Periodic Reporting for period 5 - MYCO-CARB (FUNCTIONAL BIOLOGY AND ECOLOGY OF PLANKTONIC MARINE FUNGI – Revealing the mechanistic basis of the roles of mycoplankton in the marine carbon cycle)
Okres sprawozdawczy: 2024-05-01 do 2024-10-31
Marine fungi have been largely ignored compared to other microbial groups, especially the roles that they fulfil in marine ecosystems, representing a major knowledge gap in our understanding of marine environment (Cunliffe 2023 Environ Microbiol). MYCO-CARB addressed this knowledge gap through an innovative programme of research. Fungi were assessed across a range of ecosystems; from surface coastal waters to the deep open ocean. Innovative approaches established the impact of fungal saprotrophs on the carbon cycle. A culture collection of marine saprotrophic fungi was developed to produce ecologically-relevant model fungi. Complementary culture-dependent and -independent systems biology methodologies determined the underpinning biological machinery of saprotrophic fungi. MYCO-CARB opened the marine fungal ‘black box’, revealing fungal functional biology and ecology, and establishing their roles in the carbon cycle.
MYCO-CARB sampled a range of marine ecosystems, including in the Atlantic Ocean and at the long term coastal marine observatories off Plymouth (UK). We also undertook a year-long seasonal transect from the coastal marine sites off Plymouth along an adjacent estuarine – freshwater gradient. Marine ecosystem sampling was supplemented with additional samples gifted from collaborators and other cruises including from polar regions and the Southern Ocean, and a unique preexisting eDNA time-series. DNA and RNA based assessment of marine fungal diversity was successful, including development and optimization of metabarcoding approaches for marine fungi.
We developed an innovative approach to study active saprotrophic fungi associated with marine particles. Individual organic particles were isolated from seawater, assessed via microscopy and subsequently used for single particle RNA extraction. From the single particle RNA, we were able to determine the activity of attached saprotrophic fungi. We also undertook alternative strategies to explore the potential for active fungal saprotrophy in the open ocean using high volume bulk in situ filtration and subsequent RNA-based assessment of fungal activity.
Over 500 strains have been successfully isolated from seawater, sediments and seaweeds, including from the open Atlantic Ocean, Antarctic and Arctic. All strains have been identified and are maintained cryopreserved at the Marine Biological Association. Strains from the collection have been used to explore the biology of marine fungi (summarised below) and are a resource for future research.
We explored the fundamental biology of saprotrophic marine fungi, including determining substrate ranges and responses to experimental variables across a range of marine fungal isolates. On selected models, we have shown how marine fungi are adapted. Selected models from the culture collection have undergone genome sequencing. We also worked on saprotrophic chytrid fungi, including determining interaction with particulate organic matter, aspects of the chytrid cell cycle and role of chytrids in particle microbiome interaction.
We developed an innovative approach to study active saprotrophic fungi associated with marine particles. Individual organic particles were isolated from seawater, assessed via microscopy and subsequently used for single particle RNA extraction. From the single particle RNA, we were able to determine the activity of attached saprotrophic fungi. We also undertook alternative strategies to explore the potential for active fungal saprotrophy in the open ocean using high volume bulk in situ filtration and subsequent RNA-based assessment of fungal activity.
Over 500 strains have been successfully isolated from seawater, sediments and seaweeds, including from the open Atlantic Ocean, Antarctic and Arctic. All strains have been identified and are maintained cryopreserved at the Marine Biological Association. Strains from the collection have been used to explore the biology of marine fungi (summarised below) and are a resource for future research.
We explored the fundamental biology of saprotrophic marine fungi, including determining substrate ranges and responses to experimental variables across a range of marine fungal isolates. On selected models, we have shown how marine fungi are adapted. Selected models from the culture collection have undergone genome sequencing. We also worked on saprotrophic chytrid fungi, including determining interaction with particulate organic matter, aspects of the chytrid cell cycle and role of chytrids in particle microbiome interaction.
If and how marine fungi show long-term intra- and inter-annual diversity patterns was previously unknown, preventing a comprehensive understanding of marine fungal ecology. We produced a unique 17-year eDNA time-series to determine long-term marine fungal diversity patterns. Our work has shown (for the first time) that marine fungal community structure progresses at seasonal and monthly scales, and that communities restructure every 52-weeks suggesting long-term stability (Chrismas et al 2023 Proc. R. Soc. B). Our work on marine fungal diversity forms the basis for better understanding the ecology of marine fungi and how they fit in the structure of the wider coastal marine ecosystem.
We explored the likelihood that fungi in the open ocean are biologically analogous to their coastal counterparts, including performing saprotrophy and degrading complex organic substrates using carbohydrate-active enzymes (CAZymes). We investigated the prevalence of transcribed fungal CAZyme genes and revealed an abundance of glycoside hydrolases in the open ocean, including high numbers that act upon cellulose (Chrismas & Cunliffe 2020 ISME Journal). Our work demonstrated that fungi are active saprotrophs in the open ocean and paves the way for future research into the roles of marine fungi in oceanic carbon cycling.
The establishment of the Marine Fungi Culture Collection is significant achievement. Research outputs already from the culture collection include assessing macromolecular composition and substrate range across major marine fungi cell types (Thomas et al 2022 FEMS Microbes), a genome sequence of the marine yeast Metschnikowia zobellii (one of the few marine fungal genomes available) (Cunliffe at al 2023 Wellcome Open Research) and characterising cell morphological plasticity in response to substrate availability in fungi from the open ocean (Diver et al Mycologia; Diver at al FEMS Micro Eco). The Marine Fungi Culture Collection will act as a legacy from the project and a future research resource.
The chytrids are an early-diverging lineage that are significant aquatic saprotrophs, yet their biology has received relatively little attention (Laundon & Cunliffe 2021 Front. Fungal Biol.). The work on chytrids was unexpected and happened in response to limitations caused by the COVID crisis. We determine saprotrophic chytrid biology using a range of cutting-edge approaches. We showed that chytrid cell development resembles development in multicellular fungi and is adaptive to carbon availability (Laundon et al 2020 Proc. R. Soc. B). We produced the first bioatlas of the chytrid cell cycle, revealing the key transitions in their development (Laundon et al 2022 eLife). We also showed that chytrids act as ecosystem facilitators through saprotrophic feeding by producing ‘public goods’ from carbon degradation that impact bacterial microbiomes (Roberts et al 2020 Biology Letters).
Lichens are exemplar symbioses based upon organic carbon exchange. Our work on marine lichens was unexpected and happened in response to limitations caused by the COVID crisis. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores (Chrismas et al 2023 The Lichenologist). We discovered that L. pygmaea has a complex photobiont community (Chrismas et al 2021 JMBA). We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont to investigate carbon exchange. We discovered saprotrophic extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea, a process not typically associated with lichens (Chrismas et al 2024 New Phytologist).
We explored the likelihood that fungi in the open ocean are biologically analogous to their coastal counterparts, including performing saprotrophy and degrading complex organic substrates using carbohydrate-active enzymes (CAZymes). We investigated the prevalence of transcribed fungal CAZyme genes and revealed an abundance of glycoside hydrolases in the open ocean, including high numbers that act upon cellulose (Chrismas & Cunliffe 2020 ISME Journal). Our work demonstrated that fungi are active saprotrophs in the open ocean and paves the way for future research into the roles of marine fungi in oceanic carbon cycling.
The establishment of the Marine Fungi Culture Collection is significant achievement. Research outputs already from the culture collection include assessing macromolecular composition and substrate range across major marine fungi cell types (Thomas et al 2022 FEMS Microbes), a genome sequence of the marine yeast Metschnikowia zobellii (one of the few marine fungal genomes available) (Cunliffe at al 2023 Wellcome Open Research) and characterising cell morphological plasticity in response to substrate availability in fungi from the open ocean (Diver et al Mycologia; Diver at al FEMS Micro Eco). The Marine Fungi Culture Collection will act as a legacy from the project and a future research resource.
The chytrids are an early-diverging lineage that are significant aquatic saprotrophs, yet their biology has received relatively little attention (Laundon & Cunliffe 2021 Front. Fungal Biol.). The work on chytrids was unexpected and happened in response to limitations caused by the COVID crisis. We determine saprotrophic chytrid biology using a range of cutting-edge approaches. We showed that chytrid cell development resembles development in multicellular fungi and is adaptive to carbon availability (Laundon et al 2020 Proc. R. Soc. B). We produced the first bioatlas of the chytrid cell cycle, revealing the key transitions in their development (Laundon et al 2022 eLife). We also showed that chytrids act as ecosystem facilitators through saprotrophic feeding by producing ‘public goods’ from carbon degradation that impact bacterial microbiomes (Roberts et al 2020 Biology Letters).
Lichens are exemplar symbioses based upon organic carbon exchange. Our work on marine lichens was unexpected and happened in response to limitations caused by the COVID crisis. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores (Chrismas et al 2023 The Lichenologist). We discovered that L. pygmaea has a complex photobiont community (Chrismas et al 2021 JMBA). We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont to investigate carbon exchange. We discovered saprotrophic extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea, a process not typically associated with lichens (Chrismas et al 2024 New Phytologist).