Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

Neha Garg; Yi Zeng; Anna Edlund; Alexey V Melnik; Laura M Sanchez; Hosein Mohimani; Alexey Gurevich; Vivian Miao; Stefan Schiffler; Yan Wei Lim; Tal Luzzatto-Knaan; Shengxin Cai; Forest Rohwer; Pavel A Pevzner; Robert H Cichewicz; Theodore Alexandrov; Pieter C Dorrestein

doi:10.1128/mSystems.00139-16

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

mSystems. 2016 Dec 20;1(6):e00139-16. doi: 10.1128/mSystems.00139-16. eCollection 2016 Nov-Dec.

Authors

Neha Garg¹, Yi Zeng², Anna Edlund³, Alexey V Melnik¹, Laura M Sanchez⁴, Hosein Mohimani⁵, Alexey Gurevich⁶, Vivian Miao⁷, Stefan Schiffler⁸, Yan Wei Lim⁹, Tal Luzzatto-Knaan¹, Shengxin Cai¹⁰, Forest Rohwer⁹, Pavel A Pevzner⁵, Robert H Cichewicz¹⁰, Theodore Alexandrov¹¹, Pieter C Dorrestein¹²

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA.
² Department of Chemistry and Biochemistry, University of California, San Diego, California, USA.
³ Genomic Medicine, J. Craig Venter Institute, La Jolla, California, USA.
⁴ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA; Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA.
⁵ Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.
⁶ Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
⁷ Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
⁸ SCiLS GmbH, Bremen, Germany.
⁹ Department of Biology, San Diego State University, San Diego, California, USA.
¹⁰ Natural Products Discovery Group, Department of Chemistry and Biochemistry, Institute for Natural Products Applications and Research Technologies, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
¹¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA; SCiLS GmbH, Bremen, Germany; European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
¹² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA; Department of Chemistry and Biochemistry, University of California, San Diego, California, USA; Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.

Abstract

Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level.

Keywords: lichen; mass spectrometry; metagenomics; microbial assemblages; natural products.

Abstract

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