Evidence for a mutualistic relationship between the cyanobacteria Nostoc and fungi Aspergilli in different environments

Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion

Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.

A thallus-forming N-fixing fungus-cyanobacterium symbiosis from subtropical forests

Fungi engage in diverse symbiotic relationships with phototrophs. Lichens, symbiotic complexes involving fungi and either cyanobacteria, green algae, or both, have fungi forming the external layer and much of the interior. We found an erect thallus resembling a lichen yet with an unexpected thallus structure composed of interwoven cyanobacterial filaments with numerous fungal hyphae inserted within individual cyanobacterial sheaths, contrasting with typical lichen structure. Phylogenetics identified the fungus as a previously undescribed species, Serendipita cyanobacteriicola, closely related to endophytes, and the cyanobacterium belongs to the family Coleofasciculaceae, representing a genus and species not yet classified, Symbiothallus taiwanensis. These thalli exhibit nitrogen-fixing activity similar to mosses but lower than cyanolichens. Both symbiotic partners are distinct from known lichen-forming symbionts, uncovering a phylogenetically and morphologically unprecedented thallus-forming fungus-cyanobacterium symbiosis. We propose the name "phyllosymbia" for these thalli to underscore their unique symbiotic nature and leaf-like appearance. This finding marks a previously unknown instance of fungi solely residing within structures generated by cyanobacteria.

Mixed and membrane-separated culturing of synthetic cyanobacteria-yeast consortia reveals metabolic cross-talk mimicking natural cyanolichens

Metabolite exchange mediates crucial interactions in microbial communities, significantly impacting global carbon and nitrogen cycling. Understanding these chemically-mediated interactions is essential for elucidating natural community functions and developing engineered synthetic communities. This study investigated membrane-separated bioreactors (mBRs) as a novel tool to identify transient metabolites and their producers/consumers in mixed microbial communities. We compared three co-culture methods (direct mixed, 2-chamber mBR, and 3-chamber mBR) to grow a synthetic binary community of the cyanobacterium Synechococcus elongatus PCC 7942 and the fungus Rhodotorula toruloides NBRC 0880, as well as axenic S. elongatus. Despite not being natural lichen constituents, these organisms exhibited interactions resembling those in cyanolichens. S. elongatus fixed CO2 into sugars as the primary shared metabolite, while R. toruloides secreted various biochemicals, predominantly sugar alcohols, mirroring the metabolite exchange observed in natural lichens. The mBR systems successfully captured metabolite gradients and revealed rapidly consumed compounds, including TCA cycle intermediates and amino acids. Our approach demonstrated that the 2-chamber mBR optimally balanced metabolite exchange and growth dynamics. This study provides insights into cross-species metabolic interactions and presents a valuable tool for investigating and engineering synthetic microbial communities with potential applications in biotechnology and environmental science.

Cyanobacteria-Fungi Co-Cultures: Which Partner Contributes to Antifungal Activity?

Cyanobacteria synthesize secondary metabolites with antifungal activity, making them potential biopesticide agents for sustainable, eco-friendly agriculture. Programmes to identify Cyanobacterial strains with effective bioactivity generally screen strains maintained in culture collections. These strains are often monoclonal but non-axenic and this may potentially influence the bioactivity of the generated biomass. The present study investigated in vitro antifungal activity of Nostoc muscorum MACC-189 and N. linckia MACC-612 strains co-isolated with fungal co-partners and maintained in the Mosonmagyaróvár Algal Culture Collection (MACC). The fungal co-partners were isolated from the Cyanobacterial stock cultures and identified as Purpureocillium lilacinum and Sarocladium sp., respectively. The cultures were tested against seven phytopathogens. The phytopathogenic fungi were grown on potato dextrose agar plates and suspension cultures of the Cyanobacteria-fungi and isolated fungal co-partners were placed in the centre of the plate. Antifungal effects were assessed semi-quantitatively after 10 days of incubation. The Cyanobacteria-fungal co-cultures had antifungal activity against Monilinia fructigena and Aspergillus sp. with the N. muscorum/P. lilacinum culture being the most effective. The fungal isolates inhibited M. fructigena with P. lilacinum having a dose-dependent response but did not inhibit Aspergillus sp. This suggested that the antifungal effect of the Cyanobacterial cultures on M. fructigena was due to the fungal partner rather than the cyanobacterium while the antifungal effect on Aspergillus sp. was due to the cyanobacterium partner. As it was not possible to maintain living axenic N. muscorum and N. linckia cultures, this could not be conclusively confirmed. These results highlight the importance of either using axenic cultures or identifying the co-isolates when testing Cyanobacteria cultures for antifungal bioactivity.

Machine learning predicts the growth of cyanobacterial genera in river systems and reveals their different environmental responses

Cyanobacterial blooms are a common and serious problem in global freshwater environments. However, the response mechanisms of various cyanobacterial genera to multiple nutrients and pollutants, as well as the factors driving their competitive dominance, remain unclear or controversial. The relative abundance and cell density of two dominant cyanobacterial genera (i.e., Cyanobium and Microcystis) in river ecosystems along a gradient of anthropogenic disturbance were predicted by random forest with post-interpretability based on physicochemical indices. Results showed that the optimized predictions all reached strong fitting with R2 > 0.75, and conventional water quality indices played a dominant role. One-dimensional and two-dimensional partial dependence plot (PDP) revealed that the responses of Cyanobium and Microcystis to nutrients and temperature were similar, but they showed differences in preferrable nutrient utilization and response to pollutants. Further prediction and PDP for the ratio of Cyanobium and Microcystis unveiled that their distinct responses to PAHs and SPAHs were crucial drivers for their competitive dominance over each other. This study presents a new way for analyzing the response of cyanobacterial genera to multiple environmental factors and their dominance relationships by interpretable machine learning, which is suitable for the identification and interpretation of high-dimensional nonlinear ecosystems with complex interactions.

Erythromycin mediates co-flocculation between cyanobacterium Synechocystis sp. PCC 6803 and filamentous fungi in liquid cultivation without organic compounds

Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. The fungi in the co-flocculated biomass were isolated and found to consist of five species with the filamentous Purpureocillium lilacinum and Aspergillus protuberus making up 71% of the overall fungal population. The optimal co-cultivation for flocculation was an initial 5 mg (fresh weight) of fungi, an initial cell density of Synechocystis of 0.2 OD730, 10 µM EM, and 14 days of cultivation in 100 mL of BG11 medium with no organic compound. This yielded 248 ± 28 mg/L of the Synechocystis-fungi flocculated biomass from 560 ± 35 mg/L of total biomass, a 44 ± 2% biomass flocculation efficiency. Furthermore, the EM treated Synechocystis cells in the Synechocystis-fungi flocculate had a normal cell color and morphology, while those in the axenic suspension exhibited strong chlorosis. Thus, the occurrence of the Synechocystis-fungi flocculation was mediated by EM, and the co-flocculation with the fungi protected Synechocystis against the development of chlorosis. Transcriptomic analysis suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. The CuSO4 stress can also mediate Synechocystis-fungi flocculation but at a lower flocculation efficiency than that caused by EM. The EM treatment may be applied in the co-culture between other cyanobacteria and fungi to mediate cell bio-flocculation.

Fungal symbionts impact cyanobacterial biofilm durability and photosynthetic efficiency

Cyanobacteria contribute to over 25% of the world's net primary photosynthetic production and are pivotal in mitigating greenhouse gas emissions.1 This study unveils a previously unobserved symbiotic relationship between benthic cyanobacteria and fungi that have also adapted to life as a plant endophyte. The interaction suggests an initial phase of lichenization. We isolated Leptolyngbya frigida from the Naracauli stream, which emanates from abandoned Zn industrial waste in Sardinia. Seasonally, L. frigida participates in a biomineralization processes, mitigating the Zn transfer to rivers and, subsequently, the sea.2,3,4L. frigida is a benthic cyanobacterium that establishes a biofilm on the stream bed. Notably, the area predominantly features Juncus acutus. From these roots, endophytic fungi were predominantly isolated as Clonostachys rosea, a fungus recognized for its biocontrol capabilities against plant pathogens. An intriguing observation was made when L. frigida was cultured with C. rosea on a low-carbohydrate agar medium: the fungal mycelium transformed into wall-less forms, a phenomenon not documented previously. In liquid environments, the resulting biofilm first settled at the container's bottom. Even upon rising to the surface, this biofilm remained pigment rich. Concurrently, a secondary biofilm began its formation at the bottom. These fungal-integrated biofilms displayed enhanced resilience and superior photosynthetic performance compared to those without fungal presence. Moreover, the symbiotic relationship significantly amplified O2 emission and CO2 sequestration by the biofilm.

Synthetic Light-Driven Consortia for Carbon-Negative Biosynthesis

Synthetic light-driven consortia composed of phototrophs and heterotrophs have attracted increasing attention owing to their potential to be used in sustainable biotechnology. In recent years, synthetic phototrophic consortia have been used to produce bulk chemicals, biofuels, and other valuable bioproducts. In addition, autotrophic-heterotrophic symbiosis systems have potential applications in wastewater treatment, bioremediation, and as a method for phytoplankton bloom control. Here, we discuss progress made on the biosynthesis of phototrophic microbial consortia. In addition, strategies for optimizing the synthetic light-driven consortia are summarized. Moreover, we highlight current challenges and future research directions for the development of robust and controllable synthetic light-driven consortia.

Transcriptomics Reveals the Effect of Strain Interactions on the Growth of A. Oryzae and Z. Rouxii

The microbial community structure in traditional fermented foods is quite complex, making the relationship between strains unclear. In this regard, the co-culture system can simulate microbial interactions during food fermentation and reveal the morphological changes, metabolic processes, and gene expression of microbial communities. The present study sought to investigate the effects of microbial interactions on the growth of Aspergillus oryzae and Zygosaccharomyces rouxii through omics. After co-cultivation, the pH value and dry weight were consistent with the pure culture of Z. rouxii. Additionally, the consumption of reducing sugar decreased, and the enzymatic activity increased compared with the pure culture of fungus. The analysis of volatile organic compounds (VOCs) and transcriptomics showed that co-culture significantly promoted the effect on Z. rouxii. A total of 6 different VOCs and 2202 differentially expressed genes were identified in the pure and co-culture of Z. rouxii. The differentially expressed genes were mainly related to the endonucleolytic cleavage of rRNA, ribosome biogenesis in eukaryotes, and RNA polymerase metabolic pathways. The study results will provide insights into the effect of microbial interactions on the growth of A. oryzae and Z. rouxii.

A rapid and simplified method for evaluating the performance of fungi-algae pellets: A hierarchical analysis model

Microbial pellets technology has undergone extensive research recently and has increasingly matured, showing significant promise. However, the performance of microbial pellets cannot be predicted quickly by the current evaluating methods because they are complicated to operate, take a long time, and pose a risk to the environment. In this study, a representative microbial pellet, fungi-algae pellet, was selected as the research object. Eight evaluation parameters and four evaluation indices were chosen to construct the performance evaluation system of the fungal-algal pellets using the analytic hierarchy process (AHP) and weighting method. Combining the correlation analysis and expert opinion, we found that among the eight parameters selected, the adsorption saturation rate of mycelial pellets on algae had the most significant influence weight on the performance of fungi-algae pellet, followed by algal culture time and fungal incubation time. This research proposes and validates the Performance Evaluation Value (PEV) of fungi-algae pellet and its calculation method. We also discuss the effectiveness of this new evaluation system in saving time, cost, and emission reductions. The results of this paper enable the rapid evaluation of fungi-algae pellets and promote the better development of fungi-algae pellets technology and even other multi-microbial symbiotic pellet technologies.

Incorporating Microbial Species Interaction in Management of Freshwater Toxic Cyanobacteria: A Systems Science Challenge

Water resources are critically important, but also pose risks of exposure to toxic and pathogenic microbes. Increasingly, a concern is toxic cyanobacteria, which have been linked to the death and disease of humans, domesticated animals, and wildlife in freshwater systems worldwide. Management approaches successful at reducing cyanobacterial abundance and toxin production have tended to be short-term solutions applied on small scales (e.g., algaecide application) or solutions that entail difficult multifaceted investments (e.g., modification of landscape and land use to reduce nutrient inputs). However, implementation of these approaches can be undermined by microbial species interactions that (a) provide toxic cyanobacteria with protection against the method of control or (b) permit toxic cyanobacteria to be replaced by other significant microbial threats. Understanding these interactions is necessary to avoid such scenarios and can provide a framework for novel strategies to enhance freshwater resource management via systems science (e.g., pairing existing physical and chemical approaches against cyanobacteria with ecological strategies such as manipulation of natural enemies, targeting of facilitators, and reduction of benthic occupancy and recruitment). Here, we review pertinent examples of the interactions and highlight potential applications of what is known.

New Strain of Cyphellophora olivacea Exhibits Striking Tolerance to Sodium Bicarbonate

The cyanobacterium strain Synechococcus cedrorum SAG 88.79 stock culture has fungal contamination stated by the Sammlung von Algenkulturen der Universität Göttingen itself. In this recent work, this particular fungal strain was isolated, identified, and morphologically characterised. The fungal strain AGSC12 belongs to the species Cyphellophora olivacea, with respect to the sequence similarity, phylogeny, and morphology of the strain. Colony morphology and growth capability were examined on SMA, EMMA, PDA, MEA, YEA, and YPA plates. Growth of the colonies was the most successful on YPA plates, followed by PDA and MEA containing plates. Surprisingly, the AGSC12 strain showed extreme tolerance to NaHCO3, albeit it, is is considered a general fungistatic compound. Moreover, positive association between the AGSC12 and SAG 88.79 strains was revealed, as the SAG 88.79 strain always attained higher cell density in co-cultures with the fungus than in mono-cultures. Besides, a taxonomic note on the SAG 88.79 strain itself was also stated.

Mechanism of enhanced production of triterpenoids in algal-fungal consortium

Chlorella pyrenoidosa-Ganoderma lucidum symbiotic systems were constructed. The mechanism of enhanced production of triterpenoids in algal-fungal consortium by comparing the contents of triterpenoids in individual fungal systems and algal-fungal consortium systems was investigated. The production of triterpenoids in C. pyrenoidosa-G. lucidum consortium increased significantly (P < 0.05). The categories and relative abundances of metabolites in the individual systems and algal-fungal systems were measured and analyzed by metabonomic tests. There were 57 significant different metabolites (VIP > 1 and P < 0.05) including 12 downregulated metabolites and 45 upregulated metabolites were obtained. The significant enriched metabolic pathways (VIP > 1 and P < 0.05) of citrate cycle (TCA cycle), tyrosine metabolism, glycolysis, and terpenoid backbone biosynthesis in algal-fungal consortium were obtained. The relative abundances of important precursors of triterpenoids including mevalonic acid, lanosterol, and hydroquinone were 1.4 times, 1.7 times, and 2 times, respectively, in algal-fungal consortium than that in the individual fungal systems. The presence of C. pyrenoidosa in algal-fungal consortium promoted the biosynthesis of triterpenoids in G. lucidum.

Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing

The application of microbial co-cultures is now recognized in the fields of biotechnology, ecology, and medicine. Understanding the biological interactions that govern the association of microorganisms would shape the way in which artificial/synthetic co-cultures or consortia are developed. The ability to accurately predict and control cell-to-cell interactions fully would be a significant enabler in synthetic biology. Co-culturing method development holds the key to strategically engineer environments in which the co-cultured microorganism can be monitored. Various approaches have been employed which aim to emulate the natural environment and gain access to the untapped natural resources emerging from cross-talk between partners. Amongst these methods are the use of a communal liquid medium for growth, use of a solid-liquid interface, membrane separation, spatial separation, and use of microfluidics systems. Maximizing the information content of interactions monitored is one of the major challenges that needs to be addressed by these designs. This review critically evaluates the significance and drawbacks of the co-culturing approaches used to this day in biotechnological applications, relevant to biomanufacturing. It is recommended that experimental results for a co-cultured species should be validated with different co-culture approaches due to variations in interactions that could exist as a result of the culturing method selected.

Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives

Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.