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Phototrophic Co-Cultures from Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research

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Phototrophic Co-Cultures from Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research UC Davis UC Davis Previously Published Works Title Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research. Permalink https://escholarship.org/uc/item/3pf804wf Authors Shaw, Claire Brooke, Charles Hawley, Erik et al. Publication Date 2020 DOI 10.3389/fmicb.2020.572131 Peer reviewed eScholarship.org Powered by the California Digital Library University of California fmicb-11-572131 November 2, 2020 Time: 17:31 # 1 ORIGINAL RESEARCH published: 06 November 2020 doi: 10.3389/fmicb.2020.572131 Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research Claire Shaw1, Charles Brooke1, Erik Hawley2, Morgan P. Connolly3, Javier A. Garcia4, Miranda Harmon-Smith5, Nicole Shapiro5, Michael Barton5, Susannah G. Tringe5, Tijana Glavina del Rio5, David E. Culley6, Richard Castenholz7 and Matthias Hess1* 1 Systems Microbiology and Natural Products Laboratory, University of California, Davis, Davis, CA, United States, 2 Bayer, Pittsburg, PA, United States, 3 Microbiology Graduate Group, University of California, Davis, Davis, CA, United States, Edited by: 4 Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of California, Davis, Davis, CA, Daniel Ducat, United States, 5 Department of Energy, Joint Genome Institute, Berkeley, CA, United States, 6 Greenlight Biosciences, Inc., Michigan State University, Medford, MA, United States, 7 Department of Biology, University of Oregon, Eugene, OR, United States United States Reviewed by: Ralf Steuer, Cyanobacteria are found in most illuminated environments and are key players in global Humboldt University of Berlin, carbon and nitrogen cycling. Although significant efforts have been made to advance Germany Alison Gail Smith, our understanding of this important phylum, still little is known about how members of University of Cambridge, the cyanobacteria affect and respond to changes in complex biological systems. This United Kingdom lack of knowledge is in part due to our dependence on pure cultures when determining *Correspondence: the metabolism and function of a microorganism. We took advantage of the Culture Matthias Hess [email protected] Collection of Microorganisms from Extreme Environments (CCMEE), a collection of more than 1,000 publicly available photosynthetic co-cultures maintained at the Pacific Specialty section: This article was submitted to Northwest National Laboratory, and assessed via 16S rRNA amplicon sequencing if Microbiotechnology, samples readily available from public culture collection could be used in the future a section of the journal to generate new insights into the role of microbial communities in global and local Frontiers in Microbiology carbon and nitrogen cycling. Results from this work support the existing notion that Received: 12 June 2020 Accepted: 13 October 2020 culture depositories in general hold the potential to advance fundamental and applied Published: 06 November 2020 research. Although it remains to be seen if co-cultures can be used at large scale to Citation: infer roles of individual organisms, samples that are publicly available from existing co- Shaw C, Brooke C, Hawley E, Connolly MP, Garcia JA, cultures depositories, such as the CCMEE, might be an economical starting point for Harmon-Smith M, Shapiro N, such studies. Access to archived biological samples, without the need for costly field Barton M, Tringe SG, work, might in some circumstances be one of the few remaining ways to advance Glavina del Rio T, Culley DE, Castenholz R and Hess M (2020) the field and to generate new insights into the biology of ecosystems that are not Phototrophic Co-cultures From easily accessible. The current COVID-19 pandemic, which makes sampling expeditions Extreme Environments: Community Structure and Potential Value almost impossible without putting the health of the participating scientists on the line, is for Fundamental and Applied a very timely example. Research. Front. Microbiol. 11:572131. Keywords: biodiversity, biotechnology, culture collection, cyanobacteria, extreme environments, fundamental doi: 10.3389/fmicb.2020.572131 research, microbial ecology and diversity Frontiers in Microbiology| www.frontiersin.org 1 November 2020| Volume 11| Article 572131 fmicb-11-572131 November 2, 2020 Time: 17:31 # 2 Shaw et al. Phototrophic Co-cultures From Extreme Environments INTRODUCTION Culture collections provide the possibility of preserving microbial isolates over extended periods of time without Cyanobacteria are photosynthetic prokaryotes that are found introducing significant genetic changes (McCluskey, 2017) in the majority of illuminated habitats and are known to be and they provide easy access to these isolates and their some of the most morphologically diverse prokaryotes on our associated metadata (Boundy-Mills et al., 2015). Although planet (Whitton and Potts, 2000). The global cyanobacterial culture collections hold enormous potential for capturing and biomass is estimated to total ∼3 × 1014 g of carbon (Garcia- preserving microbial biodiversity, there are numerous challenges Pichel et al., 2003) and cyanobacteria may account for 20–30% in maintaining these biological depositories. With recent of Earth’s primary photosynthetic productivity (Pisciotta et al., advances in DNA sequencing technologies and the accessibility 2010). The efficient photosynthetic machinery of cyanobacteria of 16S rRNA gene-based microbial community profiling, we are has inspired growing interest in the utilization of cyanobacteria now well positioned to re-inventory, and standardize existing and cyanobacteria containing co-cultures in microbial fuel cells culture collections, which will be essential for preserving and (Zhao et al., 2012; Gajda et al., 2015). In addition to having cataloging the planet’s microbial biodiversity. a global effect on the carbon cycle, cyanobacteria-mediated To explore the potential of culture collections, specifically nitrogen fixation has been estimated to supply 20–50% of the those that maintain samples of microbial co-cultures, we nitrogen input in some marine environments (Karl et al., 1997). reexamined the biodiversity of 26 historical phototrophic samples A detailed comprehension of cyanobacteria and their role in from the Culture Collection of Microorganisms from Extreme global carbon and nitrogen cycling is therefore indispensable Environments (CCMEE). While some of the samples, selected for a multi-scalar and holistic understanding of these globally for this project were studied previously (Supplementary Table 1) important nutrient cycles. using cloned-based 16S rRNA profiling and morphological Besides their ecological relevance, cyanobacteria have characterization (Camacho et al., 1996; Miller and Castenholz, potential applications in biotechnology: cyanobacteria facilitate 2000; Nadeau and Castenholz, 2000; Nadeau et al., 2001; Dillon the assimilation of carbon dioxide, a cheap and abundant et al., 2002; Dillon and Castenholz, 2003; Norris and Castenholz, substrate, to synthesize a variety of value-added compounds with 2006; Toplin et al., 2008), the diversity and the overall community industrial relevance (Al-Haj et al., 2016). Although monocultures assemblage of these co-cultures have not yet been characterized. have dominated in microbial biomanufacturing, controlled We selected samples from environments with distinct and co-cultures have been recognized as valuable alternatives, due extreme physical properties from across the globe, suggesting to their potential for reducing the risk of costly contaminations each co-culture would yield a unique microbial consortium. and in some cases enabling increasing product yield (Wang et al., Although reasonable to assume that these consortia have changed 2015; Yen et al., 2015; Padmaperuma et al., 2018). Numerous over time in composition and function (due to their cultivation), cyanobacterial strains have been investigated for their potential it is very likely that results obtained during this work will to produce bioactive compounds, biofertilizer, biofuels, and still provide insights into the microbial biodiversity of extreme bioplastics (Abed et al., 2009; Woo and Lee, 2017; Miao et al., habitats, some of which may no longer be accessible. 2018); and co-expression of non-cyanobacterial genes as well as co-cultivation of cyanobacteria with non-photosynthetic bacteria has resulted in self-sustained systems and improved desirable cyanobacterial phenotypes (de-Bashan et al., 2002; MATERIALS AND METHODS Subashchandrabose et al., 2011; Formighieri and Melis, 2016). Genes coding for enzymes capable of catalyzing reactions Sample Collection and Sample that result in unique products, such as modified trichamide, Description a cyclic peptide suggested to protect the bloom-forming Co-cultures selected for this study are part of a larger culture Trichodesmium erythraeum against predation (Sudek et al., collection and were collected from different locations (Table 1) 2006); and prochlorosins, a family of lanthipeptides with between 1988 and 2002. Isolates were collected using sterile diverse functions that are synthesized by various strains of techniques, kept in the dark and stored on ice as soon as possible. Prochlorococcus and Synechococcus (Li et al., 2010; Cubillos-Ruiz Samples were transported to the laboratory where aliquots were et al., 2017), have been identified from cyanobacterial genomes prepared preservation at −80◦C and cultivation.
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