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Miller IR, Bui H, Wood JB, Fields MW, Gerlach R. Understanding phycosomal dynamics to improve industrial microalgae cultivation. Trends Biotechnol 2024; 42:680-698. [PMID: 38184438 DOI: 10.1016/j.tibtech.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/08/2024]
Abstract
Algal-bacterial interactions are ubiquitous in both natural and industrial systems, and the characterization of these interactions has been reinvigorated by potential applications in biosystem productivity. Different growth conditions can be used for operational functions, such as the use of low-quality water or high pH/alkalinity, and the altered operating conditions likely constrain microbial community structure and function in unique ways. However, research is necessary to better understand whether consortia can be designed to improve the productivity, processing, and sustainability of industrial-scale cultivations through different controls that can constrain microbial interactions for maximal light-driven outputs. The review highlights current knowledge and gaps for relevant operating conditions, as well as suggestions for near-term and longer-term improvements for large-scale cultivation and polyculture engineering.
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Affiliation(s)
- Isaac R Miller
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Huyen Bui
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Jessica B Wood
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Matthew W Fields
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; Department of Civil Engineering, Montana State University, Bozeman, MT, USA; Energy Research Institute, Montana State University, Bozeman, MT, USA.
| | - Robin Gerlach
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA; Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; Energy Research Institute, Montana State University, Bozeman, MT, USA; Department of Biological and Chemical Engineering, Bozeman, MT, USA
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2
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Kim KH, Kim JM, Baek JH, Jeong SE, Kim H, Yoon HS, Jeon CO. Metabolic relationships between marine red algae and algae-associated bacteria. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:298-314. [PMID: 38827136 PMCID: PMC11136935 DOI: 10.1007/s42995-024-00227-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/28/2023] [Indexed: 06/04/2024]
Abstract
Mutualistic interactions between marine phototrophs and associated bacteria are an important strategy for their successful survival in the ocean, but little is known about their metabolic relationships. Here, bacterial communities in the algal sphere (AS) and bulk solution (BS) of nine marine red algal cultures were analyzed, and Roseibium and Phycisphaera were identified significantly more abundantly in AS than in BS. The metabolic features of Roseibium RMAR6-6 (isolated and genome-sequenced), Phycisphaera MAG 12 (obtained by metagenomic sequencing), and a marine red alga, Porphyridium purpureum CCMP1328 (from GenBank), were analyzed bioinformatically. RMAR6-6 has the genetic capability to fix nitrogen and produce B vitamins (B1, B2, B5, B6, B9, and B12), bacterioferritin, dimethylsulfoniopropionate (DMSP), and phenylacetate that may enhance algal growth, whereas MAG 12 may have a limited metabolic capability, not producing vitamins B9 and B12, DMSP, phenylacetate, and siderophores, but with the ability to produce bacitracin, possibly modulating algal microbiome. P. purpureum CCMP1328 lacks the genetic capability to fix nitrogen and produce vitamin B12, DMSP, phenylacetate, and siderophore. It was shown that the nitrogen-fixing ability of RMAR6-6 promoted the growth of P. purpureum, and DMSP reduced the oxidative stress of P. purpureum. The metabolic interactions between strain RMAR6-6 and P. purpureum CCMP1328 were also investigated by the transcriptomic analyses of their monoculture and co-culture. Taken together, potential metabolic relationships between Roseibium and P. purpureum were proposed. This study provides a better understanding of the metabolic relationships between marine algae and algae-associated bacteria for successful growth. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00227-z.
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Affiliation(s)
- Kyung Hyun Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, 34054 Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
| | - Hocheol Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974 Republic of Korea
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Wienhausen G, Moraru C, Bruns S, Tran DQ, Sultana S, Wilkes H, Dlugosch L, Azam F, Simon M. Ligand cross-feeding resolves bacterial vitamin B 12 auxotrophies. Nature 2024; 629:886-892. [PMID: 38720071 DOI: 10.1038/s41586-024-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 04/08/2024] [Indexed: 05/24/2024]
Abstract
Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes1,2. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics2-4. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.
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Affiliation(s)
- Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Stefan Bruns
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.
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4
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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5
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Eigemann F, Tait K, Temperton B, Hellweger FL. Internal carbon recycling by heterotrophic prokaryotes compensates for mismatches between phytoplankton production and heterotrophic consumption. THE ISME JOURNAL 2024; 18:wrae103. [PMID: 38861418 PMCID: PMC11217553 DOI: 10.1093/ismejo/wrae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/18/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Molecular observational tools are useful for characterizing the composition and genetic endowment of microbial communities but cannot measure fluxes, which are critical for the understanding of ecosystems. To overcome these limitations, we used a mechanistic inference approach to estimate dissolved organic carbon (DOC) production and consumption by phytoplankton operational taxonomic units and heterotrophic prokaryotic amplicon sequence variants and inferred carbon fluxes between members of this microbial community from Western English Channel time-series data. Our analyses focused on phytoplankton spring and summer blooms, as well as bacteria summer blooms. In spring blooms, phytoplankton DOC production exceeds heterotrophic prokaryotic consumption, but in bacterial summer blooms heterotrophic prokaryotes consume three times more DOC than produced by the phytoplankton. This mismatch is compensated by heterotrophic prokaryotic DOC release by death, presumably from viral lysis. In both types of summer blooms, large amounts of the DOC liberated by heterotrophic prokaryotes are reused through internal recycling, with fluxes between different heterotrophic prokaryotes being at the same level as those between phytoplankton and heterotrophic prokaryotes. In context, internal recycling accounts for approximately 75% and 30% of the estimated net primary production (0.16 vs 0.22 and 0.08 vs 0.29 μmol l-1 d-1) in bacteria and phytoplankton summer blooms, respectively, and thus represents a major component of the Western English Channel carbon cycle. We have concluded that internal recycling compensates for mismatches between phytoplankton DOC production and heterotrophic prokaryotic consumption, and we encourage future analyses on aquatic carbon cycles to investigate fluxes between heterotrophic prokaryotes, specifically internal recycling.
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Affiliation(s)
- Falk Eigemann
- Water Quality Engineering, Technical University of Berlin, 10623 Berlin, Germany
| | - Karen Tait
- Plymouth Marine Laboratory, PL1 Plymouth, United Kingdom
| | - Ben Temperton
- Faculty of Health and Life Sciences, University of Exeter, EX2 Exeter, United Kingdom
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, 10623 Berlin, Germany
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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. THE NEW PHYTOLOGIST 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] [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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7
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Paerl RW, Curtis NP, Bittner MJ, Cohn MR, Gifford SM, Bannon CC, Rowland E, Bertrand EM. Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange. mBio 2023; 14:e0006123. [PMID: 37377416 PMCID: PMC10470507 DOI: 10.1128/mbio.00061-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/17/2023] [Indexed: 06/29/2023] Open
Abstract
Vitamin B1 (thiamin) is a vital nutrient for most cells in nature, including marine plankton. Early and recent experiments show that B1 degradation products instead of B1 can support the growth of marine bacterioplankton and phytoplankton. However, the use and occurrence of some degradation products remains uninvestigated, namely N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), which has been a focus of plant oxidative stress research. We investigated the relevance of FAMP in the ocean. Experiments and global ocean meta-omic data indicate that eukaryotic phytoplankton, including picoeukaryotes and harmful algal bloom species, use FAMP while bacterioplankton appear more likely to use deformylated FAMP, 4-amino-5-aminomethyl-2-methylpyrimidine. Measurements of FAMP in seawater and biomass revealed that it occurs at picomolar concentrations in the surface ocean, heterotrophic bacterial cultures produce FAMP in the dark-indicating non-photodegradation of B1 by cells, and B1-requiring (auxotrophic) picoeukaryotic phytoplankton produce intracellular FAMP. Our results require an expansion of thinking about vitamin degradation in the sea, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as generation (dark degradation-likely via oxidation), turnover (plankton uptake), and exchange of the compound within the networks of plankton. IMPORTANCE Results of this collaborative study newly show that a vitamin B1 degradation product, N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP), can be used by diverse marine microbes (bacteria and phytoplankton) to meet their vitamin B1 demands instead of B1 and that FAMP occurs in the surface ocean. FAMP has not yet been accounted for in the ocean and its use likely enables cells to avoid B1 growth deficiency. Additionally, we show FAMP is formed in and out of cells without solar irradiance-a commonly considered route of vitamin degradation in the sea and nature. Altogether, the results expand thinking about oceanic vitamin degradation, but also the marine B1 cycle where it is now crucial to consider a new B1-related compound pool (FAMP), as well as its generation (dark degradation-likely via oxidation), turnover (plankton uptake), and exchange within networks of plankton.
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Affiliation(s)
- Ryan W. Paerl
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Nathaniel P. Curtis
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Meriel J. Bittner
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Melanie R. Cohn
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott M. Gifford
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Erin M. Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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8
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From the Sunlit to the Aphotic Zone: Assembly Mechanisms and Co-Occurrence Patterns of Protistan-Bacterial Microbiotas in the Western Pacific Ocean. mSystems 2023; 8:e0001323. [PMID: 36847533 PMCID: PMC10134807 DOI: 10.1128/msystems.00013-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
We know little about the assembly processes and association patterns of microbial communities below the photic zone. In marine pelagic systems, there are insufficient observational data regarding why and how the microbial assemblies and associations vary from photic to aphotic zones. In this study, we investigated size-fractionated oceanic microbiotas, specifically free-living (FL; 0.22 to 3 μm) and particle-associated (PA; >3 μm) bacteria and protists (0.22 to 200 μm) collected from the surface to 2,000 m in the western Pacific Ocean, to see how assembly mechanisms and association patterns changed from photic to aphotic zones. Taxonomic analysis revealed a distinct community composition between photic and aphotic zones that was largely driven by biotic associations rather than abiotic factors. Aphotic community co-occurrence was less widespread and robust than its photic counterparts, and biotic associations were crucial in microbial co-occurrence, having a higher influence on photic than aphotic co-occurrences. The decrease in biotic associations and the increase in dispersal limitation from the photic to the aphotic zone affect the deterministic-stochastic balance, leading to a more stochastic-process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to our understanding of how and why microbial assembly and co-occurrence vary from photic to aphotic zones, offering insight into the dynamics of the protistan-bacterial microbiota in the western Pacific's photic and aphotic zones. IMPORTANCE We know little about the assembly processes and association patterns of microbial communities below the photic zone in marine pelagic systems. We discovered that community assembly processes differed between photic and aphotic zones, with all three microbial groups studied (protists and FL and PA bacteria) being more influenced by stochastic processes than in the photic zone. The decrease in organismic associations and the increase in dispersal limitation from the photic to the aphotic zone both have an impact on the deterministic-stochastic balance, resulting in a more stochastic process-driven community assembly for all three microbial groups in the aphotic zone. Our findings significantly contribute to the understanding of how and why microbial assembly and co-occurrence change between photic and aphotic zones, offering insight into the dynamics of the protist-bacteria microbiota in the western Pacific oceans.
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Koester I, Quinlan ZA, Nothias LF, White ME, Rabines A, Petras D, Brunson JK, Dührkop K, Ludwig M, Böcker S, Azam F, Allen AE, Dorrestein PC, Aluwihare LI. Illuminating the dark metabolome of Pseudo-nitzschia-microbiome associations. Environ Microbiol 2022; 24:5408-5424. [PMID: 36222155 PMCID: PMC9707391 DOI: 10.1111/1462-2920.16242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/09/2022] [Indexed: 11/28/2022]
Abstract
The exchange of metabolites mediates algal and bacterial interactions that maintain ecosystem function. Yet, while thousands of metabolites are produced, only a few molecules have been identified in these associations. Using the ubiquitous microalgae Pseudo-nitzschia sp., as a model, we employed an untargeted metabolomics strategy to assign structural characteristics to the metabolites that distinguished specific diatom-microbiome associations. We cultured five species of Pseudo-nitzschia, including two species that produced the toxin domoic acid, and examined their microbiomes and metabolomes. A total of 4826 molecular features were detected by tandem mass spectrometry. Only 229 of these could be annotated using available mass spectral libraries, but by applying new in silico annotation tools, characterization was expanded to 2710 features. The metabolomes of the Pseudo-nitzschia-microbiome associations were distinct and distinguished by structurally diverse nitrogen compounds, ranging from simple amines and amides to cyclic compounds such as imidazoles, pyrrolidines and lactams. By illuminating the dark metabolomes, this study expands our capacity to discover new chemical targets that facilitate microbial partnerships and uncovers the chemical diversity that underpins algae-bacteria interactions.
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Affiliation(s)
- Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Zachary A. Quinlan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Margot E. White
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Ariel Rabines
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Daniel Petras
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - John K. Brunson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Kai Dührkop
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Marcus Ludwig
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich Schiller University, Jena, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - Andrew E. Allen
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
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10
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Nagarajan D, Lee DJ, Varjani S, Lam SS, Allakhverdiev SI, Chang JS. Microalgae-based wastewater treatment - Microalgae-bacteria consortia, multi-omics approaches and algal stress response. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157110. [PMID: 35787906 DOI: 10.1016/j.scitotenv.2022.157110] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Sustainable environmental management is one of the important aspects of sustainable development goals. Increasing amounts of wastewaters (WW) from exponential economic growth is a major challenge, and conventional treatment methods entail a huge carbon footprint in terms of energy use and GHG emissions. Microalgae-based WW treatment is a potential candidate for sustainable WW treatment. The nutrients which are otherwise unutilized in the conventional processes are recovered in the beneficial microalgal biomass. This review presents comprehensive information regarding the potential of microalgae as sustainable bioremediation agents. Microalgae-bacterial consortia play a critical role in synergistic nutrient removal, supported by the complex nutritional and metabolite exchange between microalgae and the associated bacteria. Design of effective microalgae-bacteria consortia either by screening or by recent technologies such as synthetic biology approaches are highly required for efficient WW treatment. Furthermore, this review discusses the crucial research gap in microalgal WW treatment - the application of a multi-omics platform for understanding microalgal response towards WW conditions and the design of effective microalgal or microalgae-bacteria consortia based on genetic information. While metagenomics helps in the identification and monitoring of the microbial community throughout the treatment process, transcriptomics, proteomics and metabolomics aid in studying the algal cellular response towards the nutrients and pollutants in WW. It has been established that the integration of microalgal processes into conventional WW treatment systems is feasible. In this direction, future research directions for microalgal WW treatment emphasize the need for identifying the niche in WW treatment, while highlighting the pilot sale plants in existence. Microalgae-based WW treatment could be a potential phase in the waste hierarchy of circular economy and sustainability, considering WWs are a rich secondary source of finite resources such as nitrogen and phosphorus.
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Affiliation(s)
- Dillirani Nagarajan
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, Gujarat 382 010, India
| | - Su Shiung Lam
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India
| | - Suleyman I Allakhverdiev
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taiwan.
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11
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Weber L, Soule MK, Longnecker K, Becker CC, Huntley N, Kujawinski EB, Apprill A. Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs. ISME COMMUNICATIONS 2022; 2:101. [PMID: 37938276 PMCID: PMC9723752 DOI: 10.1038/s43705-022-00184-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 09/02/2023]
Abstract
Benthic organisms are the architectural framework supporting coral reef ecosystems, but their community composition has recently shifted on many reefs. Little is known about the metabolites released from these benthic organisms and how compositional shifts may influence other reef life, including prolific microorganisms. To investigate the metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting alga, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial abundances and community composition using 16 S rRNA gene sequencing in relation to exudate source and three specific metabolites. Exudates were enriched in amino acids, nucleosides, vitamins, and indole-based metabolites, showing that benthic organisms contribute labile organic matter to reefs. Furthermore, exudate compositions were species-specific, and riboflavin and pantothenic acid emerged as significant coral-produced metabolites, while caffeine emerged as a significant invasive algal-produced metabolite. Microbial abundances and individual microbial taxa responded differently to exudates from stony corals and octocorals, demonstrating that exudate mixtures released from different coral species select for specific bacteria. In contrast, microbial communities did not respond to individual additions of riboflavin, pantothenic acid, or caffeine. This work indicates that recent shifts in benthic organisms alter exudate composition and likely impact microbial communities on coral reefs.
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Affiliation(s)
- Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
| | - Melissa Kido Soule
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Krista Longnecker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Cynthia C Becker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, MA, USA
| | - Naomi Huntley
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Marine and Environmental Science Department, University of the Virgin Islands, Charlotte Amalie West, St Thomas, Charlotte Amalie, VI, 00802, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Elizabeth B Kujawinski
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
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12
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Giri S, Yousif G, Shitut S, Oña L, Kost C. Prevalent emergence of reciprocity among cross-feeding bacteria. ISME COMMUNICATIONS 2022; 2:71. [PMID: 37938764 PMCID: PMC9723789 DOI: 10.1038/s43705-022-00155-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 05/25/2023]
Abstract
Explaining the de novo evolution of obligate cooperative cross-feeding interactions among bacteria is a fundamental problem. A critical step during this process is the emergence of reciprocity among two interaction partners, because a mutually beneficial exchange of metabolic byproducts can subsequently favour the evolution of cooperative cross-feeding. However, so far, the propensity with which unidirectional cross-feeding interactions transition into bidirectional interactions remains unknown. To address this issue, we systematically cocultured four amino acid auxotrophic genotypes of two bacterial species with potential amino acid donors belonging to 25 different bacterial species. Surprisingly, the results of this experiment revealed that in around 40% of all cases analysed, both the auxotrophic recipient and the metabolically autonomous donor gained a significant growth advantage in coculture. Subsequent experiments clarified that the auxotrophy-causing mutation did not induce the growth-enhancing effect of recipients, but that it was rather due to a generally high propensity of different species to engage in synergistic metabolic interactions. Together, these findings show that reciprocity commonly emerges spontaneously in unidirectional cross-feeding interactions, thus paving the way for the evolution of even tighter metabolic interactions.
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Affiliation(s)
- Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany.
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Ghada Yousif
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Shraddha Shitut
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany.
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13
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Wienhausen G, Bruns S, Sultana S, Dlugosch L, Groon LA, Wilkes H, Simon M. The overlooked role of a biotin precursor for marine bacteria - desthiobiotin as an escape route for biotin auxotrophy. THE ISME JOURNAL 2022; 16:2599-2609. [PMID: 35963899 PMCID: PMC9561691 DOI: 10.1038/s41396-022-01304-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022]
Abstract
Biotin (vitamin B7) is involved in a wide range of essential biochemical reactions and a crucial micronutrient that is vital for many pro- and eukaryotic organisms. The few biotin measurements in the world’s oceans show that availability is subject to strong fluctuations. Numerous marine microorganisms exhibit biotin auxotrophy and therefore rely on supply by other organisms. Desthiobiotin is the primary precursor of biotin and has recently been detected at concentrations similar to biotin in seawater. The last enzymatic reaction in the biotin biosynthetic pathway converts desthiobiotin to biotin via the biotin synthase (BioB). The role of desthiobiotin as a precursor of biotin synthesis in microbial systems, however, is largely unknown. Here we demonstrate experimentally that bacteria can overcome biotin auxotrophy if they retain the bioB gene and desthiobiotin is available. A genomic search of 1068 bacteria predicts that the biotin biosynthetic potential varies greatly among different phylogenetic groups and that 20% encode solely bioB and thus can potentially overcome biotin auxotrophy. Many Actino- and Alphaproteobacteria cannot synthesize biotin de novo, but some possess solely bioB, whereas the vast majority of Gammaproteobacteria and Flavobacteriia exhibit the last four crucial biotin synthesis genes. We detected high intra- and extracellular concentrations of the precursor relative to biotin in the prototrophic bacterium, Vibrio campbellii, with extracellular desthiobiotin reaching up to 1.09 ± 0.15*106 molecules per cell during exponential growth. Our results provide evidence for the ecological role of desthiobiotin as an escape route to overcome biotin auxotrophy for bacteria in the ocean and presumably in other ecosystems.
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14
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Deore P, Barlow CK, Schittenhelm RB, Beardall J, Noronha S. Profiling of grazed cultures of the chlorophyte alga Dunaliella tertiolecta using an untargeted LC-MS approach. JOURNAL OF PHYCOLOGY 2022; 58:568-581. [PMID: 35506918 DOI: 10.1111/jpy.13254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Extracellular signals are reported to mediate chemical cross-talk among pelagic microbes, including microalgal prey and predators. Water-soluble mediator compounds play a crucial role in extracellular communication which is vital for prey recognition, attraction, capture, and predator deterrence. A range of exo-metabolites including oxylipins and vitamins are released by prey in response to grazing stress. The temporal dynamics of such exo-metabolites largely remains unknown, especially in large-scale cultivation of microalgae such as closed or open ponds. In open ponds, infestation of predators is almost inevitable but highly undesirable due to the imminent threat of culture collapse. The early production of exo-metabolites emitted by microalgal prey in response to predator attack could be leveraged as diagnostic markers of possible culture collapse. This study uses an untargeted approach for temporal profiling of Dunaliella tertiolecta-specific exo-metabolites under grazing pressure from Oxyrrhis marina. We report 24 putatively identified metabolites, belonging to various classes such as short peptides, lipids, indole-derivatives, and free amino acids, as potential markers of grazing-mediated stress. In addition, this study outlines a clear methodology for screening of exo-metabolites in marine algal samples, the analysis of which is frequently hindered by high salt concentrations. In future, a chemistry-based targeted detection of these metabolites could enable a quick and on-site screening of predators in microalgal cultures.
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Affiliation(s)
- Pranali Deore
- IITB-MONASH Research Academy, Mumbai, 400076, India
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Christopher K Barlow
- Monash Proteomic and Metabolomic Facility, Monash University, Clayton, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Ralf B Schittenhelm
- Monash Proteomic and Metabolomic Facility, Monash University, Clayton, Victoria, 3800, Australia
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
- Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Cheras, 56000, Malaysia
| | - Santosh Noronha
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
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15
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Xiao L, Chen Z, Yang Y, Liu Z. Growth promotion of Chlorella by symbiotic bacteria under adverse environments. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Srinivas S, Berger M, Brinkhoff T, Niggemann J. Impact of Quorum Sensing and Tropodithietic Acid Production on the Exometabolome of Phaeobacter inhibens. Front Microbiol 2022; 13:917969. [PMID: 35801100 PMCID: PMC9253639 DOI: 10.3389/fmicb.2022.917969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/03/2022] [Indexed: 11/29/2022] Open
Abstract
Microbial interactions shape ecosystem diversity and chemistry through production and exchange of organic compounds, but the impact of regulatory mechanisms on production and release of these exometabolites is largely unknown. We studied the extent and nature of impact of two signaling molecules, tropodithietic acid (TDA) and the quorum sensing molecule acyl homoserine lactone (AHL) on the exometabolome of the model bacterium Phaeobacter inhibens DSM 17395, a member of the ubiquitous marine Roseobacter group. Exometabolomes of the wild type, a TDA and a QS (AHL-regulator) negative mutant were analyzed via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Based on a total of 996 reproducibly detected molecular masses, exometabolomes of the TDA and QS negative mutant were ∼70% dissimilar to each other, and ∼90 and ∼60% dissimilar, respectively, to that of the wild type. Moreover, at any sampled growth phase, 40–60% of masses detected in any individual exometabolome were unique to that strain, while only 10–12% constituted a shared “core exometabolome.” Putative annotation revealed exometabolites of ecological relevance such as vitamins, amino acids, auxins, siderophore components and signaling compounds with different occurrence patterns in the exometabolomes of the three strains. Thus, this study demonstrates that signaling molecules, such as AHL and TDA, extensively impact the composition of bacterial exometabolomes with potential consequences for species interactions in microbial communities.
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Affiliation(s)
- Sujatha Srinivas
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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17
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Zhang Y, Gallant É, Park JD, Seyedsayamdost MR. The Small-Molecule Language of Dynamic Microbial Interactions. Annu Rev Microbiol 2022; 76:641-660. [PMID: 35679616 PMCID: PMC10171915 DOI: 10.1146/annurev-micro-042722-091052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although microbes are routinely grown in monocultures in the laboratory, they are almost never encountered as single species in the wild. Our ability to detect and identify new microorganisms has advanced significantly in recent years, but our understanding of the mechanisms that mediate microbial interactions has lagged behind. What makes this task more challenging is that microbial alliances can be dynamic, consisting of multiple phases. The transitions between phases, and the interactions in general, are often mediated by a chemical language consisting of small molecules, also referred to as secondary metabolites or natural products. In this microbial lexicon, the molecules are like words and through their effects on recipient cells they convey meaning. The current review highlights three dynamic microbial interactions in which some of the words and their meanings have been characterized, especially those that mediate transitions in selected multiphasic associations. These systems provide insights into the principles that govern microbial symbioses and a playbook for interrogating similar associations in diverse ecological niches. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Yifan Zhang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; ,
| | - Étienne Gallant
- Department of Chemistry, Princeton University, Princeton, New Jersey, USA; ,
| | - Jong-Duk Park
- Department of Chemistry, Princeton University, Princeton, New Jersey, USA; ,
| | - Mohammad R Seyedsayamdost
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; , .,Department of Chemistry, Princeton University, Princeton, New Jersey, USA; ,
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18
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Heinrichs ME, Heyerhoff B, Arslan-Gatz BS, Seidel M, Niggemann J, Engelen B. Deciphering the Virus Signal Within the Marine Dissolved Organic Matter Pool. Front Microbiol 2022; 13:863686. [PMID: 35694303 PMCID: PMC9184803 DOI: 10.3389/fmicb.2022.863686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are ubiquitously distributed in the marine environment, influencing microbial population dynamics and biogeochemical cycles on a large scale. Due to their small size, they fall into the oceanographic size-class definition of dissolved organic matter (DOM; <0.7 μm). The purpose of our study was to investigate if there is a detectable imprint of virus particles in natural DOM following standard sample preparation and molecular analysis routines using ultrahigh-resolution mass spectrometry (FT-ICR-MS). Therefore, we tested if a molecular signature deriving from virus particles can be detected in the DOM fingerprint of a bacterial culture upon prophage induction and of seawater containing the natural microbial community. Interestingly, the virus-mediated lysate of the infected bacterial culture differed from the cell material of a physically disrupted control culture in its molecular composition. Overall, a small subset of DOM compounds correlated significantly with virus abundances in the bacterial culture setup, accounting for <1% of the detected molecular formulae and <2% of the total signal intensity of the DOM dataset. These were phosphorus- and nitrogen-containing compounds and they were partially also detected in DOM samples from other studies that included high virus abundances. While some of these formulae matched with typical biomolecules that are constituents of viruses, others matched with bacterial cell wall components. Thus, the identified DOM molecular formulae were probably not solely derived from virus particles but were partially also derived from processes such as the virus-mediated bacterial cell lysis. Our results indicate that a virus-derived DOM signature is part of the natural DOM and barely detectable within the analytical window of ultrahigh-resolution mass spectrometry when a high natural background is present.
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Affiliation(s)
- Mara E. Heinrichs
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Benedikt Heyerhoff
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Berin S. Arslan-Gatz
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Michael Seidel
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Bert Engelen
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
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19
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Bioactive Compounds for Quorum Sensing Signal-Response Systems in Marine Phycosphere. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10050699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Quorum sensing in the phycosphere refers to a sensor system in which bacteria secrete bioactive compounds to coordinate group behavior relying on cell density. It is an important way for algae and bacteria to communicate with each other and achieve interactions. It has been determined that quorum sensing is widely presented in the marine phycosphere, which involves a variety of bioactive compounds. Focused on these compounds in marine phycosphere, this review summarizes the types and structures of the compounds, describes the methods in detection and functional evaluation, discusses the ecological functions regulated by the compounds, such as modulating microbial colonization, achieving algae–bacteria mutualism or competition and contributing to marine biogeochemical cycles. Meanwhile, the application prospects of the compounds are also proposed, including controlling harmful algal blooms and producing biofuel. Future research should focus on improving detection techniques, developing more model systems and investigating the effects of climate change on the quorum-sensing pathway to further understand the mechanism and application potential of quorum sensing compounds. This review aims to present an overview of current research carried out in order to provide the reader with perspective on bioactive compounds involved in quorum sensing.
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20
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Availability of vitamin B 12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems. THE ISME JOURNAL 2022; 16:2002-2014. [PMID: 35585186 PMCID: PMC9296465 DOI: 10.1038/s41396-022-01250-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 01/22/2023]
Abstract
Genome analyses predict that the cofactor cobalamin (vitamin B12, called B12 herein) is produced by only one-third of all prokaryotes but almost all encode at least one B12-dependent enzyme, in most cases methionine synthase. This implies that the majority of prokaryotes relies on exogenous B12 supply and interacts with producers. B12 consists of a corrin ring centred around a cobalt ion and the lower ligand 5’6-dimethylbenzimidazole (DMB). It has never been tested whether availability of this pivotal cofactor, DMB or its intermediate α-ribazole affect growth and composition of prokaryotic microbial communities. Here we show that in the subtropical, equatorial and polar frontal Pacific Ocean supply of B12 and α-ribazole enhances heterotrophic prokaryotic production and alters the composition of prokaryotic and heterotrophic protist communities. In the polar frontal Pacific, the SAR11 clade and Oceanospirillales increased their relative abundances upon B12 supply. In the subtropical Pacific, Oceanospirillales increased their relative abundance upon B12 supply as well but also downregulated the transcription of the btuB gene, encoding the outer membrane permease for B12. Surprisingly, Prochlorococcus, known to produce pseudo-B12 and not B12, exhibited significant upregulation of genes encoding key proteins of photosystem I + II, carbon fixation and nitrate reduction upon B12 supply in the subtropical Pacific. These findings show that availability of B12 and α-ribazole affect growth and composition of prokaryotic and protist communities in oceanic systems thus revealing far-reaching consequences of methionine biosynthesis and other B12-dependent enzymatic reactions on a community level.
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21
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Koçak E, Nigiz Ş, Özkan E, Erdoğan Kablan S, Hazirolan G, Nemutlu E, Kır S, Sağıroğlu M, Özkul C. Exometabolomic Analysis of Susceptible and Multi-Drug Resistant Pseudomonas aeruginosa. Lett Appl Microbiol 2022; 75:234-242. [PMID: 35419823 DOI: 10.1111/lam.13719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Multidrug resistant (MDR) Pseudomonas aeruginosa strains have recently become one of the major public health concerns worldwide leading to difficulties in selecting appropriate antibiotic treatment. Thus, it is important to elucidate the characteristics of MDR isolates. Herein, we aimed to determine the unique exometabolome profile of P. aeruginosa clinical isolates in monocultures that comprise high resistance to multiple antibiotics, and compare the differential metabolite profiles obtained from susceptible isolates by using GC/MS. Our results showed that partial least square-discriminant analysis (PLS-DA) score plot clearly discriminated the MDR and susceptible isolates indicating the altered exometabolite profiles, and highlighted the significantly enriched levels of trehalose and glutamic acid in MDR isolates. Expression of trehalose synthase (treS) was also 1.5 fold higher in MDR isolates, relatively to susceptible isolates. Overall, our study provides insights into the distinct footprints of MDR P. aeruginosa isolates in mono-culture.
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Affiliation(s)
- Engin Koçak
- Department of Analytical Chemistry, Faculty of Gulhane Pharmacy, Health Sciences University, Ankara, Turkey
| | - Şeyma Nigiz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ece Özkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Başkent University, Ankara, Turkey
| | - Sevilay Erdoğan Kablan
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Gülşen Hazirolan
- Department of Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Emirhan Nemutlu
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Sedef Kır
- Department of Analytical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Meral Sağıroğlu
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Ceren Özkul
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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22
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Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
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Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
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23
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Zoccarato L, Sher D, Miki T, Segrè D, Grossart HP. A comparative whole-genome approach identifies bacterial traits for marine microbial interactions. Commun Biol 2022; 5:276. [PMID: 35347228 PMCID: PMC8960797 DOI: 10.1038/s42003-022-03184-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
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Affiliation(s)
- Luca Zoccarato
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, 3498838, Haifa, Israel.
| | - Takeshi Miki
- Faculty of Advanced Science and Technology, Ryukoku University, 520-2194, Otsu, Japan
| | - Daniel Segrè
- Departments of Biology, Biomedical Engineering, Physics, Boston University, 02215, Boston, MA, USA
- Bioinformatics Program & Biological Design Center, Boston University, 02215, Boston, MA, USA
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.
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24
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Yu JSL, Correia-Melo C, Zorrilla F, Herrera-Dominguez L, Wu MY, Hartl J, Campbell K, Blasche S, Kreidl M, Egger AS, Messner CB, Demichev V, Freiwald A, Mülleder M, Howell M, Berman J, Patil KR, Alam MT, Ralser M. Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance. Nat Microbiol 2022; 7:542-555. [PMID: 35314781 PMCID: PMC8975748 DOI: 10.1038/s41564-022-01072-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 01/28/2022] [Indexed: 12/30/2022]
Abstract
Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic–prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically. Using microbiome data analysis and a self-establishing metabolically cooperating yeast community model, the authors show that the presence of auxotrophs in a microbial community increases metabolic interactions between cells and fosters antimicrobial drug tolerance.
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Affiliation(s)
- Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Francisco Zorrilla
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucia Herrera-Dominguez
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Mary Y Wu
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Johannes Hartl
- Department of Biochemistry, Charité University Medicine, Berlin, Germany
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sonja Blasche
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marco Kreidl
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vadim Demichev
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité University Medicine, Berlin, Germany.,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany
| | - Michael Howell
- High-Throughput Screening, The Francis Crick Institute, London, UK
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Kiran R Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mohammad Tauqeer Alam
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE. .,Warwick Medical School, University of Warwick, Coventry, UK.
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK. .,Department of Biochemistry, Charité University Medicine, Berlin, Germany. .,Core Facility - High Throughput Mass Spectrometry, Charité University Medicine, Berlin, Germany.
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25
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Tomasch J, Ringel V, Wang H, Freese HM, Bartling P, Brinkmann H, Vollmers J, Jarek M, Wagner-Döbler I, Petersen J. Fatal affairs - conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales. Microb Genom 2022; 8:000787. [PMID: 35254236 PMCID: PMC9176285 DOI: 10.1099/mgen.0.000787] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The roseobacter group of marine bacteria is characterized by a mosaic distribution of ecologically important phenotypes. These are often encoded on mobile extrachromosomal replicons. So far, conjugation had only been experimentally proven between the two model organisms Phaeobacter inhibens and Dinoroseobacter shibae. Here, we show that two large natural RepABC-type plasmids from D. shibae can be transferred into representatives of all known major Rhodobacterales lineages. Complete genome sequencing of the newly established Phaeobacter inhibens transconjugants confirmed their genomic integrity. The conjugated plasmids were stably maintained as single copy number replicons in the genuine as well as the new host. Co-cultivation of Phaeobacter inhibens and the transconjugants with the dinoflagellate Prorocentrum minimum demonstrated that Phaeobacter inhibens is a probiotic strain that improves the yield and stability of the dinoflagellate culture. The transconjugant carrying the 191 kb plasmid, but not the 126 kb sister plasmid, killed the dinoflagellate in co-culture.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Science – Centre Algatech, Třeboň, Czech Republic
- *Correspondence: Jürgen Tomasch,
| | - Victoria Ringel
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hui Wang
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Heike M. Freese
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pascal Bartling
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Present address: Schülke & Mayr GmbH, Norderstedt, Germany
| | - Henner Brinkmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5: Biotechnology and Microbial Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michael Jarek
- Group Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Jörn Petersen
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- *Correspondence: Jörn Petersen,
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26
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Hou C, Qu T, Zhao X, Xu J, Zhong Y, Guan C, Zhang H, Lin Z, Tang X, Wang Y. Diel metabolism of Yellow Sea green tide algae alters bacterial community composition under in situ seawater acidification of coastal areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150759. [PMID: 34619190 DOI: 10.1016/j.scitotenv.2021.150759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Ocean acidification in coastal seawaters is a complex process, with coastal pH being affected by numerous factors including watershed and biological processes that also support metabolically diverse bacterial communities. The world's largest macroalgal blooms have occurred consecutively in the Yellow Sea over the last 13 years. In particular, algal mats formed by Yellow Sea green tides (YSGT) significantly influence coastal environments. Herein, we hypothesized that 1) inorganic carbonate chemistry in coastal areas is altered by diel metabolism of these giant algal mats and that 2) bacterial community composition in diffusive boundary layers might be altered along diel cycles due to algal mat metabolism. In situ studies indicated that algal mat metabolism led to changes in diel pH and CO2 in affected seawaters. Such metabolic activities could intensify diel pH fluctuations in algal mat diffusive boundary layers, as noted by pH fluctuations of 0.22 ± 0.01 units, and pCO2 fluctuations of 214.62 ± 29.37 μatm per day. In contrast, pH fluctuations of 0.11 ± 0.02 units and pCO2 fluctuations of 79.02 ± 42.70 μatm were noted in unaffected areas. Furthermore, the bacterial community composition associated with diffusive algal boundary layers, including those of ambient bacteria and epiphytic bacteria, exhibited diel changes, while endophytic bacterial communities were relatively stable. Flavobacteriaceae were particularly highly abundant taxa in the ambient and epiphytic bacterial communities and exhibited increased abundances at night but sharp decreases in abundances during daytime. Flavobacteriaceae are heterotrophic taxa that could contribute to coastal area acidification at night due to the transformation of organic carbon to inorganic carbon. These results provide new insights to understand the variability in coastal ocean acidification via harmful algal blooms while providing a framework for evaluating the effects of YSGT on costal carbon cycling.
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Affiliation(s)
- Chengzong Hou
- College of Marine Life Sciences, Ocean University of China, China.
| | - Tongfei Qu
- College of Marine Life Sciences, Ocean University of China, China.
| | - Xinyu Zhao
- College of Marine Life Sciences, Ocean University of China, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, China
| | - Jinhui Xu
- College of Marine Life Sciences, Ocean University of China, China.
| | - Yi Zhong
- College of Marine Life Sciences, Ocean University of China, China.
| | - Chen Guan
- College of Marine Life Sciences, Ocean University of China, China.
| | - Huanxin Zhang
- College of Geography and Environment, Shandong Normal University, Jinan 250000, China
| | - Zhihao Lin
- College of Marine Life Sciences, Ocean University of China, China.
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, China.
| | - Ying Wang
- College of Marine Life Sciences, Ocean University of China, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, China.
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27
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Selak L, Osterholz H, Stanković I, Hanžek N, Udovič MG, Dittmar T, Orlić S. Adaptations of microbial communities and dissolved organics to seasonal pressures in a mesotrophic coastal Mediterranean lake. Environ Microbiol 2022; 24:2282-2298. [PMID: 35106913 DOI: 10.1111/1462-2920.15924] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/29/2022]
Abstract
In lake ecosystems, changes in eukaryotic and prokaryotic microbes and the concentration and availability of dissolved organic matter (DOM) produced within or supplied to the system by allochthonous sources are components that characterize complex processes in the microbial loop. We address seasonal changes of microbial communities and DOM in the largest Croatian lake, Vrana. This shallow lake is connected to the Adriatic Sea and is impacted by agricultural activity. Microbial community and DOM structure were driven by several environmental stressors, including drought, seawater intrusion, and heavy precipitation events. Bacterial composition of different lifestyles (free-living and particle-associated) differed and only a part of the particle-associated bacteria correlated with microbial eukaryotes. Oscillations of cyanobacterial relative abundance along with chlorophyll a revealed a high primary production season characterized by increased levels of autochthonous DOM that promoted bacterial processes of organic matter degradation. From our results, we infer that in coastal freshwater lakes dependent on precipitation-evaporation balance, prolonged dry season coupled with heavy irrigation impact microbial communities at different trophic levels even if salinity increases only slightly and allochthonous DOM inputs decrease. These pressures, if applied more frequently or at higher concentrations, could have the potential to overturn the trophic state of the lake. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Helena Osterholz
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany.,Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Igor Stanković
- Hrvatske vode, Central Water Management Laboratory, Zagreb, Croatia
| | - Nikola Hanžek
- Hrvatske vode, Central Water Management Laboratory, Zagreb, Croatia
| | - Marija Gligora Udovič
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, Zagreb, Croatia
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Sandi Orlić
- Ruđer Bošković Institute, Zagreb, Croatia.,Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
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28
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Durán P, Flores-Uribe J, Wippel K, Zhang P, Guan R, Melkonian B, Melkonian M, Garrido-Oter R. Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota. Nat Commun 2022; 13:406. [PMID: 35058457 PMCID: PMC8776852 DOI: 10.1038/s41467-022-28055-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Microscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Using synthetic communities derived from C. reinhardtii and Arabidopsis thaliana, we show that phycosphere and root bacteria assemble into taxonomically similar communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggest the existence of shared ecological principles driving the assembly of the A. thaliana root and C. reinhardtii phycosphere microbiota, despite the vast evolutionary distance between these two photosynthetic organisms.
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Affiliation(s)
- Paloma Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences, 40225, Düsseldorf, Germany
| | - José Flores-Uribe
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Kathrin Wippel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Rui Guan
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Barbara Melkonian
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Michael Melkonian
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, 40225, Düsseldorf, Germany.
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29
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Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, Garcia SL. A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Front Microbiol 2022; 12:761869. [PMID: 35069467 PMCID: PMC8767057 DOI: 10.3389/fmicb.2021.761869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/15/2021] [Indexed: 01/09/2023] Open
Abstract
Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Julia K. Nuy
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Sarahi L. Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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30
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Lücken L, Lennartz ST, Froehlich J, Blasius B. Emergent Diversity and Persistent Turnover in Evolving Microbial Cross-Feeding Networks. FRONTIERS IN NETWORK PHYSIOLOGY 2022; 2:834057. [PMID: 36926111 PMCID: PMC10013070 DOI: 10.3389/fnetp.2022.834057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022]
Abstract
A distinguishing feature of many ecological networks in the microbial realm is the diversity of substrates that could potentially serve as energy sources for microbial consumers. The microorganisms are themselves the agents of compound diversification via metabolite excretion or overflow metabolism. It has been suggested that the emerging richness of different substrates is an important condition for the immense biological diversity in microbial ecosystems. In this work, we study how complex cross-feeding networks (CFN) of microbial species may develop from a simple initial community given some elemental evolutionary mechanisms of resource-dependent speciation and extinctions using a network flow model. We report results of several numerical experiments and report an in-depth analysis of the evolutionary dynamics. We find that even in stable environments, the system is subject to persisting turnover, indicating an ongoing co-evolution. Further, we compare the impact of different parameters, such as the ratio of mineralization, as well as the metabolic versatility and variability on the evolving community structure. The results imply that high microbial and molecular diversity is an emergent property of evolution in cross-feeding networks, which affects transformation and accumulation of substrates in natural systems, such as soils and oceans, with potential relevance to biotechnological applications.
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Affiliation(s)
- Leonhard Lücken
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Sinikka T Lennartz
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.,Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jule Froehlich
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Bernd Blasius
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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31
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OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6585976. [DOI: 10.1093/femsre/fuac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
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32
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Sichert A, Cordero OX. Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology. Front Microbiol 2021; 12:705082. [PMID: 34690949 PMCID: PMC8531407 DOI: 10.3389/fmicb.2021.705082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.
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33
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Marine dissolved organic matter: a vast and unexplored molecular space. Appl Microbiol Biotechnol 2021; 105:7225-7239. [PMID: 34536106 PMCID: PMC8494709 DOI: 10.1007/s00253-021-11489-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/02/2023]
Abstract
Abstract Marine dissolved organic matter (DOM) comprises a vast and unexplored molecular space. Most of it resided in the oceans for thousands of years. It is among the most diverse molecular mixtures known, consisting of millions of individual compounds. More than 1 Eg of this material exists on the planet. As such, it comprises a formidable source of natural products promising significant potential for new biotechnological purposes. Great emphasis has been placed on understanding the role of DOM in biogeochemical cycles and climate attenuation, its lifespan, interaction with microorganisms, as well as its molecular composition. Yet, probing DOM bioactivities is in its infancy, largely because it is technically challenging due to the chemical complexity of the material. It is of considerable interest to develop technologies capable to better discern DOM bioactivities. Modern screening technologies are opening new avenues allowing accelerated identification of bioactivities for small molecules from natural products. These methods diminish a priori the need for laborious chemical fractionation. We examine here the application of untargeted metabolomics and multiplexed high-throughput molecular-phenotypic screening techniques that are providing first insights on previously undetectable DOM bioactivities. Key points • Marine DOM is a vast, unexplored biotechnological resource. • Untargeted bioscreening approaches are emerging for natural product screening. • Perspectives for developing bioscreening platforms for marine DOM are discussed.
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34
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Isaac A, Francis B, Amann RI, Amin SA. Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales. Front Microbiol 2021; 12:718297. [PMID: 34447362 PMCID: PMC8383342 DOI: 10.3389/fmicb.2021.718297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.
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Affiliation(s)
- Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ben Francis
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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35
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Wang R, Gallant É, Wilson MZ, Wu Y, Li A, Gitai Z, Seyedsayamdost MR. Algal p-coumaric acid induces oxidative stress and siderophore biosynthesis in the bacterial symbiont Phaeobacter inhibens. Cell Chem Biol 2021; 29:670-679.e5. [PMID: 34437838 DOI: 10.1016/j.chembiol.2021.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/18/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
Abstract
The marine alpha-proteobacterium Phaeobacter inhibens engages in intermittent symbioses with microalgae. The symbiosis is biphasic and concludes in a parasitic phase, during which the bacteria release algaecidal metabolites in response to algal p-coumaric acid (pCA). The cell-wide effects of pCA on P. inhibens remain unknown. Herein, we report a microarray-based transcriptomic study and find that genes related to the oxidative stress response and secondary metabolism are upregulated most, while those associated with energy production and motility are downregulated in the presence of pCA. Among genes upregulated is a previously unannotated biosynthetic gene cluster and, using a combination of gene deletions and metabolic profiling, we show that it gives rise to an unreported siderophore, roseobactin. The simultaneous production of algaecides and roseobactin in the parasitic phase allows the bacteria to take up any iron that is released from dying algal cells, thereby securing a limited micronutrient.
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Affiliation(s)
- Rurun Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Étienne Gallant
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Maxwell Z Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihan Wu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Anran Li
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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36
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Periphytic microbial response to environmental phosphate bioavailability - relevance to P management in paddy fields. Appl Environ Microbiol 2021; 87:e0120121. [PMID: 34347511 DOI: 10.1128/aem.01201-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Periphyton occurs widely in shallow-water ecosystems such as paddy fields and plays critical parts in regulating local phosphorus cycling. As such, understanding the mechanisms of the biofilm's response to environmental P variability may lead to better perceptions of P utilization and retention in rice farms. Present study aims at exploring the biological and biochemical processes underlying periphyton's P buffering capability through examining changes in community structure, phosphorus uptake and storage, and molecular makeup of exometabolome at different levels of P availability. Under stressed (both excessive and scarce) phosphorus conditions, we found increased populations of the bacterial genus capable of transforming orthophosphate to polyphosphate, as well as mixotrophic algae who can survive through phagotrophy. These results were corroborated by observed polyphosphate buildup under low and high P treatment. Exometabolomic analyses further revealed that periphytic organisms may substitute S-containing lipids for phospholipids, use siderophores to dissolve iron (hydr)oxides to scavenge adsorbed P, and synthesize auxins to resist phosphorus starvation. These findings not only shed light on the mechanistic insights responsible for driving the periphytic P buffer but attest to the ecological roles of periphyton in aiding plants such as rice to overcome P limitations in natural environment. Importance The ability of periphyton to buffer environmental P in shallow aquatic ecosystems may be a natural lesson on P utilization and retention in paddy fields. This work revealed the routes and tools through which periphytic organisms adapt to and regulate ambient P fluctuation. The mechanistic understanding further implicates that the biofilm may serve rice plants to alleviate P stress. Additional results from extracellular metabolite analyses suggest the dissolved periphytic exometabolome can be a valuable nutrient source for soil microbes and plants to reduce biosynthetic costs. These discoveries have the potential to improve our understanding of biogeochemical cycling of phosphorus in general and to refine P management strategies for rice farm in particular.
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37
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Ortega-Retuerta E, Devresse Q, Caparros J, Marie B, Crispi O, Catala P, Joux F, Obernosterer I. Dissolved organic matter released by two marine heterotrophic bacterial strains and its bioavailability for natural prokaryotic communities. Environ Microbiol 2021; 23:1363-1378. [PMID: 33185969 DOI: 10.1111/1462-2920.15306] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/04/2020] [Indexed: 01/04/2023]
Abstract
Marine heterotrophic prokaryotes (HP) play a key role in organic matter processing in the ocean; however, the view of HP as dissolved organic matter (DOM) sources remains underexplored. In this study, we quantified and optically characterized the DOM produced by two single marine bacterial strains. We then tested the availability of these DOM sources to in situ Mediterranean Sea HP communities. Two bacterial strains were used: Photobacterium angustum (a copiotrophic gammaproteobacterium) and Sphingopyxis alaskensis (an oligotrophic alphaproteobacterium). When cultivated on glucose as the sole carbon source, the two strains released from 7% to 23% of initial glucose as bacterial derived DOM (B-DOM), the quality of which (as enrichment in humic or protein-like substances) differed between strains. B-DOM induced significant growth and carbon consumption of natural HP communities, suggesting that it was partly labile. However, B-DOM consistently promoted lower prokaryotic growth efficiencies than in situ DOM. In addition, B-DOM changed HP exoenzymatic activities, enhancing aminopeptidase activity when degrading P. angustum DOM, and alkaline phosphatase activity when using S. alaskensis DOM, and promoted differences in HP diversity and composition. DOM produced by HP affects in situ prokaryotic metabolism and diversity, thus changing the pathways for DOM cycling (e.g. respiration over biomass production) in the ocean.
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Affiliation(s)
- Eva Ortega-Retuerta
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Quentin Devresse
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France.,Geomar Helmholtz Centre for Ocean Research Kiel, Germany
| | - Jocelyne Caparros
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Barbara Marie
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Olivier Crispi
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Philippe Catala
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Fabien Joux
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Ingrid Obernosterer
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
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38
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Goto S, Tada Y, Suzuki K, Yamashita Y. Evaluation of the Production of Dissolved Organic Matter by Three Marine Bacterial Strains. Front Microbiol 2020; 11:584419. [PMID: 33178167 PMCID: PMC7593260 DOI: 10.3389/fmicb.2020.584419] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 11/17/2022] Open
Abstract
A large part of marine dissolved organic matter (DOM) is considered to be recalcitrant DOM (RDOM) produced by marine bacteria. However, it is still unclear whether differences in bacterial species and/or physiology control the efficiency of RDOM production. Here, batch culture experiments with glucose as the sole carbon source were carried out using three model marine bacterial strains, namely, Alteromonas macleodii (Alt), Vibrio splendidus (Vib), and Phaeobacter gallaeciensis (Pha). Dissolved organic carbon (DOC) concentrations drastically decreased during the exponential growth phases of these bacteria due to the consumption of glucose. The efficiency of bacterial DOC production at the end of incubation was largely different among the strains and was higher for Vib (20%) than for the other two strains (Alt, 4%; Pha, 6%). All strains produced fluorescent DOM (FDOM), including humic-like FDOM which is considered as recalcitrant component in the ocean, even though the composition of bacterial FDOM was also different among the strains. The efficiency of humic-like FDOM production during the exponential growth phase was different among the bacterial strains; that is, Pha produced humic-like FDOM efficiently compared with the other two species. The efficiency of humic-like FDOM production with mineralization of organic matter was lower during the exponential growth phase than during the stationary phase of Alt and Pha. Four processes for the production of bacterially derived recalcitrant humic-like FDOM are suggested from this study: (1) production during active growing (in all strains), (2) production with the reutilization of bacterial DOM (Alt), (3) production with the consumption of cellular materials (Pha), and (4) release from lysis (Vib). Our results suggest that bacterial species and physiology can regulate RDOM production and accumulation in the ocean.
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Affiliation(s)
- Shuji Goto
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Yuya Tada
- National Institute for Minamata Disease, Minamata, Japan
| | - Koji Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Youhei Yamashita
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan.,Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
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39
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Shibl AA, Isaac A, Ochsenkühn MA, Cárdenas A, Fei C, Behringer G, Arnoux M, Drou N, Santos MP, Gunsalus KC, Voolstra CR, Amin SA. Diatom modulation of select bacteria through use of two unique secondary metabolites. Proc Natl Acad Sci U S A 2020; 117:27445-27455. [PMID: 33067398 PMCID: PMC7959551 DOI: 10.1073/pnas.2012088117] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world's oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.
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Affiliation(s)
- Ahmed A Shibl
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ashley Isaac
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- International Max Planck Research School of Marine Microbiology, University of Bremen, Bremen 28334, Germany
| | - Michael A Ochsenkühn
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz 78467, Germany
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Cong Fei
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Gregory Behringer
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Marc Arnoux
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Nizar Drou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Miraflor P Santos
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz 78467, Germany
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Shady A Amin
- Marine Microbial Ecology Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates;
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40
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Liu S, Baetge N, Comstock J, Opalk K, Parsons R, Halewood E, English CJ, Giovannoni S, Bolaños LM, Nelson CE, Vergin K, Carlson CA. Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability. Front Microbiol 2020; 11:580397. [PMID: 33117322 PMCID: PMC7575717 DOI: 10.3389/fmicb.2020.580397] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/03/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using 13C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant 13C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant 13C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.
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Affiliation(s)
- Shuting Liu
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nicholas Baetge
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Jacqueline Comstock
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Rachel Parsons
- Bermuda Institute of Ocean Sciences, Saint George, Bermuda
| | - Elisa Halewood
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Chance J English
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Luis M Bolaños
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Hawai'i Sea Grant, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Kevin Vergin
- Microbial DNA Analytics, Phoenix, OR, United States
| | - Craig A Carlson
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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41
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Zecher K, Hayes KR, Philipp B. Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere. Front Microbiol 2020; 11:533894. [PMID: 33123096 PMCID: PMC7574528 DOI: 10.3389/fmicb.2020.533894] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/10/2020] [Indexed: 11/13/2022] Open
Abstract
Dissolved organic nitrogen (DON) compounds such as methylamines (MAs) and glycine betaine (GBT) occur at detectable concentrations in marine habitats and are also produced and released by microalgae. For many marine bacteria, these DON compounds can serve as carbon, energy, and nitrogen sources, but microalgae usually cannot metabolize them. Interestingly though, it was previously shown that Donghicola sp. strain KarMa—a member of the marine Rhodobacteraceae—can cross-feed ammonium such that the ammonium it produces upon degrading monomethylamine (MMA) then serves as nitrogen source for the diatom Phaeodactylum tricornutum; thus, these organisms form a mutual metabolic interaction under photoautotrophic conditions. In the present study, we investigated whether this interaction plays a broader role in bacteria–diatom interactions in general. Results showed that cross-feeding between strain KarMa and P. tricornutum was also possible with di- and trimethylamine as well as with GBT. Further, cross-feeding of strain KarMa was also observed in cocultures with the diatoms Amphora coffeaeformis and Thalassiosira pseudonana with MMA as the sole nitrogen source. Regarding cross-feeding involving other Rhodobacteraceae strains, the in silico analysis of MA and GBT degradation pathways indicated that algae-associated Rhodobacteraceae-type strains likely interact with P. tricornutum in a similar manner as the strain KarMa does. For these types of strains (such as Celeribacter halophilus, Roseobacter denitrificans, Roseovarius indicus, Ruegeria pomeroyi, and Sulfitobacter noctilucicola), ammonium cross-feeding after methylamine degradation showed species-specific patterns, whereas bacterial GBT degradation always led to diatom growth. Overall, the degradation of DON compounds by the Rhodobacteraceae family and the subsequent cross-feeding of ammonium may represent a widespread, organism-specific, and regulated metabolic interaction for establishing and stabilizing associations with photoautotrophic diatoms in the oceans.
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Affiliation(s)
- Karsten Zecher
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Kristiane Rebecca Hayes
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Bodo Philipp
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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42
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Kasuga I, Suzuki M, Kurisu F, Furumai H. Molecular-level characterization of biodegradable organic matter causing microbial regrowth in drinking water by non-target screening using Orbitrap mass spectrometry. WATER RESEARCH 2020; 184:116130. [PMID: 32731039 DOI: 10.1016/j.watres.2020.116130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/14/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Ikuro Kasuga
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan.
| | - Miyu Suzuki
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8656, Japan
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43
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Dell'Anno F, Brunet C, van Zyl LJ, Trindade M, Golyshin PN, Dell'Anno A, Ianora A, Sansone C. Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments. Microorganisms 2020; 8:E1402. [PMID: 32933071 PMCID: PMC7564820 DOI: 10.3390/microorganisms8091402] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 01/08/2023] Open
Abstract
Investigations on the ability of bacteria to enhance removal of hydrocarbons and reduce heavy metal toxicity in sediments are necessary to design more effective bioremediation strategies. In this study, five bacterial strains, Halomonas sp. SZN1, Alcanivorax sp. SZN2, Pseudoalteromonas sp. SZN3, Epibacterium sp. SZN4, and Virgibacillus sp. SZN7, were isolated from polluted sediments from an abandoned industrial site in the Gulf of Naples, Mediterranean Sea, and tested for their bioremediation efficiency on sediment samples collected from the same site. These bacteria were added as consortia or as individual cultures into polluted sediments to assess biodegradation efficiency of polycyclic aromatic hydrocarbons and heavy metal immobilisation capacity. Our results indicate that these bacteria were able to remove polycyclic aromatic hydrocarbons, with a removal rate up to ca. 80% for dibenzo-anthracene. In addition, these bacteria reduced arsenic, lead, and cadmium mobility by promoting their partitioning into less mobile and bioavailable fractions. Microbial consortia generally showed higher performance toward pollutants as compared with pure isolates, suggesting potential synergistic interactions able to enhance bioremediation capacity. Overall, our findings suggest that highly polluted sediments select for bacteria efficient at reducing the toxicity of hazardous compounds, paving the way for scaled-up bioremediation trials.
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Affiliation(s)
- Filippo Dell'Anno
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa Comunale, 80121 Napoli, Italy
| | - Christophe Brunet
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa Comunale, 80121 Napoli, Italy
| | - Leonardo Joaquim van Zyl
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - Marla Trindade
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - Peter N Golyshin
- Centre for Environmental Biotechnology (CEB), School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Antonio Dell'Anno
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Adrianna Ianora
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa Comunale, 80121 Napoli, Italy
| | - Clementina Sansone
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa Comunale, 80121 Napoli, Italy
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44
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Hach PF, Marchant HK, Krupke A, Riedel T, Meier DV, Lavik G, Holtappels M, Dittmar T, Kuypers MMM. Rapid microbial diversification of dissolved organic matter in oceanic surface waters leads to carbon sequestration. Sci Rep 2020; 10:13025. [PMID: 32747679 PMCID: PMC7400608 DOI: 10.1038/s41598-020-69930-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/14/2020] [Indexed: 11/09/2022] Open
Abstract
The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years. Little is known however, about the transformation and cycling that labile DOM undergoes in the first hours upon its release from phytoplankton. Here we provide direct experimental evidence showing that within hours of labile DOM release, its breakdown and recombination with ambient DOM leads to the formation of a diverse array of new molecules in oligotrophic North Atlantic surface waters. Furthermore, our results reveal a preferential breakdown of N and P containing molecules versus those containing only carbon. Hence, we show the preferential breakdown and molecular diversification are the crucial first steps in the eventual formation of carbon rich DOM that is resistant to microbial remineralization.
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Affiliation(s)
- Philipp F Hach
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Hannah K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Andreas Krupke
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Thomas Riedel
- IWW Water Centre, Moritzstr. 26, 45476, Mülheim an der Ruhr, Germany
| | - Dimitri V Meier
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Moritz Holtappels
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Thorsten Dittmar
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), at the Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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Sokolovskaya OM, Shelton AN, Taga ME. Sharing vitamins: Cobamides unveil microbial interactions. Science 2020; 369:369/6499/eaba0165. [PMID: 32631870 DOI: 10.1126/science.aba0165] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda N Shelton
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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46
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Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal. Sci Rep 2020; 10:9449. [PMID: 32523048 PMCID: PMC7287063 DOI: 10.1038/s41598-020-65941-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.
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47
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Bock C, Jensen M, Forster D, Marks S, Nuy J, Psenner R, Beisser D, Boenigk J. Factors shaping community patterns of protists and bacteria on a European scale. Environ Microbiol 2020; 22:2243-2260. [PMID: 32202362 DOI: 10.1111/1462-2920.14992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/18/2020] [Indexed: 01/19/2023]
Abstract
Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.
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Affiliation(s)
- Christina Bock
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Manfred Jensen
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Str. 14, 67663, Kaiserslautern, Germany
| | - Sabina Marks
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Julia Nuy
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Roland Psenner
- Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Daniela Beisser
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
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Cook KV, Li C, Cai H, Krumholz LR, Hambright KD, Paerl HW, Steffen MM, Wilson AE, Burford MA, Grossart H, Hamilton DP, Jiang H, Sukenik A, Latour D, Meyer EI, Padisák J, Qin B, Zamor RM, Zhu G. The global Microcystis interactome. LIMNOLOGY AND OCEANOGRAPHY 2020; 65:S194-S207. [PMID: 32051648 PMCID: PMC7003799 DOI: 10.1002/lno.11361] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/22/2019] [Accepted: 09/24/2019] [Indexed: 05/06/2023]
Abstract
Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.
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Affiliation(s)
- Katherine V. Cook
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
- Program in Ecology and Evolutionary Biology and the Geographical Ecology Group, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Chuang Li
- Department of Microbiology and Plant Biology and Institute for Energy and the EnvironmentThe University of OklahomaNormanOklahoma
| | - Haiyuan Cai
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Lee R. Krumholz
- Department of Microbiology and Plant Biology and Institute for Energy and the EnvironmentThe University of OklahomaNormanOklahoma
| | - K. David Hambright
- Plankton Ecology and Limnology Laboratory, Department of BiologyThe University of OklahomaNormanOklahoma
- Program in Ecology and Evolutionary Biology and the Geographical Ecology Group, Department of BiologyThe University of OklahomaNormanOklahoma
| | - Hans W. Paerl
- Institute of Marine Sciences, The University of North Carolina at Chapel HillMorehead CityNorth Carolina
| | | | - Alan E. Wilson
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabama
| | - Michele A. Burford
- Australian Rivers Institute and School of Environment and Science, Griffith UniversityNathanQueenslandAustralia
| | - Hans‐Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Stechlin, and Institute for Biochemistry and BiologyPotsdam UniversityPotsdamGermany
| | - David P. Hamilton
- Australian Rivers Institute and School of Environment and Science, Griffith UniversityNathanQueenslandAustralia
- Environmental Research Institute, University of WaikatoWaikatoNew Zealand
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
| | - Assaf Sukenik
- Israel Oceanographic and Limnological ResearchThe Yigal Allon Kinneret Limnological LaboratoryMigdalIsrael
| | | | - Elisabeth I. Meyer
- Institute for Evolution and Biodiversity, University of MünsterMünsterGermany
| | - Judit Padisák
- Department of LimnologyInstitute of Environmental Science, University of PannoniaVeszprémHungary
| | - Boqiang Qin
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
| | | | - Guangwei Zhu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjingChina
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Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography-Mass Spectrometry. mSystems 2019; 4:4/6/e00638-19. [PMID: 31822601 PMCID: PMC6906741 DOI: 10.1128/msystems.00638-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other “omics” (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats. Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes in vitro and in vivo. First, we measured the production and consumption of metabolites during the culture of a heterotrophic bacterium, Marinobacter adhaerens. Our approach revealed successional uptake of amino acids, while sugars were not consumed. These results show that exocellular metabolomics provides insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered high concentrations of sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a nontargeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans. IMPORTANCE Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other “omics” (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.
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50
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Bayer B, Hansman RL, Bittner MJ, Noriega-Ortega BE, Niggemann J, Dittmar T, Herndl GJ. Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean. Environ Microbiol 2019; 21:4062-4075. [PMID: 31336026 PMCID: PMC6899801 DOI: 10.1111/1462-2920.14755] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/25/2023]
Abstract
Ammonia‐oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen‐containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%–1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.
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Affiliation(s)
- Barbara Bayer
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria
| | - Roberta L Hansman
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria.,International Atomic Energy Agency - Environment Laboratories, Radioecology Laboratory, 98000, Monaco, Monaco
| | - Meriel J Bittner
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria
| | - Beatriz E Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Jutta Niggemann
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Gerhard J Herndl
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, 1790, AB Den Burg, Texel, The Netherlands
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