BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event
Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sort...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1176751/full |
| _version_ | 1827916457750560768 |
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| author | Ryan V. Trexler Marc W. Van Goethem Marc W. Van Goethem Danielle Goudeau Nandita Nath Rex R. Malmstrom Trent R. Northen Trent R. Northen Estelle Couradeau Estelle Couradeau |
| author_facet | Ryan V. Trexler Marc W. Van Goethem Marc W. Van Goethem Danielle Goudeau Nandita Nath Rex R. Malmstrom Trent R. Northen Trent R. Northen Estelle Couradeau Estelle Couradeau |
| author_sort | Ryan V. Trexler |
| collection | DOAJ |
| description | Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event. |
| first_indexed | 2024-03-13T03:14:22Z |
| format | Article |
| id | doaj.art-c426c2838e2b4f1386363f0d5274365c |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-13T03:14:22Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-c426c2838e2b4f1386363f0d5274365c2023-06-26T05:20:06ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-06-011410.3389/fmicb.2023.11767511176751BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up eventRyan V. Trexler0Marc W. Van Goethem1Marc W. Van Goethem2Danielle Goudeau3Nandita Nath4Rex R. Malmstrom5Trent R. Northen6Trent R. Northen7Estelle Couradeau8Estelle Couradeau9Intercollege Graduate Degree Program in Ecology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United StatesEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesBiological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaLawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesLawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United StatesEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United StatesDepartment of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United StatesDetermining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1176751/fullBONCATbiocrustsoil metagenomicsactive microorganismssoil wetting |
| spellingShingle | Ryan V. Trexler Marc W. Van Goethem Marc W. Van Goethem Danielle Goudeau Nandita Nath Rex R. Malmstrom Trent R. Northen Trent R. Northen Estelle Couradeau Estelle Couradeau BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event Frontiers in Microbiology BONCAT biocrust soil metagenomics active microorganisms soil wetting |
| title | BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event |
| title_full | BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event |
| title_fullStr | BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event |
| title_full_unstemmed | BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event |
| title_short | BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event |
| title_sort | boncat facs seq reveals the active fraction of a biocrust community undergoing a wet up event |
| topic | BONCAT biocrust soil metagenomics active microorganisms soil wetting |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1176751/full |
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