Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research

Shaw, Claire; Brooke, Charles; Hawley, Erik R.; Connolly, Morgan P; Garcia, Javier A.; Harmon-Smith, Miranda; Shapiro, Nicole; Barton, Michael D.; Tringe, Susannah G.; Rio, Tijana Glavina del; Culley, David E.; Castenholz, Richard W.; Hess, Matthias

doi:10.3389/fmicb.2020.572131

Cited by 4 publications

(4 citation statements)

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“…The figure was created by the authors using Biorender.com. 10.3389/fmicb.2023.1167718 Frontiers in Microbiology 04 frontiersin.org the natural environment (Ferrari et al, 2008;Benaud et al, 2022), co-culture approaches (Nichols et al, 2008;Shaw et al, 2020), and in situ cultivation using diffusion-based devices (Kaeberlein et al, 2002;Nichols et al, 2010;Pope et al, 2022) could overcome challenges in mimicking the natural environment and isolating hard-to-culture microbes (Figure 1; Table 1).…”

Section: Moving Forward: Advances In Microbial Cultivationmentioning

confidence: 99%

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

et al. 2023

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More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth’s microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed “microbial dark matter.” Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.

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Section: Moving Forward: Advances In Microbial Cultivationmentioning

confidence: 99%

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

et al. 2023

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“…The co-culture of photosynthetic extremophilic microorganisms isolated from extreme environments opens up new possibilities for applied research, especially in industry-related applications. Here, costly effective strategies have demonstrated enhanced production yields and a reduction in contamination risks, which can prove economically advantageous [103]. To our knowledge, few studies have focused on the analysis of silent genes or chemical characterization of unknown molecules through co-cultures of extremophilic microorganisms, including the promising I. galbana.…”

Section: Swine Wastewater Treatmentmentioning

confidence: 99%

Insights into Co-Cultivation of Photosynthetic Microorganisms for Novel Molecule Discovery and Enhanced Production of Specialized Metabolites

Rojas-Villalta,

Gómez-Espinoza,

Murillo-Vega

et al. 2023

Fermentation

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Meso- and extremophilic microalgae and cyanobacteria have a wide range of biotechnological applications. However, the industrial demand for bioactive molecules and the redundancy of these molecules has resulted in a need for new methodologies for enhanced production and the discovery of specialized metabolites. Co-cultivation has been established as a promising approach to addressing these challenges. In this context, this work aimed to describe the state of the art of the co-cultivation method involving meso- and extremophilic photosynthetic microorganisms, as well as discuss the advantages, challenges, and limitations of this approach. Co-culture is defined as an ecology-driven method in which various symbiotic interactions involving cyanobacteria and microalgae can be used to explore new compounds and enhanced production. Promising results regarding new bioactive metabolite expression and increased production through co-cultivation-based research support that idea. Also, the metabolic diversity and evolutionary adaptations of photosynthetic microorganisms to thrive in extreme environments could improve the efficiency of co-cultivation by allowing the implementation of these microorganisms. However, the complexity of ecological interactions and lack of standardization for co-cultivation protocols are obstacles to its success and scientific validation. Further research in symbiotic interplays using -omics and genetic engineering, and predictive experimental designs for co-cultures are needed to overcome these limitations.

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“…Heterotrophic bacteria associated with cyanobacteria are more often species with flexible universal metabolism, most of the strains belong to Proteobacteria . Highthroughput sequencing allows a detailed inventory of cyanobacteria-heterotrophic bacteria associations without cultivating (Shaw et al, 2020). For example, Nostoc macrocolony communities from lakes have been found to repeat partly a plankton-lake motif, but members of Shingomonadaceae, Rhodobacteriaceae, Comamonadaceae become distinctive .…”

Section: Introductionmentioning

confidence: 99%

“…Ассоциированные с цианобактериями гетеротрофные бактерии чаще являются культивируемыми видами с пластичным универсальным метаболизмом, большая часть штаммов принадлежит Proteobacteria . Высокопроизводительное секвенирование дает возможность провести детальную инвентаризацию ассоциаций цианобактерий с гетеротрофами без получения штаммов бактерий (Shaw et al, 2020). Например, выявлено, что сообщества макроколоний цианобактерии Nostoc из озерной прибрежной зоны в целом похожи на планктонные, но в них выше представ-ленность бактерий семейств Shingomonadaceae, Rhodobacteriaceae, Comamonadaceae .…”

Section: Introductionunclassified

Bacterial diversity and metabolism in microbial consortium of non-axenic culture Tychonema sp. BBK16

Krasnopeev A.Yu.,

Tikhonova I.V.,

Podlesnaya G.V.

et al. 2023

LFWB

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We performed high-throughput sequencing of microbial community with cyanobacterium Tychonema sp. BBK16 and heterotrophic bacteria in vitro. Representatives of the phylum Pseudomonadota/Proteobacteria, the bacteria Hydrogenophaga, Sphingomonas, Paucibacter, Aminobacter, Devosia, Tahibacter, and Bosea dominate and coexist with the cyanobacterium for a long period of cultivation. It was found that this cyanobacterium is an edificator of this community providing the microbiome with organic matter. Metabolic features of heterotrophic bacteria based on reconstructed genomes are presented. The main processes of carbon and nitrogen metabolism in the biofilm are carbohydrate and amino acid metabolism, as well as processes regulating the relationships between members of this consortium. Hydrogenophaga sp. and Tychonema sp. BBK16 show carbon autotrophy due to the Calvin–Benson–Bassham (СВВ) cycle, while Sphingomonas sp. due to the glyoxylate pathway of metabolism. The biofilm also contains the anoxygenic photoheterotroph Bosea sp. using light energy to transform organic matter. Aminobacter sp. is an active degrader of complex organics, which possesses methylotrophy and supplies hydrogen for oxidation by Hydrogenophaga sp., Paucibacter sp., also supplies hydrogen for this community. Sphingomonas, Tychonema and Paucibacter release phosphate from organic compounds providing phosphorus to this consortium.

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Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research

Cited by 4 publications

References 73 publications

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

Insights into Co-Cultivation of Photosynthetic Microorganisms for Novel Molecule Discovery and Enhanced Production of Specialized Metabolites

Bacterial diversity and metabolism in microbial consortium of non-axenic culture Tychonema sp. BBK16

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