1
|
Nauer PA, Kessler AJ, Hall P, Popa ME, ten Hietbrink S, Hutchinson T, Wong WW, Attard K, Glud RN, Greening C, Cook PLM. Pulses of labile carbon cause transient decoupling of fermentation and respiration in permeable sediments. LIMNOLOGY AND OCEANOGRAPHY 2023; 68:2141-2152. [PMID: 38516532 PMCID: PMC10952694 DOI: 10.1002/lno.12411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/07/2022] [Accepted: 07/15/2023] [Indexed: 03/23/2024]
Abstract
Dihydrogen (H2) is an important intermediate in anaerobic microbial processes, and concentrations are tightly controlled by thermodynamic limits of consumption and production. However, recent studies reported unusual H2 accumulation in permeable marine sediments under anoxic conditions, suggesting decoupling of fermentation and sulfate reduction, the dominant respiratory process in anoxic permeable marine sediments. Yet, the extent, prevalence and potential triggers for such H2 accumulation and decoupling remain unknown. We surveyed H2 concentrations in situ at different settings of permeable sand and found that H2 accumulation was only observed during a coral spawning event on the Great Barrier Reef. A flume experiment with organic matter addition to the water column showed a rapid accumulation of hydrogen within the sediment. Laboratory experiments were used to explore the effect of oxygen exposure, physical disturbance and organic matter inputs on H2 accumulation. Oxygen exposure had little effect on H2 accumulation in permeable sediments suggesting both fermenters and sulfate reducers survive and rapidly resume activity after exposure to oxygen. Mild physical disturbance mimicking sediment resuspension had little effect on H2 accumulation; however, vigorous shaking led to a transient accumulation of H2 and release of dissolved organic carbon suggesting mechanical disturbance and cell destruction led to organic matter release and transient decoupling of fermenters and sulfate reducers. In summary, the highly dynamic nature of permeable sediments and its microbial community allows for rapid but transient decoupling of fermentation and respiration after a C pulse, leading to high H2 levels in the sediment.
Collapse
Affiliation(s)
- Philipp A. Nauer
- Water StudiesSchool of Chemistry, Monash UniversityClaytonVictoriaAustralia
| | - Adam J. Kessler
- School of Earth Atmosphere and Environment, Monash UniversityClaytonVictoriaAustralia
| | | | - Maria Elena Popa
- Institute for Marine and Atmospheric research Utrecht (IMAU), Utrecht UniversityUtrechtNetherlands
| | - Sophie ten Hietbrink
- Institute for Marine and Atmospheric research Utrecht (IMAU), Utrecht UniversityUtrechtNetherlands
| | - Tess Hutchinson
- Water StudiesSchool of Chemistry, Monash UniversityClaytonVictoriaAustralia
| | - Wei Wen Wong
- Water StudiesSchool of Chemistry, Monash UniversityClaytonVictoriaAustralia
| | - Karl Attard
- Nordcee and HADAL, Department of BiologyUniversity of Southern DenmarkOdense MDenmark
- Danish Institute for Advanced Study, University of Southern DenmarkOdense MDenmark
| | - Ronnie N. Glud
- Nordcee and HADAL, Department of BiologyUniversity of Southern DenmarkOdense MDenmark
- Danish Institute for Advanced Study, University of Southern DenmarkOdense MDenmark
- Department of Ocean and Environmental SciencesTokyo University of Marine Science and TechnologyTokyoJapan
| | - Chris Greening
- Department of MicrobiologyBiomedicine Discovery InstituteClaytonVictoriaAustralia
| | - Perran L. M. Cook
- Water StudiesSchool of Chemistry, Monash UniversityClaytonVictoriaAustralia
| |
Collapse
|
2
|
Dent MR, Weaver BR, Roberts MG, Burstyn JN. Carbon Monoxide-Sensing Transcription Factors: Regulators of Microbial Carbon Monoxide Oxidation Pathway Gene Expression. J Bacteriol 2023; 205:e0033222. [PMID: 37154694 PMCID: PMC10210986 DOI: 10.1128/jb.00332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Carbon monoxide (CO) serves as a source of energy and carbon for a diverse set of microbes found in anaerobic and aerobic environments. The enzymes that bacteria and archaea use to oxidize CO depend upon complex metallocofactors that require accessory proteins for assembly and proper function. This complexity comes at a high energetic cost and necessitates strict regulation of CO metabolic pathways in facultative CO metabolizers to ensure that gene expression occurs only when CO concentrations and redox conditions are appropriate. In this review, we examine two known heme-dependent transcription factors, CooA and RcoM, that regulate inducible CO metabolism pathways in anaerobic and aerobic microorganisms. We provide an analysis of the known physiological and genomic contexts of these sensors and employ this analysis to contextualize known biochemical properties. In addition, we describe a growing list of putative transcription factors associated with CO metabolism that potentially use cofactors other than heme to sense CO.
Collapse
Affiliation(s)
- Matthew R. Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian R. Weaver
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Madeleine G. Roberts
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| |
Collapse
|
3
|
Michellod D, Bien T, Birgel D, Violette M, Kleiner M, Fearn S, Zeidler C, Gruber-Vodicka HR, Dubilier N, Liebeke M. De novo phytosterol synthesis in animals. Science 2023; 380:520-526. [PMID: 37141360 PMCID: PMC11139496 DOI: 10.1126/science.add7830] [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: 07/13/2022] [Accepted: 03/03/2023] [Indexed: 05/06/2023]
Abstract
Sterols are vital for nearly all eukaryotes. Their distribution differs in plants and animals, with phytosterols commonly found in plants whereas most animals are dominated by cholesterol. We show that sitosterol, a common sterol of plants, is the most abundant sterol in gutless marine annelids. Using multiomics, metabolite imaging, heterologous gene expression, and enzyme assays, we show that these animals synthesize sitosterol de novo using a noncanonical C-24 sterol methyltransferase (C24-SMT). This enzyme is essential for sitosterol synthesis in plants, but not known from most bilaterian animals. Our phylogenetic analyses revealed that C24-SMTs are present in representatives of at least five animal phyla, indicating that the synthesis of sterols common to plants is more widespread in animals than currently known.
Collapse
Affiliation(s)
- Dolma Michellod
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Tanja Bien
- Institute of Hygiene, University of Münster, Robert-Koch-Str. 41, 48149, Münster, Germany
| | - Daniel Birgel
- Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, Bundesstraße 55, 20146 Hamburg, Germany
| | - Marlene Violette
- Department of Plant and Microbial Biology NC State University, Raleigh, NC 27695, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology NC State University, Raleigh, NC 27695, USA
| | - Sarah Fearn
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Caroline Zeidler
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| |
Collapse
|
4
|
Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolić N, Sachsenberg T, McCalder J, Lipton MS, Strous M. Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. MICROBIOME 2023; 11:24. [PMID: 36755313 PMCID: PMC9909930 DOI: 10.1186/s40168-022-01454-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. RESULTS Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50-99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC-MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. CONCLUSIONS We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
Collapse
Affiliation(s)
- Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Marlene Violette
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Grace D'Angelo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Yihua Liu
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- Max Planck Institute for Biology, Tübingen, Germany
| | - Abigail Korenek
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Nikola Tolić
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Janine McCalder
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Mary S Lipton
- Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
5
|
Molecular hydrogen in seawater supports growth of diverse marine bacteria. Nat Microbiol 2023; 8:581-595. [PMID: 36747116 DOI: 10.1038/s41564-023-01322-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/05/2023] [Indexed: 02/08/2023]
Abstract
Molecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2 to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.
Collapse
|
6
|
Sato Y, Wippler J, Wentrup C, Ansorge R, Sadowski M, Gruber-Vodicka H, Dubilier N, Kleiner M. Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium. MICROBIOME 2022; 10:178. [PMID: 36273146 PMCID: PMC9587655 DOI: 10.1186/s40168-022-01372-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/15/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species. RESULTS In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted. CONCLUSIONS We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.
Collapse
Affiliation(s)
- Yui Sato
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Juliane Wippler
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Cecilia Wentrup
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Rebecca Ansorge
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Miriam Sadowski
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
| |
Collapse
|
7
|
Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae. Sci Rep 2022; 12:169. [PMID: 34997021 PMCID: PMC8742107 DOI: 10.1038/s41598-021-03973-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 01/23/2023] Open
Abstract
The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host’s ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.
Collapse
|
8
|
Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses. Annu Rev Microbiol 2021; 75:695-718. [PMID: 34351792 DOI: 10.1146/annurev-micro-051021-123130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; ,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| |
Collapse
|
9
|
A brief history of carbon monoxide and its therapeutic origins. Nitric Oxide 2021; 111-112:45-63. [PMID: 33838343 DOI: 10.1016/j.niox.2021.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/03/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023]
Abstract
It is estimated that 10% of carbon throughout the cosmos is in the form of carbon monoxide (CO). Earth's earliest prebiotic atmosphere included the trinity of gasotransmitters CO, nitric oxide (NO), and hydrogen sulfide (H2S), for which all of life has co-evolved with. The history of CO can be loosely traced to mythological and prehistoric origins with rudimentary understanding emerging in the middle ages. Ancient literature is focused on CO's deadly toxicity which is understandable in the context of our primitive relationship with coal and fire. Scientific inquiry into CO appears to have emerged throughout the 1700s followed by chemical and toxicological profiling throughout the 1800s. Despite CO's ghastly reputation, several of the 18th and 19th century scientists suggested a therapeutic application of CO. Since 2000, the fundamental understanding of CO as a deadly nuisance has undergone a paradigm shift such that CO is now recognized as a neurotransmitter and viable pharmaceutical candidate. This review is intended to provide a brief history on the trace origins pertaining to endogenous formation and therapeutic application of CO.
Collapse
|
10
|
Petersen JM, Yuen B. The symbiotic 'all-rounders': Partnerships between marine animals and chemosynthetic nitrogen-fixing bacteria. Appl Environ Microbiol 2021; 87:AEM.02129-20. [PMID: 33355107 PMCID: PMC8090883 DOI: 10.1128/aem.02129-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogen fixation is a widespread metabolic trait in certain types of microorganisms called diazotrophs. Bioavailable nitrogen is limited in various habitats on land and in the sea, and accordingly, a range of plant, animal, and single-celled eukaryotes have evolved symbioses with diverse diazotrophic bacteria, with enormous economic and ecological benefits. Until recently, all known nitrogen-fixing symbionts were heterotrophs such as nodulating rhizobia, or photoautotrophs such as cyanobacteria. In 2016, the first chemoautotrophic nitrogen-fixing symbionts were discovered in a common family of marine clams, the Lucinidae. Chemosynthetic nitrogen-fixing symbionts use the chemical energy stored in reduced sulfur compounds to power carbon and nitrogen fixation, making them metabolic 'all-rounders' with multiple functions in the symbiosis. This distinguishes them from heterotrophic symbionts that require a source of carbon from their host, and their chemosynthetic metabolism distinguishes them from photoautotrophic symbionts that produce oxygen, a potent inhibitor of nitrogenase. In this review, we consider evolutionary aspects of this discovery, by comparing strategies that have evolved for hosting intracellular nitrogen-fixing symbionts in plants and animals. The symbiosis between lucinid clams and chemosynthetic nitrogen-fixing bacteria also has important ecological impacts, as they form a nested symbiosis with endangered marine seagrasses. Notably, nitrogen fixation by lucinid symbionts may help support seagrass health by providing a source of nitrogen in seagrass habitats. These discoveries were enabled by new techniques for understanding the activity of microbial populations in natural environments. However, an animal (or plant) host represents a diverse landscape of microbial niches due to its structural, chemical, immune and behavioural properties. In future, methods that resolve microbial activity at the single cell level will provide radical new insights into the regulation of nitrogen fixation in chemosynthetic symbionts, shedding new light on the evolution of nitrogen-fixing symbioses in contrasting hosts and environments.
Collapse
Affiliation(s)
- Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna
| | - Benedict Yuen
- Centre for Microbiology and Environmental Systems Science, University of Vienna
| |
Collapse
|
11
|
Yang Y, Sun J, Sun Y, Kwan YH, Wong WC, Zhang Y, Xu T, Feng D, Zhang Y, Qiu JW, Qian PY. Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts. THE ISME JOURNAL 2020; 14:135-150. [PMID: 31595051 PMCID: PMC6908572 DOI: 10.1038/s41396-019-0520-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/11/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022]
Abstract
Deep-sea hydrothermal vents and methane seeps are often densely populated by animals that host chemosynthetic symbiotic bacteria, but the molecular mechanisms of such host-symbiont relationship remain largely unclear. We characterized the symbiont genome of the seep-living siboglinid Paraescarpia echinospica and compared seven siboglinid-symbiont genomes. Our comparative analyses indicate that seep-living siboglinid endosymbionts have more virulence traits for establishing infections and modulating host-bacterium interaction than the vent-dwelling species, and have a high potential to resist environmental hazards. Metatranscriptome and metaproteome analyses of the Paraescarpia holobiont reveal that the symbiont is highly versatile in its energy use and efficient in carbon fixation. There is close cooperation within the holobiont in production and supply of nutrients, and the symbiont may be able to obtain nutrients from host cells using virulence factors. Moreover, the symbiont is speculated to have evolved strategies to mediate host protective immunity, resulting in weak expression of host innate immunity genes in the trophosome. Overall, our results reveal the interdependence of the tubeworm holobiont through mutual nutrient supply, a pathogen-type regulatory mechanism, and host-symbiont cooperation in energy utilization and nutrient production, which is a key adaptation allowing the tubeworm to thrive in deep-sea chemosynthetic environments.
Collapse
Affiliation(s)
- Yi Yang
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanan Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yick Hang Kwan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dong Feng
- CAS Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, China
- Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, 266061, Qingdao, China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
| |
Collapse
|
12
|
Hydrogen Does Not Appear To Be a Major Electron Donor for Symbiosis with the Deep-Sea Hydrothermal Vent Tubeworm Riftia pachyptila. Appl Environ Microbiol 2019; 86:AEM.01522-19. [PMID: 31628148 DOI: 10.1128/aem.01522-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/09/2019] [Indexed: 12/23/2022] Open
Abstract
Use of hydrogen gas (H2) as an electron donor is common among free-living chemolithotrophic microorganisms. Given the presence of this dissolved gas at deep-sea hydrothermal vents, it has been suggested that it may also be a major electron donor for the free-living and symbiotic chemolithoautotrophic bacteria that are the primary producers at these sites. Giant Riftia pachyptila siboglinid tubeworms and their symbiotic bacteria ("Candidatus Endoriftia persephone") dominate many vents in the Eastern Pacific, and their use of sulfide as a major electron donor has been documented. Genes encoding hydrogenase are present in the "Ca Endoriftia persephone" genome, and proteome data suggest that these genes are expressed. In this study, high-pressure respirometry of intact R. pachyptila and incubations of trophosome homogenate were used to determine whether this symbiotic association could also use H2 as a major electron donor. Measured rates of H2 uptake by intact R. pachyptila in high-pressure respirometers were similar to rates measured in the absence of tubeworms. Oxygen uptake rates in the presence of H2 were always markedly lower than those measured in the presence of sulfide, as was the incorporation of 13C-labeled dissolved inorganic carbon. Carbon fixation by trophosome homogenate was not stimulated by H2, nor was hydrogenase activity detectable in these samples. Though genes encoding [NiFe] group 1e and [NiFe] group 3b hydrogenases are present in the genome and transcribed, it does not appear that H2 is a major electron donor for this system, and it may instead play a role in intracellular redox homeostasis.IMPORTANCE Despite the presence of hydrogenase genes, transcripts, and proteins in the "Ca Endoriftia persephone" genome, transcriptome, and proteome, it does not appear that R. pachyptila can use H2 as a major electron donor. For many uncultivable microorganisms, omic analyses are the basis for inferences about their activities in situ However, as is apparent from the study reported here, there are dangers in extrapolating from omics data to function, and it is essential, whenever possible, to verify functions predicted from omics data with physiological and biochemical measurements.
Collapse
|
13
|
Seah BKB, Antony CP, Huettel B, Zarzycki J, Schada von Borzyskowski L, Erb TJ, Kouris A, Kleiner M, Liebeke M, Dubilier N, Gruber-Vodicka HR. Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO 2 Fixation. mBio 2019; 10:e01112-19. [PMID: 31239380 PMCID: PMC6593406 DOI: 10.1128/mbio.01112-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 01/25/2023] Open
Abstract
Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO2 by the symbionts drives these nutritional associations. In this study, we investigated "Candidatus Kentron," the clade of symbionts hosted by Kentrophoros, a diverse genus of ciliates which are found in marine coastal sediments around the world. Despite being the main food source for their hosts, Kentron bacteria lack the key canonical genes for any of the known pathways for autotrophic carbon fixation and have a carbon stable isotope fingerprint that is unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic analyses instead found metabolic features consistent with growth on organic carbon, especially organic and amino acids, for which they have abundant uptake transporters. All known thiotrophic symbionts have converged on using reduced sulfur to gain energy lithotrophically, but they are diverse in their carbon sources. Some clades are obligate autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with heterotrophic capabilities similar to those in Kentron. Here we show that Kentron bacteria are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or the reverse tricarboxylic acid cycle for autotrophy.IMPORTANCE Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, "Candidatus Kentron," associated with marine ciliates. They lack genes for known autotrophic pathways and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead, they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.
Collapse
Affiliation(s)
| | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Angela Kouris
- Energy Bioengineering and Geomicrobiology Group, University of Calgary, Calgary, Alberta, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | |
Collapse
|
14
|
Abstract
Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the "expressed" metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.
Collapse
|
15
|
Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula. Proc Natl Acad Sci U S A 2019; 116:8505-8514. [PMID: 30962361 PMCID: PMC6486704 DOI: 10.1073/pnas.1818995116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Animals typically store their primary energy reserves in specialized cells. Here, we show that in the small marine flatworm Paracatenula, this function is performed by its bacterial chemosynthetic symbiont. The intracellular symbiont occupies half of the biomass in the symbiosis and has a highly reduced genome but efficiently stocks up and maintains carbon and energy, particularly sugars. The host rarely digests the symbiont cells to access these stocks. Instead, the symbionts appear to provide the bulk nutrition by secreting outer-membrane vesicles. This is in contrast to all other described chemosynthetic symbioses, where the hosts continuously digest full cells of a small and ideally growing symbiont population that cannot provide a long-term buffering capacity during nutrient limitation. Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca. Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant’Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca. R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29–4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca. R. santandreae’s versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca. R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts—serving as the primary energy storage for its animal host.
Collapse
|
16
|
Chen SC, Weng CY, Lai MC, Tamaki H, Narihiro T. Comparative genomic analyses reveal trehalose synthase genes as the signature in genus Methanoculleus. Mar Genomics 2019; 47:100673. [PMID: 30935830 DOI: 10.1016/j.margen.2019.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 11/25/2022]
Abstract
To date, the only methanoarchaea isolated directly from methane hydrate bearing sediments were Methanoculleus submarinus Nankai-1T and Methanoculleus sp. MH98A. Here, we provide the genome of Methanoculleus taiwanensis CYW4T isolated from the deep-sea subseafloor sediment at the Deformation Front offshore southwestern Taiwan, where methane hydrate deposits are likely located. Through comparative genomics analyses of nine Methanoculleus strains from various habitats, 2-3 coding genes for trehalose synthases were found in all nine Methanoculleus genomes, which were not detected in other methanogens and are therefore suggested as a signature of genus Methanoculleus among methane-producing archaea. In addition, the structural genes adjacent to trehalose synthase genes are comprised of the signaling module of Per-Arnt-Sim (PAS) domain-containing proteins, Hsp20 family proteins, arabinose efflux permeases and multiple surface proteins with fasciclin-like (FAS) repeat. This indicates that trehalose synthase gene clusters in Methanoculleus might play roles in the response to various stresses and regulate carbon storage and modification of surface proteins through accumulation of trehalose. The non-gas hydrate-associated Methanoculleus strains harbor carbon-monoxide dehydrogenase (cooS/acsA) genes, which are important for the conversion of acetate to methane at the step of CO oxidation/CO2 reduction in acetoclastic methanogens and further implies that these strains may be able to utilize CO for methanogenesis in their natural habitats. In addition, both genomes of M. bourgensis strains MS2T and MAB1 harbor highly abundant transposase genes, which may be disseminated from microbial communities in their habitats, sewage treatment plants and biogas reactors, which are breeding grounds for antibiotic resistance. Through comparative genomic analyses, we gained insight into understanding the life of strictly anaerobic methane-producing archaea in various habitats, especially in methane-based deep-sea ecosystems.
Collapse
Affiliation(s)
- Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| |
Collapse
|
17
|
Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, Strous M. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A 2018; 115:E5576-E5584. [PMID: 29844191 PMCID: PMC6004456 DOI: 10.1073/pnas.1722325115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present "direct protein-SIF" and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts' metabolism. This confirms the usefulness of this approach to accurately determine δ13C values for different species in microbial community samples.
Collapse
Affiliation(s)
- Manuel Kleiner
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Tjorven Hinzke
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Juliane Wippler
- Symbiosis Department, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Erin Thorson
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada T2N 1N4;
| |
Collapse
|
18
|
Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae. Appl Environ Microbiol 2018; 84:AEM.02267-17. [PMID: 29330187 PMCID: PMC5861843 DOI: 10.1128/aem.02267-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/09/2018] [Indexed: 12/05/2022] Open
Abstract
Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiomes of all 22 of the other host species examined. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization revealed that I. exumae harbors cooccurring gamma-, alpha-, and deltaproteobacterial symbionts, while all other known host species harbor gamma- and either alpha- or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic sulfur oxidizer “Candidatus Thiosymbion” that occurs in all other gutless phallodriline hosts does not appear to be present in I. exumae. Instead, I. exumae harbors a bacterial endosymbiont that resembles “Ca. Thiosymbion” morphologically and metabolically but originates from a novel lineage within the class Gammaproteobacteria. This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA gene sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from that of “Ca. Thiosymbion.” Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), indicate that this symbiont is a chemoautotrophic sulfur oxidizer. Our results suggest that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae and appears to have displaced the “Ca. Thiosymbion” symbionts originally associated with these hosts. IMPORTANCE All 22 gutless marine phallodriline species examined to date live in a highly specific association with endosymbiotic, chemoautotrophic sulfur oxidizers called “Ca. Thiosymbion.” These symbionts evolved from a single common ancestor and represent the ancestral trait for this host group. They are transmitted vertically and assumed to be in transition to becoming obligate endosymbionts. It is therefore surprising that despite this ancient, evolutionary relationship between phallodriline hosts and “Ca. Thiosymbion,” these symbionts are apparently no longer present in Inanidrilus exumae. They appear to have been displaced by a novel lineage of sulfur-oxidizing bacteria only very distantly related to “Ca. Thiosymbion.” Thus, this study highlights the remarkable plasticity of both animals and bacteria in establishing beneficial associations: the phallodriline hosts were able to acquire and maintain symbionts from two very different lineages of bacteria, while sulfur-oxidizing bacteria from two very distantly related lineages were able to independently establish symbiotic relationships with phallodriline hosts.
Collapse
|
19
|
Abstract
Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.
Collapse
|
20
|
Dyksma S, Pjevac P, Ovanesov K, Mussmann M. Evidence for H 2 consumption by uncultured Desulfobacterales in coastal sediments. Environ Microbiol 2017; 20:450-461. [PMID: 28772023 DOI: 10.1111/1462-2920.13880] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/30/2017] [Indexed: 12/26/2022]
Abstract
Molecular hydrogen (H2 ) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H2 -oxidizing microorganisms is essential to keep anaerobic degradation energetically favourable. Sulfate-reducing microorganisms (SRM) are known as the main H2 scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H2 in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H2 -consuming SRM in anoxic coastal sediments. The vast majority of SRM-related H2 ase sequences were assigned to group 1b and 1c [NiFe]-H2 ases of the deltaproteobacterial order Desulfobacterales. Surprisingly, the same sequence types were similarly highly expressed in spring and summer, suggesting that these are stable and integral members of the H2 -consuming community. Notably, one sequence cluster from the SRM group 1 consistently accounted for around half of all [NiFe]-H2 ase transcripts. Using SAGs, we could link this cluster with the 16S rRNA genes of the uncultured Sva0081-group of the family Desulfobacteraceae. Sequencing of 16S rRNA gene amplicons and H2 ase gene libraries suggested consistently high in situ abundance of the Sva0081 group also in other marine sediments. Together with other Desulfobacterales these likely are important H2 -scavengers in marine sediments.
Collapse
Affiliation(s)
- Stefan Dyksma
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Kin Ovanesov
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Mussmann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| |
Collapse
|
21
|
Hoshino T, Inagaki F. Distribution of anaerobic carbon monoxide dehydrogenase genes in deep subseafloor sediments. Lett Appl Microbiol 2017; 64:355-363. [PMID: 28256106 DOI: 10.1111/lam.12727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 02/05/2023]
Abstract
Carbon monoxide (CO) is the simplest oxocarbon generated by the decomposition of organic compounds, and it is expected to be in marine sediments in substantial amounts. However, the availability of CO in the deep subseafloor sedimentary biosphere is largely unknown even though anaerobic oxidation of CO is a thermodynamically favourable reaction that possibly occurs with sulphate reduction, methanogenesis, acetogenesis and hydrogenesis. In this study, we surveyed for the first time the distribution of the CO dehydrogenase gene (cooS), which encodes the catalytic beta subunit of anaerobic CO dehydrogenase (CODH), in subseafloor sediment-core samples from the eastern flank of the Juan de Fuca Ridge, Mars-Ursa Basin, Kumano Basin, and off the Shimokita Peninsula, Japan, during Integrated Ocean Drilling Program (IODP) Expeditions 301, 308 and 315 and the D/V Chikyu shakedown cruise CK06-06, respectively. Our results show the occurrence of diverse cooS genes from the seafloor down to about 390 m below the seafloor, suggesting that microbial communities have metabolic functions to utilize CO in anoxic microbial ecosystems beneath the ocean floor, and that the microbial community potentially responsible for anaerobic CO oxidation differs in accordance with possible energy-yielding metabolic reactions in the deep subseafloor sedimentary biosphere. SIGNIFICANCE AND IMPACT OF THE STUDY Little is known about the microbial community associated with carbon monoxide (CO) in the deep subseafloor. This study is the first survey of a functional gene encoding anaerobic carbon monoxide dehydrogenase (CODH). The widespread occurrence of previously undiscovered CO dehydrogenase genes (cooS) suggests that diverse micro-organisms are capable of anaerobic oxidation of CO in the deep subseafloor sedimentary biosphere.
Collapse
Affiliation(s)
- T Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan.,Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC, Nankoku, Kochi, Japan
| | - F Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan.,Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC, Nankoku, Kochi, Japan.,Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, Kanagawa, Japan
| |
Collapse
|
22
|
Wippler J, Kleiner M, Lott C, Gruhl A, Abraham PE, Giannone RJ, Young JC, Hettich RL, Dubilier N. Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis. BMC Genomics 2016; 17:942. [PMID: 27871231 PMCID: PMC5117596 DOI: 10.1186/s12864-016-3293-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 11/15/2016] [Indexed: 02/07/2023] Open
Abstract
Background The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been gained of the symbionts, the host has remained largely unstudied. Here, we generated transcriptomes and proteomes of O. algarvensis to better understand how this annelid worm gains nutrition from its symbionts, how it adapted physiologically to a symbiotic lifestyle, and how its innate immune system recognizes and responds to its symbiotic microbiota. Results Key adaptations to the symbiosis include (i) the expression of gut-specific digestive enzymes despite the absence of a gut, most likely for the digestion of symbionts in the host's epidermal cells; (ii) a modified hemoglobin that may bind hydrogen sulfide produced by two of the worm’s symbionts; and (iii) the expression of a very abundant protein for oxygen storage, hemerythrin, that could provide oxygen to the symbionts and the host under anoxic conditions. Additionally, we identified a large repertoire of proteins involved in interactions between the worm's innate immune system and its symbiotic microbiota, such as peptidoglycan recognition proteins, lectins, fibrinogen-related proteins, Toll and scavenger receptors, and antimicrobial proteins. Conclusions We show how this worm, over the course of evolutionary time, has modified widely-used proteins and changed their expression patterns in adaptation to its symbiotic lifestyle and describe expressed components of the innate immune system in a marine oligochaete. Our results provide further support for the recent realization that animals have evolved within the context of their associations with microbes and that their adaptive responses to symbiotic microbiota have led to biological innovations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3293-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Juliane Wippler
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany. .,Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Manuel Kleiner
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany. .,Energy Bioengineering and Geomicrobiology Research Group, University of Calgary, Calgary, T2N 1N4, AB, Canada.
| | - Christian Lott
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.,HYDRA Institute for Marine Sciences, Elba Field Station, Via del Forno 80, 57034, Campo nell' Elba, (LI), Italy
| | - Alexander Gruhl
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Paul E Abraham
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Richard J Giannone
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Jacque C Young
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA.,Present Address: Saul Ewing LLP, 1500 Market Street, 37th Floor, Philadelphia, PA, 19102-2186, USA
| | - Robert L Hettich
- Oak Ridge National Laboratory, Chemical Sciences Division, Oak Ridge, Tennessee, 1 Bethel Valley Rd, Oak Ridge, TN, 37831, USA
| | - Nicole Dubilier
- Symbiosis Department, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| |
Collapse
|
23
|
Petersen JM, Kemper A, Gruber-Vodicka H, Cardini U, van der Geest M, Kleiner M, Bulgheresi S, Mußmann M, Herbold C, Seah BKB, Antony CP, Liu D, Belitz A, Weber M. Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation. Nat Microbiol 2016; 2:16195. [PMID: 27775707 PMCID: PMC6872982 DOI: 10.1038/nmicrobiol.2016.195] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/07/2016] [Indexed: 12/04/2022]
Abstract
Chemosynthetic symbioses are partnerships between invertebrate animals
and chemosynthetic bacteria. The latter are the primary producers, providing most of
the organic carbon needed for the animal host's nutrition. We sequenced genomes of
the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species
encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic
symbiont was previously known to be capable of nitrogen fixation. We detected
nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and
proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric
nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability
to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic
habitats, where nitrogen availability often limits primary productivity. The chemosynthetic symbionts of the bivalve Loripes lucinalis and nematode Laxus
oneistus are found to encode nitrogen fixation genes, with evidence for
active nitrogen fixation.
Collapse
Affiliation(s)
- Jillian M Petersen
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Anna Kemper
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Ulisse Cardini
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Matthijs van der Geest
- Centre for Marine Biodiversity, Exploitation and Conservation (MARBEC), UMR 9190, IRD-IFREMER-CNRS-UM, Université de Montpellier, Montpellier Cedex 5 34095, France.,Department of Coastal Systems and Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands
| | - Manuel Kleiner
- Department of Geoscience, University of Calgary, 2500 University Drive Northwest, Alberta T2N 1N4, Canada
| | - Silvia Bulgheresi
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Craig Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Brandon K B Seah
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Chakkiath Paul Antony
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany
| | - Dan Liu
- Department of Geoscience, University of Calgary, 2500 University Drive Northwest, Alberta T2N 1N4, Canada
| | - Alexandra Belitz
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Miriam Weber
- HYDRA Institute for Marine Sciences, Elba Field Station, Campo nell'Elba, Livorno 54037, Italy
| |
Collapse
|
24
|
Musat N, Musat F, Weber PK, Pett-Ridge J. Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol 2016; 41:114-121. [PMID: 27419912 DOI: 10.1016/j.copbio.2016.06.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/09/2016] [Accepted: 06/23/2016] [Indexed: 12/29/2022]
Abstract
The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where used to track exchanges of isotopically labelled molecules between organisms. We highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont-host nutrient sharing.
Collapse
Affiliation(s)
- Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kilian Weber
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| |
Collapse
|