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Cai Q, Obieze CC, Pyke R, Delorme K, Maynard C, Greer CW, Khasa D. Gradient of acid mine drainage regulates microbial community assembly and the diversity of species associated with native plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024:125059. [PMID: 39362621 DOI: 10.1016/j.envpol.2024.125059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/13/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024]
Abstract
Acid mine drainage (AMD) is considered as one of the most important global environmental challenges. Therefore, understanding the impact of AMD on the diversity of microbial communities associated with native plants is important for phytoremediation. In this study, the community assembly and microbial diversity associated with native plants growing along an acid mine drainage (AMD) impact gradient was investigated using metabarcoding and high throughput iChip technique. The study revealed that across both domains of bacteria and fungi, richness and species diversity decreased according to AMD impact. Bacterial species diversity was more stratified according to the pH gradient than fungi, and the AMD impact on the plant-associated microbial diversity decreased towards the plant roots. The microbial community composition of the undisturbed site was significantly different from the AMD impacted sites, and the communities in the AMD impacted sites were further stratified according to the degree of impact. The overall microbial diversity was mediated by the AMD impact, niche differences and plant species differences. Dispersal limitation was the most important community assembly process in the undisturbed site, while the homogenous selection of Burkholderia, Actinospica, Puia and Bradyrhizobium increased along the AMD impact gradient. Differential abundance analysis further revealed that Umbelopsis, Burkholderia and Sphingomonas were among the biomarkers of the AMD impacted sites. Several strains of some of these responsive genera were subsequently isolated using the iChip. Overall, this study presents novel insight into the ecology of plant-associated microbial communities that are relevant for environmental monitoring and for enhancing the revegetation of AMD impacted sites.
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Affiliation(s)
- Qinhong Cai
- Department of Natural Resource Sciences, McGill University.
| | - Chinedu C Obieze
- Institut de biologie intégrative et des systèmes, Université Laval.
| | - Ruby Pyke
- Department of Natural Resource Sciences, McGill University
| | - Karine Delorme
- Department of Natural Resource Sciences, McGill University
| | - Christine Maynard
- Energy, Mining and Environment Research Centre, National Research Council Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University; Energy, Mining and Environment Research Centre, National Research Council Canada
| | - Damase Khasa
- Institut de biologie intégrative et des systèmes, Université Laval
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2
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Gomez-Gutierrrez SV, Sic-Hernandez WR, Haridas S, LaButti K, Eichenberger J, Kaur N, Lipzen A, Barry K, Goodwin SB, Gribskov M, Grigoriev IV. Comparative genomics of the extremophile Cryomyces antarcticus and other psychrophilic Dothideomycetes. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1418145. [PMID: 39309730 PMCID: PMC11412873 DOI: 10.3389/ffunb.2024.1418145] [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: 04/16/2024] [Accepted: 08/13/2024] [Indexed: 09/25/2024]
Abstract
Over a billion years of fungal evolution has enabled representatives of this kingdom to populate almost all parts of planet Earth and to adapt to some of its most uninhabitable environments including extremes of temperature, salinity, pH, water, light, or other sources of radiation. Cryomyces antarcticus is an endolithic fungus that inhabits rock outcrops in Antarctica. It survives extremes of cold, humidity and solar radiation in one of the least habitable environments on Earth. This fungus is unusual because it produces heavily melanized, meristematic growth and is thought to be haploid and asexual. Due to its growth in the most extreme environment, it has been suggested as an organism that could survive on Mars. However, the mechanisms it uses to achieve its extremophilic nature are not known. Comparative genomics can provide clues to the processes underlying biological diversity, evolution, and adaptation. This effort has been greatly facilitated by the 1000 Fungal Genomes project and the JGI MycoCosm portal where sequenced genomes have been assembled into phylogenetic and ecological groups representing different projects, lifestyles, ecologies, and evolutionary histories. Comparative genomics within and between these groups provides insights into fungal adaptations, for example to extreme environmental conditions. Here, we analyze two Cryomyces genomes in the context of additional psychrophilic fungi, as well as non-psychrophilic fungi with diverse lifestyles selected from the MycoCosm database. This analysis identifies families of genes that are expanded and contracted in Cryomyces and other psychrophiles and may explain their extremophilic lifestyle. Higher GC contents of genes and of bases in the third positions of codons may help to stabilize DNA under extreme conditions. Numerous smaller contigs in C. antarcticus suggest the presence of an alternative haplotype that could indicate the sequenced isolate is diploid or dikaryotic. These analyses provide a first step to unraveling the secrets of the extreme lifestyle of C. antarcticus.
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Affiliation(s)
| | - Wily R. Sic-Hernandez
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Joanne Eichenberger
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Navneet Kaur
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stephen B. Goodwin
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture (USDA) - Agricultural Research Service, West Lafayette, IN, United States
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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3
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Pan X, Yue Z, She Z, He X, Wang S, Chuai X, Wang J. Eukaryotic Community Structure and Interspecific Interactions in a Stratified Acidic Pit Lake Water in Anhui Province. Microorganisms 2023; 11:microorganisms11040979. [PMID: 37110402 PMCID: PMC10142529 DOI: 10.3390/microorganisms11040979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The stratified acidic pit lake formed by the confluence of acid mine drainage has a unique ecological niche and is a model system for extreme microbial studies. Eukaryotes are a component of the AMD community, with the main members including microalgae, fungi, and a small number of protozoa. In this study, we analyzed the structural traits and interactions of eukaryotes (primarily fungi and microalgae) in acidic pit lakes subjected to environmental gradients. Based on the findings, microalgae and fungi were found to dominate different water layers. Specifically, Chlorophyta showed dominance in the well-lit aerobic surface layer, whereas Basidiomycota was more abundant in the dark anoxic lower layer. Co-occurrence network analysis showed that reciprocal relationships between fungi and microalgae were prevalent in extremely acidic environments. Highly connected taxa within this network were Chlamydomonadaceae, Sporidiobolaceae, Filobasidiaceae, and unclassified Eukaryotes. Redundancy analysis (RDA) and random forest models revealed that Chlorophyta and Basidiomycota responded strongly to environmental gradients. Further analysis indicated that eukaryotic community structure was mainly determined by nutrient and metal concentrations. This study investigates the potential symbiosis between fungi and microalgae in the acidic pit lake, providing valuable insights for future eukaryotic biodiversity studies on AMD remediation.
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Affiliation(s)
- Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
| | - Zhixiang She
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
| | - Xiao He
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Nanshan Mining Company Ltd., Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan 243000, China
| | - Shaoping Wang
- Nanshan Mining Company Ltd., Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan 243000, China
| | - Xin Chuai
- Nanshan Mining Company Ltd., Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan 243000, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
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4
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Luo ZH, Li Q, Chen N, Tang LY, Liao B, Yang TT, Huang LN. Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings. JOURNAL OF HAZARDOUS MATERIALS 2023; 447:130774. [PMID: 36641850 DOI: 10.1016/j.jhazmat.2023.130774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.
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Affiliation(s)
- Zhen-Hao Luo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ling-Yun Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Liao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao-Tao Yang
- Guangdong Heavy Metal Mine Ecological Restoration Engineering Technology Research Center, Shaoguan, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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5
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Li J, Wang X, Zou J, Yang K, Wang X, Wang Y, Zhang H, Huang H, Su X, Yao B, Luo H, Qin X. Identification and Characterization of the Determinants of Copper Resistance in the Acidophilic Fungus Acidomyces richmondensis MEY-1 Using the CRISPR/Cas9 System. Appl Environ Microbiol 2023; 89:e0210722. [PMID: 36912653 PMCID: PMC10056952 DOI: 10.1128/aem.02107-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
Copper (Cu) homeostasis has not been well documented in filamentous fungi, especially extremophiles. One of the main obstacles impeding their characterization is the lack of a powerful genome-editing tool. In this study, we applied a CRISPR/Cas9 system for efficient targeted gene disruption in the acidophilic fungus Acidomyces richmondensis MEY-1, formerly known as Bispora sp. strain MEY-1. Using this system, we investigated the basis of Cu tolerance in strain MEY-1. This strain has extremely high Cu tolerance among filamentous fungi, and the transcription factor ArAceA (A. richmondensis AceA) has been shown to be involved in this process. The ArAceA deletion mutant (ΔArAceA) exhibits specific growth defects at Cu concentrations of ≥10 mM and is transcriptionally more sensitive to Cu than the wild-type strain. In addition, the putative metallothionein ArCrdA was involved in Cu tolerance only under high Cu concentrations. MEY-1 has no Aspergillus nidulans CrpA homologs, which are targets of AceA-like transcription factors and play a role in Cu tolerance. Instead, we identified the Cu-transporting P-type ATPase ArYgA, homologous to A. nidulans YgA, which was involved in pigmentation rather than Cu tolerance. When the ΔArYgA mutant was grown on medium supplemented with Cu ions, the black color was completely restored. The lack of CrpA homologs in A. richmondensis MEY-1 and its high tolerance to Cu suggest that a novel Cu detoxification mechanism differing from the AceA-CrpA axis exists. IMPORTANCE Filamentous fungi are widely distributed worldwide and play an important ecological role as decomposers. However, the mechanisms of their adaptability to various environments are not fully understood. Various extremely acidophilic filamentous fungi have been isolated from acidic mine drainage (AMD) with extremely low pH and high heavy metal and sulfate concentrations, including A. richmondensis. The lack of genetic engineering tools, particularly genome-editing tools, hinders the study of these acidophilic and heavy metal-resistant fungi at the molecular level. Here, we first applied a CRISPR/Cas9-mediated gene-editing system to A. richmondensis MEY-1. Using this system, we identified and characterized the determinants of Cu resistance in A. richmondensis MEY-1. The conserved roles of the Cu-binding transcription factor ArAceA in Cu tolerance and the Cu-transporting P-type ATPase ArYgA in the Cu-dependent production of pigment were confirmed. Our findings provide insights into the molecular basis of Cu tolerance in the acidophilic fungus A. richmondensis MEY-1. Furthermore, the CRISPR/Cas9 system used here would be a powerful tool for studies of the mechanisms of adaptability of acidophilic fungi to extreme environments.
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Affiliation(s)
- Jinyang Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiahuan Zou
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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6
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Gevi F, Leo P, Cassaro A, Pacelli C, de Vera JPP, Rabbow E, Timperio AM, Onofri S. Metabolomic Profile of the Fungus Cryomyces antarcticus Under Simulated Martian and Space Conditions as Support for Life-Detection Missions on Mars. Front Microbiol 2022; 13:749396. [PMID: 35633719 PMCID: PMC9133366 DOI: 10.3389/fmicb.2022.749396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
The identification of traces of life beyond Earth (e.g., Mars, icy moons) is a challenging task because terrestrial chemical-based molecules may be destroyed by the harsh conditions experienced on extraterrestrial planetary surfaces. For this reason, studying the effects on biomolecules of extremophilic microorganisms through astrobiological ground-based space simulation experiments is significant to support the interpretation of the data that will be gained and collected during the ongoing and future space exploration missions. Here, the stability of the biomolecules of the cryptoendolithic black fungus Cryomyces antarcticus, grown on two Martian regolith analogues and on Antarctic sandstone, were analysed through a metabolomic approach, after its exposure to Science Verification Tests (SVTs) performed in the frame of the European Space Agency (ESA) Biology and Mars Experiment (BIOMEX) project. These tests are building a set of ground-based experiments performed before the space exposure aboard the International Space Station (ISS). The analysis aimed to investigate the effects of different mineral mixtures on fungal colonies and the stability of the biomolecules synthetised by the fungus under simulated Martian and space conditions. The identification of a specific group of molecules showing good stability after the treatments allow the creation of a molecular database that should support the analysis of future data sets that will be collected in the ongoing and next space exploration missions.
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Affiliation(s)
- Federica Gevi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Patrick Leo
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
- Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Venice, Italy
| | - Alessia Cassaro
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | | | | | - Elke Rabbow
- German Aerospace Centre, Institute of Aerospace Medicine (DLR), Cologne, Germany
| | - Anna Maria Timperio
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
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7
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Passarini MRZ, Ottoni JR, Costa PEDS, Hissa DC, Falcão RM, Melo VMM, Balbino VQ, Mendonça LAR, Lima MGDS, Coutinho HDM, Verde LCL. Fungal community diversity of heavy metal contaminated soils revealed by metagenomics. Arch Microbiol 2022; 204:255. [PMID: 35412096 DOI: 10.1007/s00203-022-02860-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Júlia Ronzella Ottoni
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | | | | | - Raul Maia Falcão
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
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8
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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9
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Aguinaga OE, White KN, Dean AP, Pittman JK. Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118064. [PMID: 34481302 DOI: 10.1016/j.envpol.2021.118064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.
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Affiliation(s)
- Oscar E Aguinaga
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK; Departamento de Ingeniería, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Keith N White
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Andrew P Dean
- Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Oxford Road, Manchester, M1 5GD, UK
| | - Jon K Pittman
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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10
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Nagel JH, Wingfield MJ, Slippers B. Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae. BMC Genomics 2021; 22:589. [PMID: 34348651 PMCID: PMC8336260 DOI: 10.1186/s12864-021-07902-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/30/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The Botryosphaeriaceae are important plant pathogens, but also have the ability to establish asymptomatic infections that persist for extended periods in a latent state. In this study, we used comparative genome analyses to shed light on the genetic basis of the interactions of these fungi with their plant hosts. For this purpose, we characterised secreted hydrolytic enzymes, secondary metabolite biosynthetic gene clusters and general trends in genomic architecture using all available Botryosphaeriaceae genomes, and selected Dothideomycetes genomes. RESULTS The Botryosphaeriaceae genomes were rich in carbohydrate-active enzymes (CAZymes), proteases, lipases and secondary metabolic biosynthetic gene clusters (BGCs) compared to other Dothideomycete genomes. The genomes of Botryosphaeria, Macrophomina, Lasiodiplodia and Neofusicoccum, in particular, had gene expansions of the major constituents of the secretome, notably CAZymes involved in plant cell wall degradation. The Botryosphaeriaceae genomes were shown to have moderate to high GC contents and most had low levels of repetitive DNA. The genomes were not compartmentalized based on gene and repeat densities, but genes of secreted enzymes were slightly more abundant in gene-sparse regions. CONCLUSION The abundance of secreted hydrolytic enzymes and secondary metabolite BGCs in the genomes of Botryosphaeria, Macrophomina, Lasiodiplodia, and Neofusicoccum were similar to those in necrotrophic plant pathogens and some endophytes of woody plants. The results provide a foundation for comparative genomic analyses and hypotheses to explore the mechanisms underlying Botryosphaeriaceae host-plant interactions.
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Affiliation(s)
- Jan H Nagel
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South Africa.
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South Africa
| | - Bernard Slippers
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0001, South Africa
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11
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Ou SN, Liang JL, Jiang XM, Liao B, Jia P, Shu WS, Li JT. Physiological, Genomic and Transcriptomic Analyses Reveal the Adaptation Mechanisms of Acidiella bohemica to Extreme Acid Mine Drainage Environments. Front Microbiol 2021; 12:705839. [PMID: 34305876 PMCID: PMC8298002 DOI: 10.3389/fmicb.2021.705839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Fungi in acid mine drainage (AMD) environments are of great concern due to their potentials of decomposing organic carbon, absorbing heavy metals and reducing AMD acidity. Based on morphological analysis and ITS/18S high-throughput sequencing technology, previous studies have provided deep insights into the diversity and community composition of fungi in AMD environments. However, knowledge about physiology, metabolic potential and transcriptome profiles of fungi inhabiting AMD environments is still scarce. Here, we reported the physiological, genomic, and transcriptomic characterization of Acidiella bohemica SYSU C17045 to improve our understanding of the physiological, genomic, and transcriptomic mechanisms underlying fungal adaptation to AMD environments. A. bohemica was isolated from an AMD environment, which has been proved to be an acidophilic fungus in this study. The surface of A. bohemica cultured in AMD solutions was covered with a large number of minerals such as jarosite. We thus inferred that the A. bohemica might have the potential of biologically induced mineralization. Taking advantage of PacBio single-molecule real-time sequencing, we obtained the high-quality genome sequences of A. bohemica (50 Mbp). To our knowledge, this was the first attempt to employ a third-generation sequencing technology to explore the genomic traits of fungi isolated from AMD environments. Moreover, our transcriptomic analysis revealed that a series of genes in the A. bohemica genome were related to its metabolic pathways of C, N, S, and Fe as well as its adaptation mechanisms, including the response to acid stress and the resistance to heavy metals. Overall, our physiological, genomic, and transcriptomic data provide a foundation for understanding the metabolic potential and adaptation mechanisms of fungi in AMD environments.
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Affiliation(s)
- Shu-Ning Ou
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiao-Min Jiang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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12
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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13
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Genome assembly of Scorias spongiosa and comparative genomics provide insights into ecological adaptation of honeydew-dependent sooty mould fungi. Genomics 2021; 113:2189-2198. [PMID: 34022339 DOI: 10.1016/j.ygeno.2021.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/04/2021] [Accepted: 05/17/2021] [Indexed: 12/28/2022]
Abstract
Sooty moulds are fungi of economic importance and with unique lifestyle mainly growing on insect honeydew. However, the lack of genomic data hinders investigation of genetic mechanisms underlying their ecological adaptation. With long-read sequencing technology, we generated the genome of Scorias spongiosa, an extraordinary sooty mould fungus associated with honeydew of colony aphids and producing large fruiting bodies. A 24.21 Mb high-quality genome assembly with a N50 length of 3.37 Mb was obtained. The genome contained 7758 protein coding genes, 97.13% of which were homologous to known genes, and approximately 0.29 Mb repeat sequences. Comparative genomics showed S. spongiosa lost relatively more gene families and contained fewer species-specific genes and gene families, with many CAZyme families and sugar transporters reduced or absent. This study not only promotes understanding of the ecological adaptation of sooty moulds, but also provides valuable genomic data resource for future comparative genomic and genetic studies.
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Liang R, Li Z, Lau Vetter MCY, Vishnivetskaya TA, Zanina OG, Lloyd KG, Pfiffner SM, Rivkina EM, Wang W, Wiggins J, Miller J, Hettich RL, Onstott TC. Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost. MICROBIOME 2021; 9:110. [PMID: 34001281 PMCID: PMC8130349 DOI: 10.1186/s40168-021-01057-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/22/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. RESULTS Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26-120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. CONCLUSIONS Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars. Video abstract.
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Affiliation(s)
- Renxing Liang
- Princeton University, B88, Guyot Hall, Princeton, NJ, 08544, USA.
| | - Zhou Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Maggie C Y Lau Vetter
- Princeton University, B88, Guyot Hall, Princeton, NJ, 08544, USA
- Present address: Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Tatiana A Vishnivetskaya
- University of Tennessee, Knoxville, TN, USA
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oksana G Zanina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | | | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Wei Wang
- Genomics Core Facility, Princeton University, Princeton, NJ, USA
| | - Jessica Wiggins
- Genomics Core Facility, Princeton University, Princeton, NJ, USA
| | - Jennifer Miller
- Genomics Core Facility, Princeton University, Princeton, NJ, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Tullis C Onstott
- Princeton University, B88, Guyot Hall, Princeton, NJ, 08544, USA
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15
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Rheault K, Lachance D, Morency MJ, Thiffault É, Guittonny M, Isabel N, Martineau C, Séguin A. Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar. Front Microbiol 2020; 11:575625. [PMID: 33329437 PMCID: PMC7719689 DOI: 10.3389/fmicb.2020.575625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 01/09/2023] Open
Abstract
Abandoned unrestored mines are an important environmental concern as they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic and unfavorable biotic conditions. However, some pioneer tree species having high levels of genetic diversity, such as balsam poplar (Populus balsamifera), can naturally colonize these sites and initiate plant succession. This suggests that some tree genotypes are likely more suited for acclimation to the conditions of mine wastes. In this study, we selected two contrasting mine waste storage facilities (waste rock from a gold mine and tailings from a molybdenum mine) from the Abitibi region of Quebec (Canada), on which poplars were found to have grown naturally. First, we assessed in situ the impact of vegetation presence on each mine waste type. The presence of balsam poplars improved soil health locally by modifying the physicochemical properties (e.g., higher nutrient content and pH) of the mine wastes and causing an important shift in their bacterial and fungal community compositions, going from lithotrophic communities that dominate mine waste environments to heterotrophic communities involved in nutrient cycling. Next, in a greenhouse experiment we assessed the impact of plant genotype when grown in these mine wastes. Ten genotypes of P. balsamifera were collected locally, found growing either at the mine sites or in the surrounding natural forest. Tree growth was monitored over two growing seasons, after which the effects of genotype-by-environment interactions were assessed by measuring the physicochemical properties of the substrates and the changes in microbial community assembly. Although substrate type was identified as the main driver of rhizosphere microbiome diversity and community structure, a significant effect due to tree genotype was also detected, particularly for bacterial communities. Plant genotype also influenced aboveground tree growth and the physicochemical properties of the substrates. These results highlight the influence of balsam poplar genotype on the soil environment and the potential importance of tree genotype selection in the context of mine waste revegetation.
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Affiliation(s)
- Karelle Rheault
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Denis Lachance
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Évelyne Thiffault
- Renewable Materials Research Centre, Department of Wood and Forest Sciences, Université Laval, Quebec City, QC, Canada
| | - Marie Guittonny
- Research Institute of Mines and Environment (RIME), Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
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16
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Yang S, Wu L, Wu B, Zhang Y, Wang H, Tan X. Diversity and structure of soil microbiota of the Jinsha earthen relic. PLoS One 2020; 15:e0236165. [PMID: 32697804 PMCID: PMC7375591 DOI: 10.1371/journal.pone.0236165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/30/2020] [Indexed: 12/02/2022] Open
Abstract
In order to define the diversity and composition of the microbial communities colonizing of the soil microbiome of the Jinsha earthen relic, we used high-throughput sequencing technology to identify and characterize the microbiota in 22 samples collected from the Jinsha earthen relic in China during 2017 and 2018. We compared the taxonomy of the microbial communities from samples taken at different times and different sites. Our results showed that the identity of the dominant bacterial phyla differed among the samples. Proteobacteria (23–86.2%) were the predominant bacterial phylum in all samples taken from site A in both 2017 and 2018. However, Actinobacteria (21–92.3%) were the most popular bacterial phylum in samples from sites B and C in 2017 and 2018. Ascomycota were identified as the only fungal phyla in samples in 2017. However, the group varied drastically in relative abundance between 2017 and 2018. Functional analysis of the soil bacterial community suggested that abundant members of the microbiota may be associated with metabolism and the specific environment. This report was the first high-throughput sequencing study of the soil of the Jinsha earthen relic microbiome. Since soil microbiota can damage soil and archeological structures, comprehensive analyses of the microbiomes at archeological sites may contribute to the understand of the influence of microorganisms on the degradation of soil, as well as to the identification of potentially beneficial or undesirable members of these microbial communities in archeological sites. The study will be helpful to provide effective data and guidance for the prevention and control of microbial corrosion of the Jinsha earthen relic.
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Affiliation(s)
- Sheng Yang
- Chengdu Institute of Cultural Relics, Chengdu, PR China
| | - Linfeng Wu
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Bin Wu
- Jinsha Site Museum, Chengdu, PR China
| | - Yizheng Zhang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Haiyan Wang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Xuemei Tan
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
- * E-mail:
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17
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Hujslová M, Gryndlerová H, Bystrianský L, Hršelová H, Gryndler M. Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic. Extremophiles 2020; 24:577-591. [PMID: 32449144 DOI: 10.1007/s00792-020-01177-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.
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Affiliation(s)
- Martina Hujslová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.
| | - Hana Gryndlerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Bystrianský
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
| | - Hana Hršelová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Milan Gryndler
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
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18
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Wise BR, Roane TM, Mosier AC. Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment. MICROBIAL ECOLOGY 2020; 79:562-575. [PMID: 31446448 DOI: 10.1007/s00248-019-01420-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.
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Affiliation(s)
- Ben R Wise
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Timberley M Roane
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA.
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19
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Chen LX, Anantharaman K, Shaiber A, Eren AM, Banfield JF. Accurate and complete genomes from metagenomes. Genome Res 2020; 30:315-333. [PMID: 32188701 PMCID: PMC7111523 DOI: 10.1101/gr.258640.119] [Citation(s) in RCA: 210] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Alon Shaiber
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois 60637, USA.,Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA.,Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA
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20
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The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes. Commun Biol 2020; 3:50. [PMID: 32005944 PMCID: PMC6994591 DOI: 10.1038/s42003-020-0770-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
Fusarium oxysporum is a cross-kingdom fungal pathogen that infects plants and humans. Horizontally transferred lineage-specific (LS) chromosomes were reported to determine host-specific pathogenicity among phytopathogenic F. oxysporum. However, the existence and functional importance of LS chromosomes among human pathogenic isolates are unknown. Here we report four unique LS chromosomes in a human pathogenic strain NRRL 32931, isolated from a leukemia patient. These LS chromosomes were devoid of housekeeping genes, but were significantly enriched in genes encoding metal ion transporters and cation transporters. Homologs of NRRL 32931 LS genes, including a homolog of ceruloplasmin and the genes that contribute to the expansion of the alkaline pH-responsive transcription factor PacC/Rim1p, were also present in the genome of NRRL 47514, a strain associated with Fusarium keratitis outbreak. This study provides the first evidence, to our knowledge, for genomic compartmentalization in two human pathogenic fungal genomes and suggests an important role of LS chromosomes in niche adaptation. Zhang, Yang et al. compare a Fusarium oxysporum isolate obtained clinically to a phytopathogenic strain to examine transfer of lineage-specific chromosomes in determining host specificity. They find four unique lineage-specific chromosomes that seem to contribute to fungal adaptation to human hosts.
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21
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Coleine C, Masonjones S, Sterflinger K, Onofri S, Selbmann L, Stajich JE. Peculiar genomic traits in the stress-adapted cryptoendolithic Antarctic fungus Friedmanniomyces endolithicus. Fungal Biol 2020; 124:458-467. [PMID: 32389308 DOI: 10.1016/j.funbio.2020.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 11/28/2022]
Abstract
Friedmanniomyces endolithicus is a highly melanized fungus endemic to the Antarctic, occurring exclusively in endolithic communities of the ice-free areas of the Victoria Land, including the McMurdo Dry Valleys, the coldest and most hyper-arid desert on Earth and accounted as the Martian analog on our planet. F. endolithicus is highly successful in these inhospitable environments, the most widespread and commonly isolated species from these peculiar niches, indicating a high degree of adaptation. The nature of its extremo tolerance has not been previously studied. To investigate this, we sequenced genome of F. endolithicus CCFEE 5311 to explore gene content and genomic patterns that could be attributed to its specialization. The predicted functional potential of the genes was assigned by similarity to InterPro and CAZy domains. The genome was compared to phylogenetically close relatives which are also melanized fungi occurring in extreme environments including Friedmanniomyces simplex, Baudoinia panamericana, Acidomyces acidophilus, Hortaea thailandica and Hortaea werneckii. We tested if shared genomic traits existed among these species and hyper-extremotolerant fungus F. endolithicus. We found that some characters for stress tolerance such as meristematic growth and cold tolerance are enriched in F. endolithicus that may be triggered by the exposure to Antarctic prohibitive conditions.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
| | - Sawyer Masonjones
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Katja Sterflinger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy; Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
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22
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Ametrano CG, Grewe F, Crous PW, Goodwin SB, Liang C, Selbmann L, Lumbsch HT, Leavitt SD, Muggia L. Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota). IMA Fungus 2019; 10:19. [PMID: 32647623 PMCID: PMC7325674 DOI: 10.1186/s43008-019-0018-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.
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Affiliation(s)
- Claudio G Ametrano
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
| | - Felix Grewe
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85176, 3508 AD Utrecht, The Netherlands
| | - Stephen B Goodwin
- USDA-ARS, Crop Production and Pest Control Research Unit and Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Chen Liang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell' Università, 01100 Viterbo, Italy.,Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | - H Thorsten Lumbsch
- Grainger Bioinformatics Center and Integrative Research Center, Science and Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605 USA
| | - Steven D Leavitt
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, 4102 Life Science Building, Provo, UT 84602 USA
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy
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23
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Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies. Curr Microbiol 2019; 77:657-674. [DOI: 10.1007/s00284-019-01771-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/09/2019] [Indexed: 11/27/2022]
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24
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Guo Y, Tu T, Zheng J, Bai Y, Huang H, Su X, Wang Y, Wang Y, Yao B, Luo H. Improvement of BsAPA Aspartic Protease Thermostability via Autocatalysis-Resistant Mutation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10505-10512. [PMID: 31462045 DOI: 10.1021/acs.jafc.9b03959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
An aspartic protease gene (Bsapa) was cloned from Bispora sp. MEY-1 and expressed in Pichia pastoris. The recombinant BsAPA showed maximal activity at pH 3.0 and 75 °C and remained stable at 70 °C and below, indicating the thermostable nature of BsAPA. However, heat inactivation still limits the application of BsAPA. To further improve its thermostability, an autocatalysis site (L205-F206) in BsAPA was identified and three mutants (F193W, K204P, and A371V) were generated based on the analysis of the structure neighboring the autocatalysis site. These mutants have improved thermostability, and their half-life at 75 °C increased by 0.5-, 0.2-, and 0.3-fold, respectively. A triple-site mutant (F193W/K204P/A371V) was generated, with 1.5-fold increased half-life at 80 and a 10.7 °C increased Tm, compared with those of the wild-type. These results indicate that autocatalysis of aspartic protease reduces enzyme thermostability. Furthermore, site-directed mutagenesis at regions near the autocatalysis site is an efficient approach to improve aspartic protease thermostability.
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Affiliation(s)
- Yujie Guo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Jie Zheng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Yaru Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute , Chinese Academy of Agricultural Sciences , No. 18 12 Zhongguancun South Street , Beijing 100081 , P. R. China
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25
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Gilbert KB, Holcomb EE, Allscheid RL, Carrington JC. Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes. PLoS One 2019; 14:e0219207. [PMID: 31339899 PMCID: PMC6655640 DOI: 10.1371/journal.pone.0219207] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/18/2019] [Indexed: 11/25/2022] Open
Abstract
The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
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Affiliation(s)
- Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Emily E. Holcomb
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Robyn L. Allscheid
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - James C. Carrington
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
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26
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Chang Y, Desirò A, Na H, Sandor L, Lipzen A, Clum A, Barry K, Grigoriev IV, Martin FM, Stajich JE, Smith ME, Bonito G, Spatafora JW. Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota. THE NEW PHYTOLOGIST 2019; 222:511-525. [PMID: 30485448 DOI: 10.1111/nph.15613] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/29/2018] [Indexed: 06/09/2023]
Abstract
Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non-Dikarya order with ectomycorrhizal members. They also form mycorrhizal-like association with some nonspermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal-lifestyle signatures and whether Endogonales originated around the same time as land plants did. We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant-cell-wall-degrading enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling. Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian-Triassic boundary and Endogonales originated in the mid-late Silurian. Mycoplasma-related endobacterium sequences were identified in three Endogonaceae genomes. Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.
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Affiliation(s)
- Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Alessandro Desirò
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Institut national de la recherche agronomique, Laboratoire d'excellence ARBRE, Centre INRA-Grand Est, Unité mixte de recherche Inra-Université de Lorraine "Interactions Arbres/Microorganismes", 54280, Champenoux, France
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
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27
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Faiza M, Huang S, Lan D, Wang Y. New insights on unspecific peroxygenases: superfamily reclassification and evolution. BMC Evol Biol 2019; 19:76. [PMID: 30866798 PMCID: PMC6417270 DOI: 10.1186/s12862-019-1394-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/20/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Unspecific peroxygenases (UPO) (EC 1.11.2.1) represent an intriguing oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity. With over 300 identified substrates, UPOs catalyze numerous oxidations including 1- or 2- electron oxygenation, selective oxyfunctionalizations, which make them most significant in organic syntheses and potentially attractive as industrial biocatalysts. There are very few UPOs available with distinct properties, notably, MroUPO which shows behavior ranging between UPO and another heme-thiolate peroxidase, called Chloroperoxidase (CPO). It prompted us to search for more UPOs in fungal kingdom which led us to studying their relationship with CPO. RESULTS In this study, we searched for novel UPOs in more than 800 fungal genomes and found 113 putative UPO-encoding sequences distributed in 35 different fungal species (or strains), amongst which single sequence per species were subjected to phylogeny study along with CPOs. Our phylogenetic study show that the UPOs are distributed in Basidiomycota and Ascomycota phyla of fungi. The sequence analysis helped to classify the UPOs into five distinct subfamilies: classic AaeUPO and four new subfamilies with potential new traits. We have also shown that each of these five subfamilies (supported by) have their own signature motifs. Surprisingly, some of the CPOs appeared to be a type of UPOs indicating that they were previously identified incorrectly. Selection pressure was observed on important motifs in UPOs which could have driven their functional divergence. Furthermore, the sites having different evolutionary rates caused by the functional divergence were also identified on some motifs along with the other relevant amino acid residues. Finally, we predicted critical amino acids responsible for the functional divergence in the UPOs and identified some sequence differences among UPOs, CPOs, and MroUPO to predict it's ranging behavior. CONCLUSION This study discovers new UPOs, provides a glimpse of their evolution from CPOs, and presents new insight on their functional divergence. We present a new classification of UPOs and shed new light on its phylogenetics. These different UPOs may exhibit a wide range of characteristics and specificities which may help in various fields of synthetic chemistry and industrial biocatalysts, and may as well lead to an advancement towards the understanding of physiological role of UPOs in fungi.
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Affiliation(s)
- Muniba Faiza
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 China
| | - Shengfeng Huang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640 China
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28
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Hujslová M, Bystrianský L, Benada O, Gryndler M. Fungi, a neglected component of acidophilic biofilms: do they have a potential for biotechnology? Extremophiles 2019; 23:267-275. [PMID: 30840146 DOI: 10.1007/s00792-019-01085-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 02/25/2019] [Indexed: 01/18/2023]
Abstract
Fungi from extreme environments, including acidophilic ones, belong to biotechnologically most attractive organisms. They can serve as a source of enzymes and metabolites with potentially uncommon properties and may actively participate within bioremediation processes. In respect of their biotechnological potential, extremophilic fungi are mostly studied as individual species. Nevertheless, microorganisms rarely live separately and they form biofilms instead. Living in biofilms is the most successful life strategy on the Earth and the biofilm is the most abundant form of life in extreme environments including highly acidic ones. Compared to bacterial fraction, fungal part of acidophilic biofilms represents a largely unexplored source of organisms with possible use in biotechnology and especially data on biofilms of highly acidic soils are missing. The functioning of the biofilm results from interactions between organisms whose metabolic capabilities are efficiently combined. When we look on acidophilic fungi and their biotechnological potential we should take this fact into account as well. The practical problem to be resolved in connection with extensive studies of exploitable properties and abilities of acidophilic fungi is the methodology of isolation of strains from the nature. In this respect, novel isolation techniques should be developed.
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Affiliation(s)
- Martina Hujslová
- Laboratory of Fungal biology, Institute of Microbiology ASCR, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Lukáš Bystrianský
- Department of Biology, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Za válcovnou 1000/8, 400 01, Ústí nad Labem, Czech Republic
| | - Oldřich Benada
- Department of Biology, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Za válcovnou 1000/8, 400 01, Ústí nad Labem, Czech Republic.,Laboratory of Molecular Structure Characterization, Institute of Microbiology ASCR, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Milan Gryndler
- Department of Biology, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Za válcovnou 1000/8, 400 01, Ústí nad Labem, Czech Republic
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29
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Interactions among microfungi and pyrite-chalcopyrite mineralizations: tolerance, mineral bioleaching, and metal bioaccumulation. Mycol Prog 2019. [DOI: 10.1007/s11557-018-01466-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Glukhova LB, Frank YA, Danilova EV, Avakyan MR, Banks D, Tuovinen OH, Karnachuk OV. Isolation, Characterization, and Metal Response of Novel, Acid-Tolerant Penicillium spp. from Extremely Metal-Rich Waters at a Mining Site in Transbaikal (Siberia, Russia). MICROBIAL ECOLOGY 2018; 76:911-924. [PMID: 29663040 DOI: 10.1007/s00248-018-1186-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
The role of fungi in metal cycling in acidic environments has been little explored to date. In this study, two acid-tolerant and metal-resistant Penicillium isolates, strains ShG4B and ShG4C, were isolated from a mine site in the Transbaikal area of Siberia (Russia). Waters at the mine site were characterized by extremely high metal concentrations: up to 18 g l-1 Fe and > 2 g l-1 each of Cu, Zn, Al, and As. Both isolates were identified as Penicillium spp. by phylogenetic analyses and they grew well in Czapek medium acidified to pH 2.5. Resistance to Cu, Cd, Ni, Co, and arsenate was in the range of 1-10 g l-1. Further experiments with Penicillium strain ShG4C demonstrated that growth in Cu-containing media was accompanied by the precipitation of Cu-oxalate (moolooite) and the formation of extracellular vesicles enriched in Cu on the mycelia. Vesicles were greatly reduced in size in Cd-containing media and were not formed in the presence of Ni or Co. Cd-oxalate was detected as a crystalline solid phase in Cd-exposed mycelia. Hydrated Ni-sulfate (retgersite) and Co-sulfate (bieberite) were detected in mycelia grown in the presence of Ni and Co, respectively. The results demonstrated that acid-tolerant and metal-resistant Penicillium constitute a component in extremophilic microbiomes, contributing to organic matter breakdown and formation of secondary solid phases at pH ranges found in acid rock drainage.
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Affiliation(s)
- Lubov B Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - Ehrzena V Danilova
- Institute of General and Experimental Biology, Russian Academy of Sciences, Sakhyanovoy St. 6, Ulan-Ude, Russia, 670047
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050
| | - David Banks
- School of Engineering, Systems Power & Energy, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
- Holymoor Consultancy Ltd., 360 Ashgate Road, Chesterfield, Derbyshire, S40 4BW, UK
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Lenin Ave. 36, Tomsk, Russia, 634050.
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31
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Genome Sequence of the Extremely Acidophilic Fungus Acidomyces richmondensis FRIK2901. Microbiol Resour Announc 2018; 7:MRA01314-18. [PMID: 30533739 PMCID: PMC6256575 DOI: 10.1128/mra.01314-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/02/2018] [Indexed: 11/20/2022] Open
Abstract
Acidomyces richmondensis is an extremophilic fungal species found in warm, acidic, and metal-rich environments. To improve upon the existing reference genome, we used PacBio and Illumina sequencing to assemble a highly contiguous 29.3-Mb genome of A. richmondensis FRIK2901. Acidomyces richmondensis is an extremophilic fungal species found in warm, acidic, and metal-rich environments. To improve upon the existing reference genome, we used PacBio and Illumina sequencing to assemble a highly contiguous 29.3-Mb genome of A. richmondensis FRIK2901.
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32
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Castelle CJ, Banfield JF. Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell 2018. [DOI: 10.1016/j.cell.2018.02.016] [Citation(s) in RCA: 322] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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33
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West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res 2018; 28:569-580. [PMID: 29496730 PMCID: PMC5880246 DOI: 10.1101/gr.228429.117] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/27/2018] [Indexed: 11/24/2022]
Abstract
Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.
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Affiliation(s)
- Patrick T West
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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34
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Zhu MZ, Li N, Wang YT, Liu N, Guo MQ, Sun BQ, Zhou H, Liu L, Wu JL. Acid/Salt/pH Gradient Improved Resolution and Sensitivity in Proteomics Study Using 2D SCX-RP LC–MS. J Proteome Res 2017; 16:3470-3475. [DOI: 10.1021/acs.jproteome.7b00443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ming-Zhi Zhu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Sino-Africa Joint
Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Na Li
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Yi-Tong Wang
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Ning Liu
- Central
Laboratory, Second Hospital of Jilin University, Changchun, China
| | - Ming-Quan Guo
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Chinese Academy of Sciences, Sino-Africa Joint
Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Bao-qing Sun
- State
Key Laboratory of Respiratory Disease, National Clinical Center for
Respiratory Diseases, Guangzhou Institute of Respiratory Diseases,
First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Hua Zhou
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Liang Liu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
| | - Jian-Lin Wu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Macao, China
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35
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Niu C, Payne GA, Woloshuk CP. Involvement of FST1 from Fusarium verticillioides in virulence and transport of inositol. MOLECULAR PLANT PATHOLOGY 2017; 18:695-707. [PMID: 27195938 PMCID: PMC6638204 DOI: 10.1111/mpp.12430] [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: 04/18/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 06/05/2023]
Abstract
Fumonisin B1 (FB1), a polyketide mycotoxin produced by Fusarium verticillioides during the colonization of maize kernels, is detrimental to human and animal health. FST1 encodes a putative protein with 12 transmembrane domains; however, its function remains unknown. The FST1 gene is highly expressed by the fungus in the endosperm of maize kernels compared with the levels of expression in germ tissues. Previous research has shown that FST1 affects FB1 production, virulence, hydrogen peroxide resistance, hydrophobicity and macroconidia production. Here, we examine the phylogeny of FST1, its expression in a Saccharomyces cerevisiae strain lacking a functional myo-inositol transporter (ITR1) and the effect of amino acid changes in the central loop and C-terminus regions of FST1 on functionality. The results indicate that expression of FST1 in an ITR1 mutant strain restores growth on myo-inositol medium to wild-type levels and restores the inhibitory effects of FB1, suggesting that FST1 can transport both myo-inositol and FB1 into yeast cells. Our results with engineered FST1 also indicate that amino acids in the central loop and C-terminus regions are important for FST1 functionality in both S. cerevisiae and F. verticillioides. Overall, this research has established the first characterized inositol transporter in filamentous fungi and has advanced our knowledge about the global regulatory functions of FST1.
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Affiliation(s)
- Chenxing Niu
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIN47907‐2054USA
| | - Gary A. Payne
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695‐7567USA
| | - Charles P. Woloshuk
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIN47907‐2054USA
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Zhang X, Liu X, Liang Y, Xiao Y, Ma L, Guo X, Miao B, Liu H, Peng D, Huang W, Yin H. Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps. Front Microbiol 2017; 8:790. [PMID: 28529505 PMCID: PMC5418355 DOI: 10.3389/fmicb.2017.00790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
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Cárdenas JP, Quatrini R, Holmes DS. Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review. Res Microbiol 2016; 167:529-38. [PMID: 27394987 DOI: 10.1016/j.resmic.2016.06.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 12/19/2022]
Abstract
High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed.
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Affiliation(s)
| | | | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
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