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Jung P, Briegel-Williams L, Büdel B, Schultz M, Nürnberg DJ, Grube M, D’Agostino PM, Kaštovský J, Mareš J, Lorenz M, González MLG, Forno MD, Westberg M, Chrismas N, Pietrasiak N, Whelan P, Dvořák P, Košuthová A, Gkelis S, Bauersachs T, Schiefelbein U, Giao VTP, Lakatos M. The underestimated fraction: diversity, challenges and novel insights into unicellular cyanobionts of lichens. ISME COMMUNICATIONS 2024; 4:ycae069. [PMID: 38966402 PMCID: PMC11222712 DOI: 10.1093/ismeco/ycae069] [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: 12/13/2023] [Revised: 04/10/2024] [Accepted: 05/03/2024] [Indexed: 07/06/2024]
Abstract
Lichens are remarkable and classic examples of symbiotic organisms that have fascinated scientists for centuries. Yet, it has only been for a couple of decades that significant advances have focused on the diversity of their green algal and/or cyanobacterial photobionts. Cyanolichens, which contain cyanobacteria as their photosynthetic partner, include up to 10% of all known lichens and, as such, studies on their cyanobionts are much rarer compared to their green algal counterparts. For the unicellular cyanobionts, i.e. cyanobacteria that do not form filaments, these studies are even scarcer. Nonetheless, these currently include at least 10 different genera in the cosmopolitan lichen order Lichinales. An international consortium (International Network of CyanoBionts; INCb) will tackle this lack of knowledge. In this article, we discuss the status of current unicellular cyanobiont research, compare the taxonomic resolution of photobionts from cyanolichens with those of green algal lichens (chlorolichens), and give a roadmap of research on how to recondition the underestimated fraction of symbiotic unicellular cyanobacteria in lichens.
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Affiliation(s)
- Patrick Jung
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Laura Briegel-Williams
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Burkhard Büdel
- Rhineland-Palatinate Technical University Kaiserslautern Landau, Kaiserslautern, Germany
| | - Matthias Schultz
- Herbarium Hamburgense, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Dennis J Nürnberg
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin Germany
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Paul M D’Agostino
- Technical University Dresden, Chair of Technical Biochemistry, Dresden, Germany
| | - Jan Kaštovský
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jan Mareš
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Maike Lorenz
- University of Goettingen, SAG Goettingen, Goettingen, Germany
| | | | | | | | | | | | | | - Petr Dvořák
- Palacký University Olomouc, Olomouc, Czech Republic
| | | | - Spyros Gkelis
- Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Thorsten Bauersachs
- Institute of Organic Biogeochemistry in Geo-Systems, RWTH Aachen University, Aachen, Germany
| | | | | | - Michael Lakatos
- Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - INCb
- International Network for research on unicellular CyanoBionts from lichens
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Tagirdzhanova G, Scharnagl K, Yan X, Talbot NJ. Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses. Sci Rep 2023; 13:21285. [PMID: 38042930 PMCID: PMC10693582 DOI: 10.1038/s41598-023-48637-w] [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: 09/13/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023] Open
Abstract
Lichen symbiosis is centered around a relationship between a fungus and a photosynthetic microbe, usually a green alga. In addition to their main photosynthetic partner (the photobiont), lichen symbioses can contain additional algae present in low abundance. The biology of these algae and the way they interact with the rest of lichen symbionts remains largely unknown. Here we present the first genome sequence of a non-photobiont lichen-associated alga. Coccomyxa viridis was unexpectedly found in 12% of publicly available lichen metagenomes. With few exceptions, members of the Coccomyxa viridis clade occur in lichens as non-photobionts, potentially growing in thalli endophytically. The 45.7 Mbp genome of C. viridis was assembled into 18 near chromosome-level contigs, making it one of the most contiguous genomic assemblies for any lichen-associated algae. Comparing the C. viridis genome to its close relatives revealed the presence of traits associated with the lichen lifestyle. The genome of C. viridis provides a new resource for exploring the evolution of the lichen symbiosis, and how symbiotic lifestyles shaped evolution in green algae.
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Affiliation(s)
- Gulnara Tagirdzhanova
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Klara Scharnagl
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- University & Jepson Herbaria, University of California Berkeley, Valley Life Sciences Building, Berkeley, CA, 94720, USA
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
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Zuo YB, Han DY, Wang YY, Yang QX, Ren Q, Liu XZ, Wei XL. Fungal-Algal Association Drives Lichens' Mutualistic Symbiosis: A Case Study with Trebouxia-Related Lichens. PLANTS (BASEL, SWITZERLAND) 2023; 12:3172. [PMID: 37687418 PMCID: PMC10490544 DOI: 10.3390/plants12173172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Biotic and abiotic factors influence the formation of fungal-algal pairings in lichen symbiosis. However, the specific determinants of these associations, particularly when distantly related fungi are involved, remain poorly understood. In this study, we investigated the impact of different drivers on the association patterns between taxonomically diverse lichenized fungi and their trebouxioid symbiotic partners. We collected 200 samples from four biomes and identified 41 species of lichenized fungi, associating them with 16 species of trebouxioid green algae, of which 62% were previously unreported. The species identity of both the fungal and algal partners had the most significant effect on the outcome of the symbiosis, compared to abiotic factors like climatic variables and geographic distance. Some obviously specific associations were observed in the temperate zone; however, the nestedness value was lower in arid regions than in cold, polar, and temperate regions according to interaction network analysis. Cophylogenetic analyses revealed congruent phylogenies between trebouxioid algae and associated fungi, indicating a tendency to reject random associations. The main evolutionary mechanisms contributing to the observed phylogenetic patterns were "loss" and "failure to diverge" of the algal partners. This study broadens our knowledge of fungal-algal symbiotic patterns in view of Trebouxia-associated fungi.
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Affiliation(s)
| | | | | | | | | | - Xin-Zhan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin-Li Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Chong JWR, Khoo KS, Chew KW, Ting HY, Show PL. Trends in digital image processing of isolated microalgae by incorporating classification algorithm. Biotechnol Adv 2023; 63:108095. [PMID: 36608745 DOI: 10.1016/j.biotechadv.2023.108095] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 12/17/2022] [Accepted: 01/01/2023] [Indexed: 01/05/2023]
Abstract
Identification of microalgae species is of importance due to the uprising of harmful algae blooms affecting both the aquatic habitat and human health. Despite this occurence, microalgae have been identified as a green biomass and alternative source due to its promising bioactive compounds accumulation that play a significant role in many industrial applications. Recently, microalgae species identification has been conducted through DNA analysis and various microscopy techniques such as light, scanning electron, transmission electron, and atomic force -microscopy. The aforementioned procedures have encouraged researchers to consider alternate ways due to limitations such as costly validation, requiring skilled taxonomists, prolonged analysis, and low accuracy. This review highlights the potential innovations in digital microscopy with the incorporation of both hardware and software that can produce a reliable recognition, detection, enumeration, and real-time acquisition of microalgae species. Several steps such as image acquisition, processing, feature extraction, and selection are discussed, for the purpose of generating high image quality by removing unwanted artifacts and noise from the background. These steps of identification of microalgae species is performed by reliable image classification through machine learning as well as deep learning algorithms such as artificial neural networks, support vector machines, and convolutional neural networks. Overall, this review provides comprehensive insights into numerous possibilities of microalgae image identification, image pre-processing, and machine learning techniques to address the challenges in developing a robust digital classification tool for the future.
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Affiliation(s)
- Jun Wei Roy Chong
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan.
| | - Kit Wayne Chew
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
| | - Huong-Yong Ting
- Drone Research and Application Centre, University of Technology Sarawak, No.1, Jalan Universiti, 96000 Sibu, Sarawak, Malaysia
| | - Pau Loke Show
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia; Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai 602105, India.
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Chiva S, Moya P, Barreno E. Lichen phycobiomes as source of biodiversity for microalgae of the Stichococcus-like genera. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01223-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractThe term phycobiome was recently introduced to designate all the microalgae (primary or non-primary) associated with lichen symbioses. Abundant non-primary symbiotic microalgae are usually obtained from lichen isolations, confirming that thalli are a source of biodiversity and new species. In this study, microalgae were isolated from thalli of Buellia zoharyi, Ramalina farinacea and Parmotrema pseudotinctorum collected in the Iberian Peninsula and the Canary Islands. Excluding Trebouxia phycobionts, 17 strains similar to Stichococcus (Prasiola clade) were obtained. Molecular identification was carried out by nuclear ITS sequencing, and a phylogenetic tree was generated from these sequences, and grouping them into 4 clades: Diplosphaera chodatti, Diplosphaera sp.1. Deuterostichocuccus sp.1. and Tritostichococcus coniocybes. It is also noteworthy that Diplosphaera sp.1 was detected and isolated from three phylogenetically distant lichenized fungi (B. zoharyi, R. farinacea and P. pseudotinctorum), which were sampled in ecologically different localities, namely Tenerife, La Gomera and Castellón. These results reinforce the idea of the constant presence of certain microalgae associated with the lichen thalli which, despite not being the main primary photobiont, probably form part of the lichen’s phycobiomes.
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Adler L, Díaz-Ramos A, Mao Y, Pukacz KR, Fei C, McCormick AJ. New horizons for building pyrenoid-based CO2-concentrating mechanisms in plants to improve yields. PLANT PHYSIOLOGY 2022; 190:1609-1627. [PMID: 35961043 PMCID: PMC9614477 DOI: 10.1093/plphys/kiac373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 05/06/2023]
Abstract
Many photosynthetic species have evolved CO2-concentrating mechanisms (CCMs) to improve the efficiency of CO2 assimilation by Rubisco and reduce the negative impacts of photorespiration. However, the majority of plants (i.e. C3 plants) lack an active CCM. Thus, engineering a functional heterologous CCM into important C3 crops, such as rice (Oryza sativa) and wheat (Triticum aestivum), has become a key strategic ambition to enhance yield potential. Here, we review recent advances in our understanding of the pyrenoid-based CCM in the model green alga Chlamydomonas reinhardtii and engineering progress in C3 plants. We also discuss recent modeling work that has provided insights into the potential advantages of Rubisco condensation within the pyrenoid and the energetic costs of the Chlamydomonas CCM, which, together, will help to better guide future engineering approaches. Key findings include the potential benefits of Rubisco condensation for carboxylation efficiency and the need for a diffusional barrier around the pyrenoid matrix. We discuss a minimal set of components for the CCM to function and that active bicarbonate import into the chloroplast stroma may not be necessary for a functional pyrenoid-based CCM in planta. Thus, the roadmap for building a pyrenoid-based CCM into plant chloroplasts to enhance the efficiency of photosynthesis now appears clearer with new challenges and opportunities.
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Affiliation(s)
| | | | - Yuwei Mao
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krzysztof Robin Pukacz
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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Trebouxia lynnae sp. nov. (Former Trebouxia sp. TR9): Biology and Biogeography of an Epitome Lichen Symbiotic Microalga. BIOLOGY 2022; 11:biology11081196. [PMID: 36009823 PMCID: PMC9405249 DOI: 10.3390/biology11081196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/06/2022] [Indexed: 12/02/2022]
Abstract
Two microalgal species, Trebouxia jamesii and Trebouxia sp. TR9, were detected as the main photobionts coexisting in the thalli of the lichen Ramalina farinacea. Trebouxia sp. TR9 emerged as a new taxon in lichen symbioses and was successfully isolated and propagated in in vitro culture and thoroughly investigated. Several years of research have confirmed the taxon Trebouxia sp. TR9 to be a model/reference organism for studying mycobiont−photobiont association patterns in lichen symbioses. Trebouxia sp. TR9 is the first symbiotic, lichen-forming microalga for which an exhaustive characterization of cellular ultrastructure, physiological traits, genetic and genomic diversity is available. The cellular ultrastructure was studied by light, electron and confocal microscopy; physiological traits were studied as responses to different abiotic stresses. The genetic diversity was previously analyzed at both the nuclear and organelle levels by using chloroplast, mitochondrial, and nuclear genome data, and a multiplicity of phylogenetic analyses were carried out to study its intraspecific diversity at a biogeographical level and its specificity association patterns with the mycobiont. Here, Trebouxia sp. TR9 is formally described by applying an integrative taxonomic approach and is presented to science as Trebouxia lynnae, in honor of Lynn Margulis, who was the primary modern proponent for the significance of symbiosis in evolution. The complete set of analyses that were carried out for its characterization is provided.
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De Carolis R, Cometto A, Moya P, Barreno E, Grube M, Tretiach M, Leavitt SD, Muggia L. Photobiont Diversity in Lichen Symbioses From Extreme Environments. Front Microbiol 2022; 13:809804. [PMID: 35422771 PMCID: PMC9002315 DOI: 10.3389/fmicb.2022.809804] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/27/2022] [Indexed: 11/19/2022] Open
Abstract
Fungal–algal relationships—both across evolutionary and ecological scales—are finely modulated by the presence of the symbionts in the environments and by the degree of selectivity and specificity that either symbiont develop reciprocally. In lichens, the green algal genus Trebouxia Puymaly is one of the most frequently recovered chlorobionts. Trebouxia species-level lineages have been recognized on the basis of their morphological and phylogenetic diversity, while their ecological preferences and distribution are still only partially unknown. We selected two cosmopolitan species complexes of lichen-forming fungi as reference models, i.e., Rhizoplaca melanophthalma and Tephromela atra, to investigate the diversity of their associated Trebouxia spp. in montane habitats across their distributional range worldwide. The greatest diversity of Trebouxia species-level lineages was recovered in the altitudinal range 1,000–2,500 m a.s.l. A total of 10 distinct Trebouxia species-level lineages were found to associate with either mycobiont, for which new photobionts are reported. One previously unrecognized Trebouxia species-level lineage was identified and is here provisionally named Trebouxia “A52.” Analyses of cell morphology and ultrastructure were performed on axenically isolated strains to fully characterize the new Trebouxia “A52” and three other previously recognized lineages, i.e., Trebouxia “A02,” T. vagua “A04,” and T. vagua “A10,” which were successfully isolated in culture during this study. The species-level diversity of Trebouxia associating with the two lichen-forming fungi in extreme habitats helps elucidate the evolutionary pathways that this lichen photobiont genus traversed to occupy varied climatic and vegetative regimes.
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Affiliation(s)
| | - Agnese Cometto
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Patricia Moya
- Botánica, ICBIBE, Faculty of CC. Biológicas, Universitat de València, Valencia, Spain
| | - Eva Barreno
- Botánica, ICBIBE, Faculty of CC. Biológicas, Universitat de València, Valencia, Spain
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Steven D Leavitt
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
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