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Liu X, Wang X, Zhou F, Xue Y, Liu C. Genomic insights into Penicillium chrysogenum adaptation to subseafloor sedimentary environments. BMC Genomics 2024; 25:4. [PMID: 38166640 PMCID: PMC10759354 DOI: 10.1186/s12864-023-09921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Penicillium chrysogenum is a filamentous fungal species with diverse habitats, yet little is known about its genetics in adapting to extreme subseafloor sedimental environments. RESULTS Here, we report the discovery of P. chrysogenum strain 28R-6-F01, isolated from deep coal-bearing sediments 2306 m beneath the seafloor. This strain possesses exceptional characteristics, including the ability to thrive in extreme conditions such as high temperature (45 °C), high pressure (35 Mpa), and anaerobic environments, and exhibits broad-spectrum antimicrobial activity, producing the antibiotic penicillin at a concentration of 358 μg/mL. Genome sequencing and assembly revealed a genome size of 33.19 Mb with a GC content of 48.84%, containing 6959 coding genes. Comparative analysis with eight terrestrial strains identified 88 unique genes primarily associated with penicillin and aflatoxins biosynthesis, carbohydrate degradation, viral resistance, and three secondary metabolism gene clusters. Furthermore, significant expansions in gene families related to DNA repair were observed, likely linked to the strain's adaptation to its environmental niche. CONCLUSIONS Our findings provide insights into the genomic and biological characteristics of P. chrysogenum adaptation to extreme anaerobic subseafloor sedimentary environments, such as high temperature and pressure.
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Xinran Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Fan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China.
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Ma Y, Zhao M, Zhou F, Liu X, Liu C. Anaerobic production and biosynthesis mechanism of exopolysaccharides in Schizophyllum commune 20R-7-F01. Int J Biol Macromol 2023; 253:127339. [PMID: 37820905 DOI: 10.1016/j.ijbiomac.2023.127339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/01/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
Exopolysaccharides (EPS) produced by microorganisms play a vital role in physiological and ecological processes. However, the mechanisms of EPS synthesis and release in anaerobic environments remain poorly understood. Here, we provide the first evidence of anaerobic EPS synthesis by the fungus Schizophyllum commune 20R-7-F01, isolated from coal-bearing sediments ~2.0 km below the seafloor. Under anaerobic conditions, the fungus exhibited significantly higher specific EPS production (1.57 times) than under aerobic conditions. Transcriptomic analysis revealed 2057 differentially expressed genes (DEGs) in the strain cultured anaerobically for 7 days compared to aerobically. Among these genes, 642 were significantly upregulated, while 1415 were significantly downregulated, mainly associated with carbon metabolism pathways. Genes involved in glycolysis and EPS synthesis, including hexokinase (HK), phosphoglucomutase (PGM), and (1 → 3)-β-glucan synthase (GLS), were significantly upregulated, while those related to the TCA cycle, respiratory chain, and pentose phosphate pathway were downregulated under anaerobic conditions. These findings highlight the oxygen-dependent regulation of EPS synthesis and suggest that EPS may serve as a key mechanism for fungal adaptation to anaerobic environments.
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Affiliation(s)
- Yunan Ma
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Mengshi Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Fan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China.
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Jiang JP, Leng S, Liao YF, Liu X, Li DX, Chu C, Yu XY, Liu CH. The potential role of subseafloor fungi in driving the biogeochemical cycle of nitrogen under anaerobic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165374. [PMID: 37422230 DOI: 10.1016/j.scitotenv.2023.165374] [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: 04/29/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023]
Abstract
Fungi represent the dominant eukaryotic group of organisms in anoxic marine sedimentary ecosystems, ranging from a few centimeters to ~ 2.5 km below seafloor. However, little is known about how fungi can colonize anaerobic subseafloor environments for tens of millions of years and whether they play a role in elemental biogeochemical cycles. Based on metabolite detection, isotope tracer and gene analysis, we examined the anaerobic nitrogen conversion pathways of 19 fungal species (40 strains) isolated from1.3 to 2.5 km coal-bearing sediments below seafloor. Our results show for the first time that almost all fungi possess anaerobic denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and nitrification pathways, but not anaerobic ammonium oxidation (anammox). Moreover, the distribution of fungi with different nitrogen-conversion abilities in subseafloor sediments was mainly determined by in situ temperature, CaCO3, and inorganic carbon contents. These findings suggest that fungi have multiple nitrogen transformation processes to cope with their requirements for a variety of nitrogen sources in nutrient deficient anaerobic subseafloor sedimentary environments.
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Affiliation(s)
- Jun-Peng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Shuang Leng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yi-Fan Liao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dong-Xu Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiang-Yang Yu
- Jiangsu Key Laboratory for Food Quality, Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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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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Ma Y, Wang Z, Arifeen MZU, Xue Y, Yuan S, Liu C. Structure and bioactivity of polysaccharide from a subseafloor strain of Schizophyllum commune 20R-7-F01. Int J Biol Macromol 2022; 222:610-619. [PMID: 36167101 DOI: 10.1016/j.ijbiomac.2022.09.189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/08/2022] [Accepted: 09/21/2022] [Indexed: 11/05/2022]
Abstract
Fungal polysaccharide is a kind of biomacromolecule with multiple biological activities, which has a wide application prospect and may play an important role in organisms to cope with extreme environments. Herein, we reported an extracellular polysaccharide (EPS) produced by Schizophyllum commune 20R-7-F01 that was isolated from subseafloor sediments at ~2 km below the seafloor, obtained during expedition 337. The monosaccharide of EPS was glucose and its molecular weight was 608.8 kDa. Methylation and NMR analysis indicated that the backbone of the EPS was (1 → 3)-β-D-glucan with a side chain (1 → 6) β-D-glucan linking at every third residue. Bio-active assays revealed that the EPS had potent antioxidant activity and could promote RAW264.7 cells viability and phagocytosis. These results suggest that fungi derived from sediments below seafloor are important and new source of polysaccharides and may be involved in the adaptation of fungi to anoxic subseafloor extreme ecosystem.
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Affiliation(s)
- Yunan Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhen Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Muhammad Zain Ul Arifeen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Sheng Yuan
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, 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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Liu X, Huang X, Chu C, Xu H, Wang L, Xue Y, Arifeen Muhammad ZU, Inagaki F, Liu C. Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments. iScience 2022; 25:104417. [PMID: 35663011 PMCID: PMC9156946 DOI: 10.1016/j.isci.2022.104417] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/30/2022] [Accepted: 05/12/2022] [Indexed: 12/15/2022] Open
Abstract
To understand the genomic evolution and adaptation strategies of fungi to subseafloor sedimentary environments, we de novo assembled the genome of Schizophyllum commune strain 20R-7-F01 isolated from ∼2.0 km-deep, ∼20-millionyearsago (Mya) coal-bearing sediments. Phylogenomics study revealed a differentiation time of 28–73 Mya between this strain and the terrestrial type-strain H4-8, in line with sediment age records. Comparative genome analyses showed that FunK1 protein kinase, NmrA family, and transposons in this strain are significantly expanded, possibly linking to the environmental adaptation and persistence in sediment for over millions of years. Re-sequencing study of 14 S. commune strains sampled from different habitats revealed that subseafloor strains have much lower nucleotide diversity, substitution rate, and homologous recombination rate than other strains, reflecting that the growth and/or reproduction of subseafloor strains are extremely slow. Our data provide new insights into the adaptation and long-term survival of the fungi in the subseafloor sedimentary biosphere. The genome of subseafloor Schizophyllum commune is distinct from that of other environmental isolates The divergence time between strains 20R-7-F01 and H4-8 of S. commune is 28–73 Mya S. commune experiences an evolutionary stasis in the subseafloor environment DNA repair, transposons, and CAZymes help fungi adapt to the subseafloor environment
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Xin Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Hui Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
- Corresponding author
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | | | - Fumio Inagaki
- Mantle Drilling Promotion Office, Institute for Marine-Earth Exploration and Engineering (MarE3), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama 236-0001, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai 980-8574, Japan
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
- Corresponding author
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