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Zheng Q, Hu Y, Kosina SM, Van Goethem MW, Tringe SG, Bowen BP, Northen TR. Conservation of beneficial microbes between the rhizosphere and the cyanosphere. New Phytol 2023; 240:1246-1258. [PMID: 37668195 DOI: 10.1111/nph.19225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/26/2023] [Indexed: 09/06/2023]
Abstract
Biocrusts are phototroph-driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth-promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host-microbe co-culture experiments between biocrust communities/biocrust isolates and a model grass (Brachypodium distachyon) or a dominant biocrust cyanobacterium (Microcoleus vaginatus), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates (Bosea sp._L1B56, Pseudarthrobacter sp._L1D14 and Pseudarthrobacter picheli_L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B. distachyon exudates, and supplementation of plant growth medium with this metabolite increased B. distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth-promoting microbes and metabolites.
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Affiliation(s)
- Qing Zheng
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuntao Hu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Marc W Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Susannah G Tringe
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Berkeley, CA, 94720, USA
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2
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Trexler RV, Van Goethem MW, Goudeau D, Nath N, Malmstrom RR, Northen TR, Couradeau E. BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event. Front Microbiol 2023; 14:1176751. [PMID: 37434715 PMCID: PMC10330726 DOI: 10.3389/fmicb.2023.1176751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
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.
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Affiliation(s)
- Ryan V. Trexler
- Intercollege Graduate Degree Program in Ecology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Marc W. Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Danielle Goudeau
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Nandita Nath
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Rex R. Malmstrom
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Estelle Couradeau
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United States
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Marasco R, Ramond JB, Van Goethem MW, Rossi F, Daffonchio D. Diamonds in the rough: Dryland microorganisms are ecological engineers to restore degraded land and mitigate desertification. Microb Biotechnol 2023. [PMID: 36641786 PMCID: PMC10364308 DOI: 10.1111/1751-7915.14216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023] Open
Abstract
Our planet teeters on the brink of massive ecosystem collapses, and arid regions experience manifold environmental and climatic challenges that increase the magnitude of selective pressures on already stressed ecosystems. Ultimately, this leads to their aridification and desertification, that is, to simplified and barren ecosystems (with proportionally less microbial load and diversity) with altered functions and food webs and modification of microbial community network. Thus, preserving and restoring soil health in such a fragile biome could help buffer climate change's effects. We argue that microorganisms and the protection of their functional properties and networks are key to fight desertification. Specifically, we claim that it is rational, possible and certainly practical to rely on native dryland edaphic microorganisms and microbial communities as well as dryland plants and their associated microbiota to conserve and restore soil health and mitigate soil depletion in newly aridified lands. Furthermore, this will meet the objective of protecting/stabilizing (and even enhancing) soil biodiversity globally. Without urgent conservation and restoration actions that take into account microbial diversity, we will ultimately, and simply, not have anything to protect anymore.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Jean-Baptiste Ramond
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marc W Van Goethem
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Federico Rossi
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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Marasco R, Fusi M, Ramond JB, Van Goethem MW, Seferji K, Maggs-Kölling G, Cowan DA, Daffonchio D. The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition. ISME Commun 2022; 2:47. [PMID: 37938683 PMCID: PMC9723607 DOI: 10.1038/s43705-022-00130-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 06/17/2023]
Abstract
Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - Marco Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marc W Van Goethem
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kholoud Seferji
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
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Graham EB, Averill C, Bond-Lamberty B, Knelman JE, Krause S, Peralta AL, Shade A, Smith AP, Cheng SJ, Fanin N, Freund C, Garcia PE, Gibbons SM, Van Goethem MW, Guebila MB, Kemppinen J, Nowicki RJ, Pausas JG, Reed SP, Rocca J, Sengupta A, Sihi D, Simonin M, Słowiński M, Spawn SA, Sutherland I, Tonkin JD, Wisnoski NI, Zipper SC. Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.588940] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Disturbances fundamentally alter ecosystem functions, yet predicting their impacts remains a key scientific challenge. While the study of disturbances is ubiquitous across many ecological disciplines, there is no agreed-upon, cross-disciplinary foundation for discussing or quantifying the complexity of disturbances, and no consistent terminology or methodologies exist. This inconsistency presents an increasingly urgent challenge due to accelerating global change and the threat of interacting disturbances that can destabilize ecosystem responses. By harvesting the expertise of an interdisciplinary cohort of contributors spanning 42 institutions across 15 countries, we identified an essential limitation in disturbance ecology: the word ‘disturbance’ is used interchangeably to refer to both the events that cause, and the consequences of, ecological change, despite fundamental distinctions between the two meanings. In response, we developed a generalizable framework of ecosystem disturbances, providing a well-defined lexicon for understanding disturbances across perspectives and scales. The framework results from ideas that resonate across multiple scientific disciplines and provides a baseline standard to compare disturbances across fields. This framework can be supplemented by discipline-specific variables to provide maximum benefit to both inter- and intra-disciplinary research. To support future syntheses and meta-analyses of disturbance research, we also encourage researchers to be explicit in how they define disturbance drivers and impacts, and we recommend minimum reporting standards that are applicable regardless of scale. Finally, we discuss the primary factors we considered when developing a baseline framework and propose four future directions to advance our interdisciplinary understanding of disturbances and their social-ecological impacts: integrating across ecological scales, understanding disturbance interactions, establishing baselines and trajectories, and developing process-based models and ecological forecasting initiatives. Our experience through this process motivates us to encourage the wider scientific community to continue to explore new approaches for leveraging Open Science principles in generating creative and multidisciplinary ideas.
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Van Goethem MW, Swenson TL, Trubl G, Roux S, Northen TR. Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust. mBio 2019; 10:e02287-19. [PMID: 31848272 PMCID: PMC6918073 DOI: 10.1128/mbio.02287-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/07/2019] [Indexed: 12/15/2022] Open
Abstract
Biological soil crusts (biocrusts) are photosynthetic "hot spots" in deserts and cover ∼12% of the Earth's terrestrial surface, and yet they face an uncertain future given expected shifts in rainfall events. Laboratory wetting of biocrust communities is known to cause a bloom of Firmicutes which rapidly become dominant community members within 2 days after emerging from a sporulated state. We hypothesized that their bacteriophages (phages) would respond to such a dramatic increase in their host's abundance. In our experiment, wetting caused Firmicutes to bloom and triggered a significant depletion of cyanobacterial diversity. We used genome-resolved metagenomics to link phage to their hosts and found that the bloom of the genus Bacillus correlated with a dramatic increase in the number of Caudovirales phages targeting these diverse spore-formers (r = 0.762). After 2 days, we observed dramatic reductions in the relative abundances of Bacillus, while the number of Bacillus phages continued to increase, suggestive of a predator-prey relationship. We found predicted auxiliary metabolic genes (AMGs) associated with sporulation in several Caudovirales genomes, suggesting that phages may influence and even benefit from sporulation dynamics in biocrusts. Prophage elements and CRISPR-Cas repeats in Firmicutes metagenome-assembled genomes (MAGs) provide evidence of recent infection events by phages, which were corroborated by mapping viral contigs to their host MAGs. Combined, these findings suggest that the blooming Firmicutes become primary targets for biocrust Caudovirales phages, consistent with the classical "kill-the-winner" hypothesis.IMPORTANCE This work forms part of an overarching research theme studying the effects of a changing climate on biological soil crust (biocrust) in the Southwestern United States. To our knowledge, this study was the first to characterize bacteriophages in biocrust and offers a view into the ecology of phages in response to a laboratory wetting experiment. The phages identified here represent lineages of Caudovirales, and we found that the dynamics of their interactions with their Firmicutes hosts explain the collapse of a bacterial bloom that was induced by wetting. Moreover, we show that phages carried host-altering metabolic genes and found evidence of proviral infection and CRISPR-Cas repeats within host genomes. Our results suggest that phages exert controls on population density by lysing dominant bacterial hosts and that they further impact biocrust by acquiring host genes for sporulation. Future research should explore how dominant these phages are in other biocrust communities and quantify how much the control and lysis of blooming populations contributes to nutrient cycling in biocrusts.
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Affiliation(s)
- Marc W Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tami L Swenson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Simon Roux
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
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7
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Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. Learning representations of microbe-metabolite interactions. Nat Methods 2019; 16:1306-1314. [PMID: 31686038 PMCID: PMC6884698 DOI: 10.1038/s41592-019-0616-3] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/19/2019] [Indexed: 12/26/2022]
Abstract
Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem by using neural networks (https://github.com/biocore/mmvec) to estimate the conditional probability that each molecule is present given the presence of a specific microorganism. We show with known environmental (desert soil biocrust wetting) and clinical (cystic fibrosis lung) examples, our ability to recover microbe-metabolite relationships, and demonstrate how the method can discover relationships between microbially produced metabolites and inflammatory bowel disease.
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Affiliation(s)
- James T Morton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - James R Foulds
- Department of Information Systems, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | | | - Tami L Swenson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Marc W Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Yoshiki Vazquez-Baeza
- Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Nicholas A Bokulich
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Aaron Watters
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Se Jin Song
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY, USA
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Computer Science Department, Courant Institute, New York, NY, USA
- Center For Data Science, New York University, New York, NY, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovaftion Center, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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8
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Porcar M, Louie KB, Kosina SM, Van Goethem MW, Bowen BP, Tanner K, Northen TR. Microbial Ecology on Solar Panels in Berkeley, CA, United States. Front Microbiol 2018; 9:3043. [PMID: 30619134 PMCID: PMC6297676 DOI: 10.3389/fmicb.2018.03043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.
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Affiliation(s)
- Manuel Porcar
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain.,Darwin Bioprospecting Excellence S.L., Parc Científic de la Universitat de València, Paterna, Spain.,Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States
| | - Katherine B Louie
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marc W Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kristie Tanner
- Darwin Bioprospecting Excellence S.L., Parc Científic de la Universitat de València, Paterna, Spain
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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9
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Van Goethem MW, Pierneef R, Bezuidt OKI, Van De Peer Y, Cowan DA, Makhalanyane TP. A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils. Microbiome 2018; 6:40. [PMID: 29471872 PMCID: PMC5824556 DOI: 10.1186/s40168-018-0424-5] [Citation(s) in RCA: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/11/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. METHODS We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. RESULTS In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and β-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r = - 0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. CONCLUSIONS ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.
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Affiliation(s)
- Marc W Van Goethem
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Rian Pierneef
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Oliver K I Bezuidt
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Yves Van De Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa.
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Van Goethem MW, Makhalanyane TP, Cowan DA, Valverde A. Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities. Front Microbiol 2017; 8:2099. [PMID: 29118751 PMCID: PMC5660985 DOI: 10.3389/fmicb.2017.02099] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/13/2017] [Indexed: 01/04/2023] Open
Abstract
Hypoliths, microbial assemblages found below translucent rocks, provide important ecosystem services in deserts. While several studies have assessed microbial diversity of hot desert hypoliths and whether these communities are metabolically active, the interactions among taxa remain unclear. Here, we assessed the structure, diversity, and co-occurrence patterns of hypolithic communities from the hyperarid Namib Desert by comparing total (DNA) and potentially active (RNA) communities. The potentially active and total hypolithic communities differed in their composition and diversity, with significantly higher levels of Cyanobacteria and Alphaproteobacteria in potentially active hypoliths. Several phyla known to be abundant in total hypolithic communities were metabolically inactive, indicating that some hypolithic taxa may be dormant or dead. The potentially active hypolith network was highly modular in structure with almost exclusively positive co-occurrences (>95% of the total) between taxa. Members of the Cyanobacteria and Alphaproteobacteria were identified as potential keystone taxa, and exhibited numerous positive co-occurrences with other microbes, suggesting that these groups might have important roles in maintaining network topological structure despite their low abundance.
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Affiliation(s)
- Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Angel Valverde
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
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Adriaenssens EM, Kramer R, Van Goethem MW, Makhalanyane TP, Hogg I, Cowan DA. Environmental drivers of viral community composition in Antarctic soils identified by viromics. Microbiome 2017; 5:83. [PMID: 28724405 PMCID: PMC5518109 DOI: 10.1186/s40168-017-0301-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 07/06/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform. Metadata on soil physico-chemistry was collected from all sites. Both read and contig datasets were analyzed with reference-independent and reference-dependent methods to assess viral community structures and the influence of environmental parameters on their distribution. RESULTS We observed a high heterogeneity in virus signatures, independent of geographical proximity. Tailed bacteriophages were dominant in all samples, but the incidences of the affiliated families Siphoviridae and Myoviridae were inversely correlated, suggesting direct competition for hosts. Viruses of the families Phycodnaviridae and Mimiviridae were present at significant levels in high-diversity soil samples and were found to co-occur, implying little competition between them. Combinations of soil factors, including pH, calcium content, and site altitude, were found to be the main drivers of viral community structure. CONCLUSIONS The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.
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Affiliation(s)
- Evelien M. Adriaenssens
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Rolf Kramer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Marc W. Van Goethem
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Thulani P. Makhalanyane
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Ian Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, 170 Laurier Avenue West, Ottawa, Ontario K1P 5V5 Canada
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
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Bezuidt OKI, Gomri MA, Pierneef R, Van Goethem MW, Kharroub K, Cowan DA, Makhalanyane TP. Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria. Stand Genomic Sci 2016; 11:68. [PMID: 27617058 PMCID: PMC5016870 DOI: 10.1186/s40793-016-0186-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/27/2016] [Indexed: 11/10/2022] Open
Abstract
The members of the genus Thermoactinomyces are known for their protein degradative capacities. Thermoactinomyces sp. strain AS95 is a Gram-positive filamentous bacterium, isolated from moderately saline water in the Thamelaht region of Algeria. This isolate is a thermophilic aerobic bacterium with the capacity to produce extracellular proteolytic enzymes. This strain exhibits up to 99 % similarity with members of the genus Thermoactinomyces, based on 16S rRNA gene sequence similarity. Here we report on the phenotypic features of Thermoactinomyces sp. strain AS95 together with the draft genome sequence and its annotation. The genome of this strain is 2,558,690 bp in length (one chromosome, but no plasmid) with an average G + C content of 47.95 %, and contains 2550 protein-coding and 60 RNA genes together with 64 ORFs annotated as proteases.
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Affiliation(s)
- Oliver K. I. Bezuidt
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Natural Sciences 2 Building, Office 3-14, Lynnwood Road, Pretoria, 0028 South Africa
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Mohamed A. Gomri
- Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments, INATAA, Université Frères Mentouri Constantine, Constantine, Algérie
| | - Rian Pierneef
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, 0028 South Africa
| | - Marc W. Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Natural Sciences 2 Building, Office 3-14, Lynnwood Road, Pretoria, 0028 South Africa
| | - Karima Kharroub
- Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments, INATAA, Université Frères Mentouri Constantine, Constantine, Algérie
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Natural Sciences 2 Building, Office 3-14, Lynnwood Road, Pretoria, 0028 South Africa
| | - Thulani P. Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Natural Sciences 2 Building, Office 3-14, Lynnwood Road, Pretoria, 0028 South Africa
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Van Goethem MW, Makhalanyane TP, Valverde A, Cary SC, Cowan DA. Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw051. [DOI: 10.1093/femsec/fiw051] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 12/18/2022] Open
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