L. Rodrigues-Filho
- Laboratório de Ecologia Aplicada e Conservação, Departamento de Engenharia de Pesca e Ciências Biológicas, Universidade Do Estado de Santa Catarina, Laguna, SC Brazil
- Programa de Pós-Graduação em Planejamento Territorial e Desenvolvimento Socioambiental (PPGPLAN)/UDESC/FAED, Universidade do Estado de Santa Catarina, Florianópolis, SC Brazil
| | - Rafael L. Macêdo
- Graduate Program in Ecology and Natural Resources, and Department of Ecology and Evolutionary Biology, Federal University of São Carlos - UFSCar, São Carlos, Brazil
| | - Hugo Sarmento
- Graduate Program in Ecology and Natural Resources, and Department of Ecology and Evolutionary Biology, Federal University of São Carlos - UFSCar, São Carlos, Brazil
- Graduate Program in Ecology of Inland Water Ecosystems (PEA), State University of Maringá (UEM), Centre of Research in Limnology, Ichthyology and Aquaculture (Nupélia), Maringá, Paraná, Brazil
| | - Victor R. A. Pimenta
- Laboratório de Ecologia Aplicada e Conservação, Departamento de Engenharia de Pesca e Ciências Biológicas, Universidade Do Estado de Santa Catarina, Laguna, SC Brazil
- Graduate Program in Ecology and Natural Resources, and Department of Ecology and Evolutionary Biology, Federal University of São Carlos - UFSCar, São Carlos, Brazil
| | - Cecilia Alonso
- Microbial Ecology of Aquatic Systems Research Group, Centro Universitario Regional del Este, Universidad de la República, Rocha, Uruguay
| | - Clarissa R. Teixeira
- Laboratório de Mamíferos Aquáticos (LAMAQ), Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Whale Habitat, Ecology & Telemetry Laboratory (WHET), Oregon State University (OSU), Newport, OR USA
| | - Paulo R. Pagliosa
- Laboratório de Biodiversidade Costeira, Coordenadoria Especial de Oceanografia, Universidade Federal de Santa Catarina, Florianópolis, SC Brazil
| | - Sérgio A. Netto
- Universidade do Sul de Santa Catarina, UNISUL, Tubarão, Santa Catarina, Brazil
| | - Natália C. L. Santos
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ Brazil
| | - Fábio G. Daura-Jorge
- Laboratório de Mamíferos Aquáticos (LAMAQ), Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Programa de Pós-Graduação em Ecologia (POSECO), Universidade Federal de Santa Catarina (UFSC), Trindade, Florianópolis, Brazil
| | - Odete Rocha
- Graduate Program in Ecology and Natural Resources, and Department of Ecology and Evolutionary Biology, Federal University of São Carlos - UFSCar, São Carlos, Brazil
| | - Paulo Horta
- Laboratório de Ficologia, Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, SC Brazil
| | - Joaquim O. Branco
- Graduate Program in Ecology and Natural Resources, and Department of Ecology and Evolutionary Biology, Federal University of São Carlos - UFSCar, São Carlos, Brazil
- Programa de Pós-Graduação em Ciência e Tecnologia Ambiental, Universidade do Vale do Itajaí, Itajaí, SC Brazil
| | - Rodrigo Sartor
- Universidade do Sul de Santa Catarina, UNISUL, Tubarão, Santa Catarina, Brazil
| | - Jean Muller
- Universidade do Sul de Santa Catarina, UNISUL, Tubarão, Santa Catarina, Brazil
| | - Vivian M. Cionek
- Programa de Pós-Graduação em Ciência e Tecnologia Ambiental, Universidade do Vale do Itajaí, Itajaí, SC Brazil
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Vuillemin A. Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia. Front Microbiol 2023; 14:1101902. [PMID: 36846760 PMCID: PMC9950273 DOI: 10.3389/fmicb.2023.1101902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.
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Liu S, Trevathan-Tackett SM, Jiang Z, Cui L, Wu Y, Zhang X, Li J, Luo H, Huang X. Nutrient loading decreases blue carbon by mediating fungi activities within seagrass meadows. ENVIRONMENTAL RESEARCH 2022; 212:113280. [PMID: 35430277 DOI: 10.1016/j.envres.2022.113280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Coastal pollution, including nutrient loading, can negatively impact seagrass health and cover and may consequently alter soil organic carbon (SOC) accumulation and preservation. Key to understanding how eutrophication impacts SOC cycling in seagrass ecosystems is how nutrient loading changes the sources of carbon being deposited and how these changes in resources, both nutrients and carbon availability, influence soil microbiota community and activity. Currently, the direction and magnitude of nutrient loading impacts on seagrass SOC dynamics are poorly understood at a meadow scale, limiting our ability to reveal the driving mechanisms of SOC remineralisation. The purpose of this study was to assess the response of surface SOC and soil microbiomes to nutrient loading within tropical seagrass meadows. To achieve this, we quantified both total SOC and recalcitrant soil organic carbon (RSOC) concentrations and sources, in addition to the composition of bacterial and fungal communities and soil extracellular enzyme activities. We found that nutrient loading elevated SOC and RSOC content, mainly facilitated by enhanced algal growth. There was no nutrient effect on the soil prokaryotic communities, however, saprotrophic fungi groups (i.e. Trapeliales, Sordaridales, Saccharomycetales and Polyporales) and fungal activities were elevated under high nutrient conditions, including extracellular enzyme activities linked to seagrass-based cellulose and lignin decomposition. This relative increase in RSOC transformation may decrease the relative contribution of seagrass carbon to RSOC pools. Additionally, significantly different fungal communities were observed between adjacent T. hemprichii and E. acoroides areas, which coincided with elevated RSOC-decomposing enzyme activity in T. hemprichii meadows, even though the mixed seagrass meadow received allochthonous SOC and RSOC from the same sources. These results suggest that nutrient loading stimulated fungal activity and community shifts specific to the local seagrass species, thereby causing fine-scale (within-meadow) variability in SOC cycling in response to nutrient loading. This study provides evidence that fungal composition and activity, mediated by human activities (e.g. nutrient loading), can be an important influence on seagrass blue carbon accumulation and remineralisation.
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Affiliation(s)
- Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Stacey M Trevathan-Tackett
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, Victoria, 3125, Australia
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Lijun Cui
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jinlong Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongxue Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya, 572100, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Zain Ul Arifeen M, Ma Y, Wu T, Chu C, Liu X, Jiang J, Li D, Xue YR, Liu CH. Anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungi isolated from anaerobic coal-associated sediments at 2.5 km below the seafloor. CHEMOSPHERE 2022; 303:135062. [PMID: 35618067 DOI: 10.1016/j.chemosphere.2022.135062] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Fungi represent the dominant eukaryotic group in the deep biosphere and well-populated in the anaerobic coal-bearing sediments up to ∼2.5 km below seafloor (kmbsf). But whether fungi are able to degrade and utilize coal to sustain growth in the anaerobic sub-seafloor environment remains unknown. Based on biodegradation investigation, we found that fungi isolated from sub-seafloor sediments at depths of ∼1.3-∼2.5 kmbsf showed a broad range of polycyclic aromatic hydrocarbons (PAHs) anaerobic degradation rates (3-25%). Among them, the white-rot fungus Schizophyllium commune 20R-7-F01 exhibited the highest degradation, 25%, 18% and 13%, of phenanthrene (Phe), pyrene (Pyr) and benzo[a]pyrene (BaP); respectively, after 10 days of anaerobic incubation. Phe was utilized well and about 40.4% was degraded by the fungus, after 20 days of anaerobic incubation. Moreover, the ability of fungi to degrade PAHs was positively correlated with the anaerobic growth of fungi, indicating that fungi can use PAHs as a sole carbon source under anoxic conditions. In addition, fungal degradation of PAHs was found to be related to the activity of carboxylases, but little or nothing to do with the activity of lignin modifying enzymes such as laccase (Lac), manganese peroxidase (MnP) and lignin peroxidase (LiP). These results suggest that sub-seafloor fungi possess a special mechanism to degrade and utilize PAHs as a carbon and energy source under anaerobic conditions. Furthermore, fungi living in sub-seafloor sediments may not only play an important role in carbon cycle in the anaerobic environments of the deep biosphere, but also be able to persist in deep sediment below seafloor for millions of years by using PAHs or related compounds as carbon and energy source. This anaerobic biodegradation ability could make these fungi suitable candidates for bioremediation of toxic pollutants such as PAHs from anoxic environments.
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Affiliation(s)
- Muhammad Zain Ul Arifeen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yunan Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tianshang Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Junpeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dongxu Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ya-Rong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
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Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf. Appl Environ Microbiol 2022; 88:e0021622. [PMID: 35404072 PMCID: PMC9088280 DOI: 10.1128/aem.00216-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using 13C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. 13C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated 13C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated 13C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated 13C-bicarbonate under sediment anoxic conditions also assimilated 13C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches. IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using 13C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.
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10
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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: 15] [Impact Index Per Article: 7.5] [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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11
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Chen Y, Zheng M, Qiu Y, Wang H, Zhang H, Tao Q, Luo H, Zhang Z. Organic Matter and Total Nitrogen Lead to Different Microbial Community Structure in Sediments Between Lagoon and Surrounding Areas by Regulating Xenococcus Abundance. Front Microbiol 2022; 13:859921. [PMID: 35531298 PMCID: PMC9069056 DOI: 10.3389/fmicb.2022.859921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Coastal lagoon is an important productive ecosystem on the Earth. In this study, we compared microbial community in the sediments between lagoon and surrounding areas, and explored mechanism for the variation of microbial community. As a result, the sediment of surrounding area showed significantly higher organic matter and total nitrogen than that of the lagoon. The linear regression analysis revealed that organic matter and total nitrogen are positively correlated with Xenococcus. Bacterial and fungal PCoA1 showed significantly positive relationships with the relative abundance of Xenococcus, indicating that Xenococcus affects the bacterial and fungal community in the sediments of both the lagoon and surrounding area. ANOSIM analysis demonstrated that there were significant differences in bacterial and fungal community structure in the sediments between the lagoon and surrounding areas. Therefore, organic matter and total nitrogen affect the microbial community structure in the sediments of lagoon and surrounding areas by regulating the abundance of Xenococcus.
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Affiliation(s)
- Yonggan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, China
| | - Minjing Zheng
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, China
| | - Yue Qiu
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Hong Wang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Haonan Zhang
- Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, China
| | - Qiongren Tao
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Hongwei Luo
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
| | - Zhenhua Zhang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, China
- Key Laboratory of Biodiversity and Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, China
- *Correspondence: Zhenhua Zhang,
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12
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6523362. [DOI: 10.1093/femsec/fiac009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/14/2022] Open
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13
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Labile organic carbon fractions drive soil microbial communities after long-term fertilization. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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14
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Perkins AK, Rose AL, Grossart HP, Rojas-Jimenez K, Barroso Prescott SK, Oakes JM. Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata. Front Microbiol 2021; 12:726138. [PMID: 34733248 PMCID: PMC8558676 DOI: 10.3389/fmicb.2021.726138] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.
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Affiliation(s)
- Anita K. Perkins
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Andrew L. Rose
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, Berlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Selva K. Barroso Prescott
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | - Joanne M. Oakes
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
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15
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Zain Ul Arifeen M, Ma ZJ, Wu S, Liu JZ, Xue YR, Liu CH. Effect of oxygen concentrations and branched-chain amino acids on the growth and development of sub-seafloor fungus, Schizophyllum commune 20R-7-F01. Environ Microbiol 2021; 23:6940-6952. [PMID: 34431210 DOI: 10.1111/1462-2920.15738] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 11/28/2022]
Abstract
Fungi have been reported to be the dominant eukaryotic group in anoxic sub-seafloor sediments, but how fungi subsist in the anoxic sub-marine sedimental environment is rarely understood. Our previous study demonstrated that the fungus, Schizophyllum commune 20R-7-F01 isolated from a ~2 km sediment below the seafloor, can grow and produce primordia in the complete absence of oxygen with enhanced production of branched-chain amino acids (BCAAs), but the primordia cannot be developed into fruit bodies without oxygen. Here, we present the individual and synergistic effects of oxygen and BCAAs on the fruit-body development of this strain. It was found that the fungus required a minimum oxygen concentration of 0.5% pO2 to generate primordia and 1% pO2 to convert primordia into mature fruit body. However, if BCAAs (20 mM) were added to the medium, the primordium could be developed into fruit body at a lower oxygen concentration up to 0.5% pO2 where genes fst4 and c2h2 playing an important role in compensating oxygen deficiency. Moreover, under hypoxic conditions, the fungus showed an increase in mitochondrial number and initiation of auto-phagocytosis. These findings suggest that the fruit-body formation of S. commune may have multiple mechanisms, including energy and amino acid metabolism in response to oxygen concentrations.
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Affiliation(s)
- Muhammad Zain Ul Arifeen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhi-Jun Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Si Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jun-Zhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ya-Rong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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16
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Abstract
Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years.
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Coskun ÖK, Vuillemin A, Schubotz F, Klein F, Sichel SE, Eisenreich W, Orsi WD. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. ISME JOURNAL 2021; 16:257-271. [PMID: 34312482 PMCID: PMC8692406 DOI: 10.1038/s41396-021-01066-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Frieder Klein
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Susanna E Sichel
- Departamento de Geologia e Geofísica/LAGEMAR-Universidade Federal Fluminense-Brazil, Niterói, RJ, Brazil
| | - Wolfgang Eisenreich
- Department of Chemistry, Bavarian NMR Center-Structural Membrane Biochemistry, Technische Universität München, Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany. .,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany.
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18
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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19
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Vuillemin A, Kerrigan Z, D'Hondt S, Orsi WD. Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay. FEMS Microbiol Ecol 2020; 96:fiaa223. [PMID: 33150943 PMCID: PMC7688785 DOI: 10.1093/femsec/fiaa223] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/03/2020] [Indexed: 01/31/2023] Open
Abstract
Chloroflexi are widespread in subsurface environments, and recent studies indicate that they represent a major fraction of the communities in subseafloor sediment. Here, we compare the abundance, diversity, metabolic potential and gene expression of Chloroflexi from three abyssal sediment cores from the western North Atlantic Gyre (water depth >5400 m) covering up to 15 million years of sediment deposition, where Chloroflexi were found to represent major components of the community at all sites. Chloroflexi communities die off in oxic red clay over 10-15 million years, and gene expression was below detection. In contrast, Chloroflexi abundance and gene expression at the anoxic abyssal clay site increase below the seafloor and peak in 2-3 million-year-old sediment, indicating a comparably higher activity. Metatranscriptomes from the anoxic site reveal increased expression of Chloroflexi genes involved in cell wall biogenesis, protein turnover, inorganic ion transport, defense mechanisms and prophages. Phylogenetic analysis shows that these Chloroflexi are closely related to homoacetogenic subseafloor clades and actively transcribe genes involved in sugar fermentations, gluconeogenesis and Wood-Ljungdahl pathway in the subseafloor. Concomitant expression of cell division genes indicates that these putative homoacetogenic Chloroflexi are actively growing in these million-year-old anoxic abyssal sediments.
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Affiliation(s)
- Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany
| | - Zak Kerrigan
- Graduate School of Oceanography, University of Rhode Island, Narragansett Bay Campus, 215 South Ferry Road, Narragansett, RI 02882, USA
| | - Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett Bay Campus, 215 South Ferry Road, Narragansett, RI 02882, USA
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, Germany
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20
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Xiao R, Guo Y, Zhang M, Pan W, Wang JJ. Stronger network connectivity with lower diversity of soil fungal community was presented in coastal marshes after sixteen years of freshwater restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140623. [PMID: 32693270 DOI: 10.1016/j.scitotenv.2020.140623] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Freshwater input for salt marsh restoration in the Yellow River Delta induced Phragmites australis expansion and thus may cause shifts of soil fungi from halophilic to desalination-adapted species for increased litter decomposition. In this study, soil fungal communities of restored and natural salt marshes were determined to reveal further details of shift in soil fungal community and its probable prediction for salt marsh restoration. Our results showed a stronger network within Ascomycota (e.g. Sordariales, Aspergillus, Hypocreales and Cladosporium herbarum) in restored marshes, but with a lower diversity of halophilic taxa (e.g. Chytridiomycota and Nematoda) in comparison with natural salt marshes. Contrarily, the occurrence of Chytridiomycota, Ichthyosporea and Discicristoidea in the soil fungal networks of the natural salt marsh emphasized the importance of salt tolerant species at the land-sea transition zone. The Sordariales was dominant and had a strong correlation with other fungal species and aggregate associated soil organic carbon (SOC), which probably contributed to SOC accumulation in restored marshes. But the reduced halophilic species specific to salt marsh elucidated that the formation of monospecific stands of P. australis along with the freshwater input induced desalination to the saline habitats changed the native patterns of vegetation and soil organisms. As the buffer between terrestrial and marine systems, a single habitat type such as dense monocultures of P. australis must be avoided and diverse saltmarsh habitats across a salinity gradient should be reserved. In this way, the diversity and specificity of coastal halophytes and related microorganisms could be maintained and thus might confer benefits in balancing various functions of the salt marsh ecosystem and preserving the system's elasticity and resistance to stress.
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Affiliation(s)
- Rong Xiao
- College of Environment and Resources, Fuzhou University, Fuzhou 350108, China.
| | - Yutong Guo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Mingxiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Wenbin Pan
- College of Environment and Resources, Fuzhou University, Fuzhou 350108, China
| | - Jian Jim Wang
- School of Plant, Environmental and Soil Sciences, Louisiana State Univ. Agricultural Center, Baton Rouge, LA 70803, USA
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21
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Vargas-Gastélum L, Riquelme M. The Mycobiota of the Deep Sea: What Omics Can Offer. Life (Basel) 2020; 10:E292. [PMID: 33228036 PMCID: PMC7699357 DOI: 10.3390/life10110292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/14/2020] [Accepted: 11/18/2020] [Indexed: 01/23/2023] Open
Abstract
The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.
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Affiliation(s)
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ctra.Ensenada-Tijuana No. 3918, Ensenada 22860, Baja California, Mexico;
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22
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Abstract
How microbial metabolism is translated into cellular reproduction under energy-limited settings below the seafloor over long timescales is poorly understood. Here, we show that microbial abundance increases an order of magnitude over a 5 million-year-long sequence in anoxic subseafloor clay of the abyssal North Atlantic Ocean. This increase in biomass correlated with an increased number of transcribed protein-encoding genes that included those involved in cytokinesis, demonstrating that active microbial reproduction outpaces cell death in these ancient sediments. Metagenomes, metatranscriptomes, and 16S rRNA gene sequencing all show that the actively reproducing community was dominated by the candidate phylum "Candidatus Atribacteria," which exhibited patterns of gene expression consistent with fermentative, and potentially acetogenic, metabolism. "Ca. Atribacteria" dominated throughout the 8 million-year-old cored sequence, despite the detection limit for gene expression being reached in 5 million-year-old sediments. The subseafloor reproducing "Ca. Atribacteria" also expressed genes encoding a bacterial microcompartment that has potential to assist in secondary fermentation by recycling aldehydes and, thereby, harness additional power to reduce ferredoxin and NAD+ Expression of genes encoding the Rnf complex for generation of chemiosmotic ATP synthesis were also detected from the subseafloor "Ca Atribacteria," as well as the Wood-Ljungdahl pathway that could potentially have an anabolic or catabolic function. The correlation of this metabolism with cytokinesis gene expression and a net increase in biomass over the million-year-old sampled interval indicates that the "Ca Atribacteria" can perform the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in millions-of-years-old anoxic sediments.IMPORTANCE The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum "Candidatus Atribacteria" dominated a deep-sea subseafloor ecosystem, where it exhibited increased transcription of genes associated with acetogenic fermentation and reproduction in million-year-old sediment. We attribute its improved fitness after burial in the seabed to its capabilities to derive energy from increasingly oxidized metabolites via a bacterial microcompartment and utilize a potentially reversible Wood-Ljungdahl pathway to help meet anabolic and catabolic requirements for growth. Our findings show that "Ca Atribacteria" can perform all the necessary catabolic and anabolic functions necessary for cellular reproduction, even under energy limitation in anoxic sediments that are millions of years old.
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Anaerobic metabolism of Foraminifera thriving below the seafloor. ISME JOURNAL 2020; 14:2580-2594. [PMID: 32641728 PMCID: PMC7490399 DOI: 10.1038/s41396-020-0708-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/09/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. Relative Foraminifera gene expression in anoxic sediment increased an order of magnitude, which was confirmed in a 10-day incubation experiment where the development of anoxia coincided with a 20–40-fold increase in the relative abundance of Foraminifera protein encoding transcripts, attributed primarily to those involved in protein synthesis, intracellular protein trafficking, and modification of the cytoskeleton. This indicated that many Foraminifera were not only surviving but thriving, under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, fumarate reduction, and potentially dissimilatory nitrate reduction. Moreover, the gene expression data indicate that under anoxia Foraminifera use the phosphogen creatine phosphate as an ATP store, allowing reserves of high-energy phosphate pool to be maintained for sudden demands of increased energy during anaerobic metabolism. This was co-expressed alongside genes involved in phagocytosis and clathrin-mediated endocytosis (CME). Foraminifera may use CME to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These anaerobic metabolic mechanisms help to explain the ecological success of Foraminifera documented in the fossil record since the Cambrian period more than 500 million years ago.
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24
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Lacerda ALDF, Proietti MC, Secchi ER, Taylor JD. Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula. Mol Ecol 2020; 29:1903-1918. [DOI: 10.1111/mec.15444] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ana L. d. F. Lacerda
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Maíra C. Proietti
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Eduardo R. Secchi
- Instituto de Oceanografia Universidade Federal do Rio Grande-FURG Rio Grande Brazil
| | - Joe D. Taylor
- School of Science, Engineering and Environment University of Salford Manchester UK
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Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments. Nat Microbiol 2019; 5:248-255. [PMID: 31873205 DOI: 10.1038/s41564-019-0630-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023]
Abstract
The genomes of the Asgard superphylum of Archaea hold clues pertaining to the nature of the host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Representatives of the Asgard candidate phylum Candidatus Lokiarchaeota (Lokiarchaeon) have the capacity for acetogenesis and fermentation5-7, but how their metabolic activity responds to environmental conditions is poorly understood. Here, we show that in anoxic Namibian shelf sediments, Lokiarchaeon gene expression levels are higher than those of bacterial phyla and increase with depth below the seafloor. Lokiarchaeon gene expression was significantly different across a hypoxic-sulfidic redox gradient, whereby genes involved in growth, fermentation and H2-dependent carbon fixation had the highest expression under the most reducing (sulfidic) conditions. Quantitative stable isotope probing revealed that anaerobic utilization of CO2 and diatomaceous extracellular polymeric substances by Lokiarchaeon was higher than the bacterial average, consistent with higher expression of Lokiarchaeon genes, including those involved in transport and fermentation of sugars and amino acids. The quantitative stable isotope probing and gene expression data demonstrate homoacetogenic activity of Candidatus Lokiarchaeota, whereby fermentative H2 production from organic substrates is coupled with the Wood-Ljungdahl carbon fixation pathway8. The high energetic efficiency provided by homoacetogenesis8 helps to explain the elevated metabolic activity of Lokiarchaeon in this anoxic, energy-limited setting.
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Vuillemin A, Wankel SD, Coskun ÖK, Magritsch T, Vargas S, Estes ER, Spivack AJ, Smith DC, Pockalny R, Murray RW, D’Hondt S, Orsi WD. Archaea dominate oxic subseafloor communities over multimillion-year time scales. SCIENCE ADVANCES 2019; 5:eaaw4108. [PMID: 31223656 PMCID: PMC6584578 DOI: 10.1126/sciadv.aaw4108] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/10/2019] [Indexed: 05/31/2023]
Abstract
Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.
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Affiliation(s)
- Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Scott D. Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ömer K. Coskun
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Tobias Magritsch
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Emily R. Estes
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
| | - Arthur J. Spivack
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - David C. Smith
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Robert Pockalny
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Richard W. Murray
- Department of Earth and Environment, Boston University, Boston, MA 02215, USA
| | - Steven D’Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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27
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Quantifying population-specific growth in benthic bacterial communities under low oxygen using H 218O. ISME JOURNAL 2019; 13:1546-1559. [PMID: 30783213 PMCID: PMC6776007 DOI: 10.1038/s41396-019-0373-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 01/09/2023]
Abstract
The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.
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Hassett BT, Borrego EJ, Vonnahme TR, Rämä T, Kolomiets MV, Gradinger R. Arctic marine fungi: biomass, functional genes, and putative ecological roles. ISME JOURNAL 2019; 13:1484-1496. [PMID: 30745572 DOI: 10.1038/s41396-019-0368-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/06/2019] [Accepted: 01/22/2019] [Indexed: 01/07/2023]
Abstract
Recent molecular evidence suggests a global distribution of marine fungi; however, the ecological relevance and corresponding biological contributions of fungi to marine ecosystems remains largely unknown. We assessed fungal biomass from the open Arctic Ocean by applying novel biomass conversion factors from cultured isolates to environmental sterol and CARD-FISH data. We found an average of 16.54 nmol m-3 of ergosterol in sea ice and seawater, which corresponds to 1.74 mg C m-3 (444.56 mg C m-2 in seawater). Using Chytridiomycota-specific probes, we observed free-living and particulate-attached cells that averaged 34.07 µg C m-3 in sea ice and seawater (11.66 mg C m-2 in seawater). Summed CARD-FISH and ergosterol values approximate 1.77 mg C m-3 in sea ice and seawater (456.23 mg C m-2 in seawater), which is similar to biomass estimates of other marine taxa generally considered integral to marine food webs and ecosystem processes. Using the GeoChip microarray, we detected evidence for fungal viruses within the Partitiviridae in sediment, as well as fungal genes involved in the degradation of biomass and the assimilation of nitrate. To bridge our observations of fungi on particulate and the detection of degradative genes, we germinated fungal conidia in zooplankton fecal pellets and germinated fungal conidia after 8 months incubation in sterile seawater. Ultimately, these data suggest that fungi could be as important in oceanic ecosystems as they are in freshwater environments.
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Affiliation(s)
- B T Hassett
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway.
| | - E J Borrego
- Texas A&M University, 435 Nagle Street, 2132 TAMU, College Station, TX, 77833, USA
| | - T R Vonnahme
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway
| | - T Rämä
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway
| | - M V Kolomiets
- Texas A&M University, 435 Nagle Street, 2132 TAMU, College Station, TX, 77833, USA
| | - R Gradinger
- UiT Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019, Tromsø, Norway
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