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MacVittie S, Doroodian S, Alberto A, Sogin M. Microbiome depletion and recovery in the sea anemone, Exaiptasia diaphana, following antibiotic exposure. mSystems 2024:e0134223. [PMID: 38757963 DOI: 10.1128/msystems.01342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Microbial species that comprise host-associated microbiomes play an essential role in maintaining and mediating the health of plants and animals. While defining the role of individual or even complex communities is important toward quantifying the effect of the microbiome on host health, it is often challenging to develop causal studies that link microbial populations to changes in host fitness. Here, we investigated the impacts of reduced microbial load following antibiotic exposure on the fitness of the anemone, Exaiptasia diaphana and subsequent recovery of the host's microbiome. Anemones were exposed to two different types of antibiotic solutions for 3 weeks and subsequently held in sterilized seawater for a 3-week recovery period. Our results revealed that both antibiotic treatments reduced the overall microbial load during and up to 1 week post-treatment. The observed reduction in microbial load was coupled with reduced anemone biomass, halted asexual reproduction rates, and for one of the antibiotic treatments, the partial removal of the anemone's algal symbiont. Finally, our amplicon sequencing results of the 16S rRNA gene revealed that anemone bacterial composition only shifted in treated individuals during the recovery phase of the experiment, where we also observed a significant reduction in the overall diversity of the microbial community. Our work implies that the E. diaphana's microbiome contributes to host fitness and that the recovery of the host's microbiome following disturbance with antibiotics leads to a reduced, but stable microbial state.IMPORTANCEExaiptasia diaphana is an emerging model used to define the cellular and molecular mechanisms of coral-algal symbioses. E. diaphana also houses a diverse microbiome, consisting of hundreds of microbial partners with undefined function. Here, we applied antibiotics to quantify the impact of microbiome removal on host fitness as well as define trajectories in microbiome recovery following disturbance. We showed that reduction of the microbiome leads to negative impacts on host fitness, and that the microbiome does not recover to its original composition while held under aseptic conditions. Rather the microbiome becomes less diverse, but more consistent across individuals. Our work is important because it suggests that anemone microbiomes play a role in maintaining host fitness, that they are susceptible to disturbance events, and that it is possible to generate gnotobiotic individuals that can be leveraged in microbiome manipulation studies to investigate the role of individual species on host health.
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Affiliation(s)
- Sophie MacVittie
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Saam Doroodian
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Aaron Alberto
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Maggie Sogin
- Department of Molecular Cell Biology, University of California, Merced, California, USA
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2
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Liao L, Qin Q, Yi D, Lai Q, Cong B, Zhang H, Shao Z, Zhang J, Chen B. Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments. Mol Ecol 2024:e17385. [PMID: 38738821 DOI: 10.1111/mec.17385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/04/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.
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Affiliation(s)
- Li Liao
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Qilong Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Dian Yi
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, China
| | - Qiliang Lai
- Third Institute of Oceanography, Ministry of Natural Resources, P. R. China, Xiamen, China
| | - Bolin Cong
- First Institute of Oceanography, Ministry of Natural Resources, P. R. China, Qingdao, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, China
| | - Zongze Shao
- Third Institute of Oceanography, Ministry of Natural Resources, P. R. China, Xiamen, China
| | - Jin Zhang
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Bo Chen
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
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3
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Liu W, Cong B, Lin J, Liu S, Deng A, Zhao L. Author Correction: Taxonomic identification and temperature stress tolerance mechanisms of Aequorivita marisscotiae sp. nov. Commun Biol 2024; 7:542. [PMID: 38714887 PMCID: PMC11076454 DOI: 10.1038/s42003-024-06257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Affiliation(s)
- Wenqi Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Bailin Cong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shenghao Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Aifang Deng
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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4
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Rodriguez Jimenez A, Breine A, Whiteway C, Dechamps E, George IF, Van der Henst C. Bactericidal effect of bacteria isolated from the marine sponges Hymeniacidon perlevis and Halichondria panicea against carbapenem-resistant Acinetobacter baumannii. Lett Appl Microbiol 2024; 77:ovae035. [PMID: 38684470 DOI: 10.1093/lambio/ovae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/19/2024] [Accepted: 04/28/2024] [Indexed: 05/02/2024]
Abstract
In this study, we evaluated the antimicrobial activity of bacteria isolated from the marine sponges Hymeniacidon perlevis and Halichondria panicea against seven Acinetobacter baumannii strains, the majority of which were clinically relevant carbapenem-resistant A. baumannii strains. We observed the inhibitory activity of 18 (out of 114) sponge-isolated bacterial strains against all A. baumanii strains using medium-throughput solid agar overlay assays. These inhibitory strains belonged to the genera Lactococcus, Pseudomonas, and Vagococcus. In addition, this antimicrobial activity was validated through a liquid co-cultivation challenge using an inhibitory strain of each genus and a green fluorescent protein-tagged A. baumanii strain. Fluorescence measurements indicated that the growth of A. baumanii was inhibited by the sponge isolates. In addition, the inability of A. baumanii to grow after spreading the co-cultures on solid medium allowed us to characterize the activity of the sponge isolates as bactericidal. In conclusion, this study demonstrates that marine sponges are a reservoir of bacteria that deserves to be tapped for antibiotic discovery against A. baumanii.
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Affiliation(s)
- Ana Rodriguez Jimenez
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Anke Breine
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Clemence Whiteway
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Etienne Dechamps
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Isabelle F George
- Ecology of Aquatic Systems, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
- Marine Biology, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Charles Van der Henst
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
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5
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Yu JS, Rowe AR, Sackett JD. Complete genome sequence of iron-oxidizing Stutzerimonas stutzeri strain FeN3W isolated from Catalina Harbor sediment. Microbiol Resour Announc 2024:e0003024. [PMID: 38700344 DOI: 10.1128/mra.00030-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
Stutzerimonas stutzeri strain FeN3W is an iron-oxidizing bacterium isolated from marine sediment. FeN3W's 5.9 Mb genome encodes complete pathways for glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, and aerobic and anaerobic (nitrate) respiration. The genome contains 32 putative heme-binding proteins predicted to localize to the cell envelope.
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Affiliation(s)
- Jin-Sang Yu
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joshua D Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
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6
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Krueger Q, Reitzel A. Draft genome sequence of Vibrio diabolicus isolated from the starlet sea anemone Nematostella vectensis. Microbiol Resour Announc 2024; 13:e0107523. [PMID: 38456697 PMCID: PMC11008165 DOI: 10.1128/mra.01075-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024] Open
Abstract
Nematostella vectensis has grown as a model organism for investigating host-bacteria interactions. Here, we report the full genome of Vibrio diabolicus NVE-VD1, an isolate from N. vectensis from the South Carolina Baruch Estuarine Reserve.
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Affiliation(s)
- Quinton Krueger
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Adam Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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7
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Lorente B, Cabral C, Frias J, Faria J, Toubarro D. Draft genome sequence of Agarivorans aestuarii strain ZMCS4, a putative CAZyme-producing bacteria isolated from the marine brown algae Cladostephus spongiosus. Microbiol Resour Announc 2024; 13:e0117823. [PMID: 38534151 PMCID: PMC11080527 DOI: 10.1128/mra.01178-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
We report the draft genome sequence of Agarivorans aestuarii strain ZMCS4, isolated from Cladostephus spongiosus. The assembled genome consists of 4.5 Mbp, comprising 25 contigs and 4,128 coding sequences. This genome will provide insights into further studies on relevant CAZymes involved in the hydrolysis of algal cell walls.
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Affiliation(s)
- Beatriz Lorente
- />CIBIO – Research Centre in Biodiversity and Genetic Resources, InBio Associate Laboratory, University of the Azores, Ponta Delgada, Portugal
| | - Carla Cabral
- Biotechnology Centre of Azores (CBA), University of the Azores, Ponta Delgada, Portugal
| | - Jorge Frias
- Biotechnology Centre of Azores (CBA), University of the Azores, Ponta Delgada, Portugal
| | - João Faria
- />CIBIO – Research Centre in Biodiversity and Genetic Resources, InBio Associate Laboratory, University of the Azores, Ponta Delgada, Portugal
| | - Duarte Toubarro
- Biotechnology Centre of Azores (CBA), University of the Azores, Ponta Delgada, Portugal
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8
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Zhong J, Osborn T, Del Rosario Hernández T, Kyrysyuk O, Tully BJ, Anderson RE. Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle. mSystems 2024; 9:e0006724. [PMID: 38380923 PMCID: PMC10949469 DOI: 10.1128/msystems.00067-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.
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Affiliation(s)
- Juntao Zhong
- Carleton College, Northfield, Minnesota, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Troy Osborn
- Carleton College, Northfield, Minnesota, USA
| | - Thais Del Rosario Hernández
- Carleton College, Northfield, Minnesota, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Oleksandr Kyrysyuk
- Carleton College, Northfield, Minnesota, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Benjamin J. Tully
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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9
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential. mBio 2024; 15:e0291823. [PMID: 38380943 PMCID: PMC10936187 DOI: 10.1128/mbio.02918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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10
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Ruiz A, Gisbert E, Andree KB. Impact of the diet in the gut microbiota after an inter-species microbial transplantation in fish. Sci Rep 2024; 14:4007. [PMID: 38369563 PMCID: PMC10874947 DOI: 10.1038/s41598-024-54519-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Inter-species microbial transplantations offer the possibility of transferring species-specific microbes and their associated functionality. As a conceptual approach, an intestinal microbiota transplant (IMT) between two marine carnivorous fish species that thrive in different environmental conditions was conducted: from donor Atlantic salmon (Salmo salar) to recipient gilthead seabream (Sparus aurata), after obliterating its basal microbiota with an antibiotic treatment. To confirm that the gut microbiota was able to recover after antibiotics without the influence of the diet, a group of gilthead seabream not submitted to the IMT was kept fasted as an internal control. To assess the effect of the diet after the IMT, two groups of gilthead seabream were respectively fed with their typical diet and with Atlantic salmon diet. At 36 days post-IMT, the gut of the individuals fed with their typical diet was dominated by the feed-associated bacteria, while those fed with the salmon diet had developed a unique microbiota from the convergence of the diet, donor, and recipient microbiota. These results suggested that an intestinal microbiota transplantation may be effective if the basal microbiota from the gut is first cleared and a targeted dietary modification is provided to maintain and enrich the novel bacteria species over time.
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Affiliation(s)
- Alberto Ruiz
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain.
| | - Enric Gisbert
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain
| | - Karl B Andree
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain
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11
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Kraemer SA, Ramachandran A, Onana VE, Li WKW, Walsh DA. A multiyear time series (2004-2012) of bacterial and archaeal community dynamics in a changing Arctic Ocean. ISME Commun 2024; 4:ycad004. [PMID: 38282643 PMCID: PMC10809757 DOI: 10.1093/ismeco/ycad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
Climate change is profoundly impacting the Arctic, leading to a loss of multiyear sea ice and a warmer, fresher upper Arctic Ocean. The response of microbial communities to these climate-mediated changes is largely unknown. Here, we document the interannual variation in bacterial and archaeal communities across a 9-year time series of the Canada Basin that includes two historic sea ice minima (2007 and 2012). We report an overall loss of bacterial and archaeal community richness and significant shifts in community composition. The magnitude and period of most rapid change differed between the stratified water layers. The most pronounced changes in the upper water layers (surface mixed layer and upper Arctic water) occurred earlier in the time series, while changes in the lower layer (Pacific-origin water) occurred later. Shifts in taxonomic composition across time were subtle, but a decrease in Bacteroidota taxa and increase in Thaumarchaeota and Euryarchaeota taxa were the clearest signatures of change. This time series provides a rare glimpse into the potential influence of climate change on Arctic microbial communities; extension to the present day should contribute to deeper insights into the trajectory of Arctic marine ecosystems in response to warming and freshening.
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Affiliation(s)
- Susanne A Kraemer
- Environment and Climate Change Canada, Montreal, Quebec, H2Y 2E7, Canada
| | - Arthi Ramachandran
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Vera E Onana
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - William K W Li
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, B2Y 4A2, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
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12
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Bittner MJ, Bannon CC, Rowland E, Sundh J, Bertrand EM, Andersson AF, Paerl RW, Riemann L. New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system. ISME Commun 2024; 4:ycad016. [PMID: 38390520 PMCID: PMC10881298 DOI: 10.1093/ismeco/ycad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024]
Abstract
Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.
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Affiliation(s)
- Meriel J Bittner
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Catherine C Bannon
- Department of Biology, Dalhousie University, Halifax, B3H 4R2, Nova Scotia, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, B3H 4R2, Nova Scotia, Canada
| | - John Sundh
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, B3H 4R2, Nova Scotia, Canada
| | - Anders F Andersson
- Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17165 Stockholm, Sweden
| | - Ryan W Paerl
- Department of Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 2769, United States
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
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13
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Meyer Cifuentes IE, Degenhardt J, Neumann-Schaal M, Jehmlich N, Ngugi DK, Öztürk B. Comparative biodegradation analysis of three compostable polyesters by a marine microbial community. Appl Environ Microbiol 2023; 89:e0106023. [PMID: 38014952 PMCID: PMC10734441 DOI: 10.1128/aem.01060-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Biodegradable plastics can be used in applications where the end product cannot be efficiently recycled due to high levels of contaminations, e.g., food or soil. Some of these plastics have a dedicated end of life, such as composting, but their degradation in the marine environment is poorly understood. In this study we showed that marine microbial communities can degrade a range of biodegradable polymers with different physical and chemical properties and use these as a sole carbon source for growth. We have also provided insights into the degradation mechanisms using a combined metagenomic and metaproteomic approach. In addition, we have identified three new enzymes that are capable of degrading both aliphatic polymers and aliphatic-aromatic copolymers, which can be used for biotechnological applications.
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Affiliation(s)
- Ingrid E. Meyer Cifuentes
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julius Degenhardt
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - David Kamanda Ngugi
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Başak Öztürk
- Junior Research Group Microbial Biotechnology, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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14
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Minch B, Akter S, Weinheimer A, Rahman MS, Parvez MAK, Rezwana Rahman S, Ahmed MF, Moniruzzaman M. Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal. mSphere 2023; 8:e0040723. [PMID: 37902318 PMCID: PMC10732071 DOI: 10.1128/msphere.00407-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE The BoB, the world's largest bay, is of significant economic importance to surrounding countries, particularly Bangladesh, which heavily relies on its coastal resources. Concurrently, the BoB holds substantial ecological relevance due to the region's high vulnerability to climate change-induced impacts. Yet, our understanding of the BoB's microbiome in relation to marine food web and biogeochemical cycling remains limited. Particularly, there are little or no data on the viral diversity and host association in the BoB. We examined the viral community in two distinct BoB coastal regions to reveal a multitude of viral species interacting with a wide range of microbial hosts, some of which play key roles in coastal biogeochemical cycling or potential pathogens. Furthermore, we demonstrate that the BoB coast harbors a diverse community of large and giant viruses, underscoring the importance of investigating understudied environments to discover novel viral lineages with complex metabolic capacities.
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Affiliation(s)
- Benjamin Minch
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
| | - Salma Akter
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | | | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | | | - Md Firoz Ahmed
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
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15
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Schober I, Bunk B, Carril G, Freese HM, Ojeda N, Riedel T, Meier-Kolthoff JP, Göker M, Spröer C, Flores-Herrera PA, Nourdin-Galindo G, Gómez F, Cárdenas C, Vásquez-Ponce F, Labra A, Figueroa J, Olivares-Pacheco J, Nübel U, Sikorski J, Marshall SH, Overmann J. Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts. ISME J 2023; 17:2247-2258. [PMID: 37853183 PMCID: PMC10689435 DOI: 10.1038/s41396-023-01531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis 16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsia comprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsia diversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming.
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Affiliation(s)
- Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gabriela Carril
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nicolás Ojeda
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Patricio A Flores-Herrera
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Guillermo Nourdin-Galindo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Fernando Gómez
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Constanza Cárdenas
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Felipe Vásquez-Ponce
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Alvaro Labra
- Laboratorio de Patógenos Acuícolas, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jaime Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jorge Olivares-Pacheco
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Milenio para la Investigación Colaborativa en Resistencia Antimicrobiana (MICROB-R), Santiago, Chile
| | - Ulrich Nübel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
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16
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Truchon AR, Chase EE, Gann ER, Moniruzzaman M, Creasey BA, Aylward FO, Xiao C, Gobler CJ, Wilhelm SW. Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research. Front Microbiol 2023; 14:1284617. [PMID: 38098665 PMCID: PMC10720644 DOI: 10.3389/fmicb.2023.1284617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.
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Affiliation(s)
- Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Emily E Chase
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, United States
| | - Brooke A Creasey
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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17
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Mara P, Geller-McGrath D, Edgcomb V, Beaudoin D, Morono Y, Teske A. Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface. Nat Commun 2023; 14:7768. [PMID: 38012208 PMCID: PMC10681998 DOI: 10.1038/s41467-023-43296-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David Geller-McGrath
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - David Beaudoin
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avantgarde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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18
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Liu W, Cong B, Lin J, Liu S, Deng A, Zhao L. Taxonomic identification and temperature stress tolerance mechanisms of Aequorivita marisscotiae sp. nov. Commun Biol 2023; 6:1186. [PMID: 37990058 PMCID: PMC10663628 DOI: 10.1038/s42003-023-05559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
The deep sea harbours microorganisms with unique life characteristics and activities due to adaptation to particular environmental conditions, but the limited sample collection and pure culture techniques available constrain the study of deep-sea microorganisms. In this study, strain Ant34-E75 was isolated from Antarctic deep-sea sediment samples and showed the highest 16 S rRNA gene sequence similarity (97.18%) with the strain Aequorivita viscosa 8-1bT. Strain Ant34-E75 is psychrotrophic and can effectively increase the cold tolerance of Chlamydomonas reinhardtii (a model organism). Subsequent transcriptome analysis revealed multiple mechanisms involved in the Ant34-E75 response to temperature stress, and weighted gene co-expression network analysis (WGCNA) showed that the peptidoglycan synthesis pathway was the key component. Overall, this study provides insights into the characteristics of a deep-sea microorganism and elucidates mechanisms of temperature adaptation at the molecular level.
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Affiliation(s)
- Wenqi Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Bailin Cong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shenghao Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Aifang Deng
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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19
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Phillips EK, Shaffer JMC, Henson MW, Coelho JT, Martin MO, Thrash JC. Genome sequences of four agarolytic bacteria from the Bacteroidia and Gammaproteobacteria. Microbiol Resour Announc 2023; 12:e0066723. [PMID: 37812006 PMCID: PMC10652895 DOI: 10.1128/mra.00667-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 10/10/2023] Open
Abstract
Here we present the genomes of four marine agarolytic bacteria belonging to the Bacteroidota and Proteobacteria. Two genomes are closed and two are in draft form, but all are at least 99% complete and offer new opportunities to study agar-degradation in marine bacteria.
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Affiliation(s)
- Elise K. Phillips
- Department of Biology, University of Puget Sound, Tacoma, Washington, USA
| | | | - Michael W. Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jordan T. Coelho
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Mark O. Martin
- Department of Biology, University of Puget Sound, Tacoma, Washington, USA
| | - J. Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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20
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Mueller AJ, Daebeler A, Herbold CW, Kirkegaard RH, Daims H. Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales. ISME J 2023; 17:2123-2133. [PMID: 37749300 PMCID: PMC10579370 DOI: 10.1038/s41396-023-01518-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.
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Affiliation(s)
- Anna J Mueller
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Anne Daebeler
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- Department of Soil Biology and Biogeochemistry, Biology Centre CAS, Na Sádkách 7, 370 05, Budweis, Czech Republic
| | - Craig W Herbold
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria
- School of Biological Sciences, University of Canterbury, Christchurch, 8041, New Zealand
| | - Rasmus H Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Holger Daims
- University of Vienna, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, Djerassiplatz 1, 1030, Vienna, Austria.
- The Comammox Research Platform, University of Vienna, Vienna, Austria.
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21
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Gavriilidou A, Avcı B, Galani A, Schorn MA, Ingham CJ, Ettema TJG, Smidt H, Sipkema D. Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle. ISME J 2023; 17:1808-1818. [PMID: 37587369 PMCID: PMC10579324 DOI: 10.1038/s41396-023-01484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 08/18/2023]
Abstract
Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
| | - Burak Avcı
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Anastasia Galani
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine BV, Verenigingstraat 36, 3515GJ, Utrecht, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, The Netherlands.
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22
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Guo W, Duan J, Shi Z, Yu X, Shao Z. Biodegradation of PET by the membrane-anchored PET esterase from the marine bacterium Rhodococcus pyridinivorans P23. Commun Biol 2023; 6:1090. [PMID: 37891241 PMCID: PMC10611731 DOI: 10.1038/s42003-023-05470-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Evidence for microbial biodegradation of polyethylene terephthalate (PET) has been reported, but little is known about the PET biodegradation process and molecular mechanism by marine microorganisms. Here, we show the biodegradation of PET by the membrane-anchored PET esterase from the marine bacterium Rhodococcus pyridinivorans P23, elucidate the properties of this enzyme, and propose the PET biodegradation by this strain in biofilm. We identify the PET-degrading enzyme dubbed PET esterase through activity tracking. In addition to depolymerizing PET, it hydrolyzes MHET into TPA under acid conditions. We prove that it is a low and constitutively transcribed, membrane-anchored protein displayed on the cell surface. Furthermore, we also investigate the microbial groups possessing PET esterase coupled with the TPA degradation pathway, mainly in the phyla Proteobacteria and Actinobacteriota. Clarification of the microbial PET biodegradation in the marine environment will contribute to the understanding of bioremediation of marine PET pollution.
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Affiliation(s)
- Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China.
| | - Jingjing Duan
- College of Environment and Ecology, Xiamen University, 361005, Xiamen, Fujian, China.
| | - Zhengguang Shi
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China
- School of Advanced Manufacturing, Fuzhou University, 362251, Jinjiang, China
| | - Xue Yu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China
- School of Advanced Manufacturing, Fuzhou University, 362251, Jinjiang, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 361005, Xiamen, Fujian, China
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Heng WL, Lau NS, Furusawa G. Complete genome sequence of marine filamentous bacterium, Saprospira grandis strain WH T. Microbiol Resour Announc 2023; 12:e0044123. [PMID: 37589468 PMCID: PMC10508125 DOI: 10.1128/mra.00441-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
Here, we report the complete genome sequence of a type strain of the genus Saprospira, Saprospira grandis strain WHT. The genome consists of one circular chromosome and plasmid comprising 4,250,550 bp and 53,161 bp with GC content of 46.6% and 46.8%, respectively.
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Affiliation(s)
- Wooi Liang Heng
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
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24
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Park H, Lim SJ, Cosme J, O'Connell K, Sandeep J, Gayanilo F, Cutter Jr. GR, Montes E, Nitikitpaiboon C, Fisher S, Moustahfid H, Thompson LR. Investigation of machine learning algorithms for taxonomic classification of marine metagenomes. Microbiol Spectr 2023; 11:e0523722. [PMID: 37695074 PMCID: PMC10580933 DOI: 10.1128/spectrum.05237-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/30/2023] [Indexed: 09/12/2023] Open
Abstract
Microbial communities play key roles in ocean ecosystems through regulation of biogeochemical processes such as carbon and nutrient cycling, food web dynamics, and gut microbiomes of invertebrates, fish, reptiles, and mammals. Assessments of marine microbial diversity are therefore critical to understanding spatiotemporal variations in microbial community structure and function in ocean ecosystems. With recent advances in DNA shotgun sequencing for metagenome samples and computational analysis, it is now possible to access the taxonomic and genomic content of ocean microbial communities to study their structural patterns, diversity, and functional potential. However, existing taxonomic classification tools depend upon manually curated phylogenetic trees, which can create inaccuracies in metagenomes from less well-characterized communities, such as from ocean water. Herein, we explore the utility of deep learning tools-DeepMicrobes and a novel Residual Network architecture-that leverage natural language processing and convolutional neural network architectures to map input sequence data (k-mers) to output labels (taxonomic groups) without reliance on a curated taxonomic tree. We trained both models using metagenomic reads simulated from marine microbial genomes in the MarRef database. The performance of both models (accuracy, precision, and percent microbe predicted) was compared with the standard taxonomic classification tool Kraken2 using 10 complex metagenomic data sets simulated from MarRef. Our results demonstrate that time, compute power, and microbial genomic diversity still pose challenges for machine learning (ML). Moreover, our results suggest that high genome coverage and rectification of class imbalance are prerequisites for a well-trained model, and therefore should be a major consideration in future ML work. IMPORTANCE Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches. Our study provides insights on the methods, results, and challenges of deep learning on marine microbial metagenomic data sets. Future machine learning approaches can be improved by rectifying genome coverage and class imbalance in the training data sets, developing alternative models, and increasing the accessibility of computational resources for model training and refinement.
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Affiliation(s)
- Helen Park
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- EPSRC/BBSRC Future Biomanufacturing Research Hub, EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Shen Jean Lim
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
- College of Marine Science, University of South Florida, St Petersburg, Florida, USA
| | | | - Kyle O'Connell
- Deloitte Consulting LLP, Biomedical Data Science Team, Arlington, Virginia, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Northwest, Washington, DC, USA
| | - Jilla Sandeep
- Harte Research Institute, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Felimon Gayanilo
- Harte Research Institute, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - George R. Cutter Jr.
- Southwest Fisheries Science Center, Antarctic Ecosystem Research Division, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Enrique Montes
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
| | - Chotinan Nitikitpaiboon
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Sam Fisher
- Deloitte Consulting LLP, Biomedical Data Science Team, Arlington, Virginia, USA
| | - Hassan Moustahfid
- NOAA/US Integrated Ocean Observing System (IOOS), Silver Spring, Maryland, USA
| | - Luke R. Thompson
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, USA
- Northern Gulf Institute, Mississippi State University, Mississippi, USA
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Schleyer G, Kuhlisch C, Ziv C, Ben-Dor S, Malitsky S, Schatz D, Vardi A. Lipid biomarkers for algal resistance to viral infection in the ocean. Proc Natl Acad Sci U S A 2023; 120:e2217121120. [PMID: 37364132 DOI: 10.1073/pnas.2217121120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to identify lipid biomarkers for the resistance of the bloom-forming alga Emiliania huxleyi to its specific virus, E. huxleyi virus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistant E. huxleyi strains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers in E. huxleyi isolates collected from induced E. huxleyi blooms and in samples collected during an open-ocean E. huxleyi bloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition of E. huxleyi cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and coevolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.
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Affiliation(s)
- Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Carmit Ziv
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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27
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Reynolds R, Hyun S, Tully B, Bien J, Levine NM. Identification of microbial metabolic functional guilds from large genomic datasets. Front Microbiol 2023; 14:1197329. [PMID: 37455725 PMCID: PMC10348482 DOI: 10.3389/fmicb.2023.1197329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/26/2023] [Indexed: 07/18/2023] Open
Abstract
Heterotrophic microbes play an important role in the Earth System as key drivers of major biogeochemical cycles. Specifically, the consumption rate of organic matter is set by the interaction between diverse microbial communities and the chemical and physical environment in which they reside. Modeling these dynamics requires reducing the complexity of microbial communities and linking directly with biogeochemical functions. Microbial metabolic functional guilds provide one approach for reducing microbial complexity and incorporating microbial biogeochemical functions into models. However, we lack a way to identify these guilds. In this study, we present a method for defining metabolic functional guilds from annotated genomes, which are derived from both uncultured and cultured organisms. This method utilizes an Aspect Bernoulli (AB) model and was tested on three large genomic datasets with 1,733-3,840 genomes each. Ecologically relevant microbial metabolic functional guilds were identified including guilds related to DMSP degradation, dissimilatory nitrate reduction to ammonia, and motile copiotrophy. This method presents a way to generate hypotheses about functions co-occurring within individual microbes without relying on cultured representatives. Applying the concept of metabolic functional guilds to environmental samples will provide new insight into the role that heterotrophic microbial communities play in setting rates of carbon cycling.
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Affiliation(s)
- Ryan Reynolds
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Sangwon Hyun
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Benjamin Tully
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
- Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Jacob Bien
- Department of Data Sciences and Operations, University of Southern California, Los Angeles, CA, United States
| | - Naomi M. Levine
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
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28
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Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
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Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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29
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Yu Y, Wang P, Cao HY, Teng ZJ, Zhu Y, Wang M, McMinn A, Chen Y, Xiang H, Zhang YZ, Chen XL, Zhang YQ. Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea. ISME J 2023; 17:537-548. [PMID: 36690779 PMCID: PMC10030869 DOI: 10.1038/s41396-023-01364-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/25/2023]
Abstract
D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.
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Affiliation(s)
- Yang Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Peng Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yanping Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Yin Chen
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hua Xiang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, the Institute of Microbiology CAS, Beijing, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
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30
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Gilbert NE, LeCleir GR, Pound HL, Strzepek RF, Ellwood MJ, Twining BS, Roux S, Boyd PW, Wilhelm SW. Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean. mSystems 2023;:e0126022. [PMID: 36794943 DOI: 10.1128/msystems.01260-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Viruses can alter the abundance, evolution, and metabolism of microorganisms in the ocean, playing a key role in water column biogeochemistry and global carbon cycles. Large efforts to measure the contribution of eukaryotic microorganisms (e.g., protists) to the marine food web have been made, yet the in situ activities of the ecologically relevant viruses that infect these organisms are not well characterized. Viruses within the phylum Nucleocytoviricota ("giant viruses") are known to infect a diverse range of ecologically relevant marine protists, yet how these viruses are influenced by environmental conditions remains under-characterized. By employing metatranscriptomic analyses of in situ microbial communities along a temporal and depth-resolved gradient, we describe the diversity of giant viruses at the Southern Ocean Time Series (SOTS), a site within the subpolar Southern Ocean. Using a phylogeny-guided taxonomic assessment of detected giant virus genomes and metagenome-assembled genomes, we observed depth-dependent structuring of divergent giant virus families mirroring dynamic physicochemical gradients in the stratified euphotic zone. Analyses of transcribed metabolic genes from giant viruses suggest viral metabolic reprogramming of hosts from the surface to a 200-m depth. Lastly, using on-deck incubations reflecting a gradient of iron availability, we show that modulating iron regimes influences the activity of giant viruses in the field. Specifically, we show enhanced infection signatures of giant viruses under both iron-replete and iron-limited conditions. Collectively, these results expand our understanding of how the water column's vertical biogeography and chemical surroundings affect an important group of viruses within the Southern Ocean. IMPORTANCE The biology and ecology of marine microbial eukaryotes is known to be constrained by oceanic conditions. In contrast, how viruses that infect this important group of organisms respond to environmental change is less well known, despite viruses being recognized as key microbial community members. Here, we address this gap in our understanding by characterizing the diversity and activity of "giant" viruses within an important region in the sub-Antarctic Southern Ocean. Giant viruses are double-stranded DNA (dsDNA) viruses of the phylum Nucleocytoviricota and are known to infect a wide range of eukaryotic hosts. By employing a metatranscriptomics approach using both in situ samples and microcosm manipulations, we illuminated both the vertical biogeography and how changing iron availability affects this primarily uncultivated group of protist-infecting viruses. These results serve as a foundation for our understanding of how the open ocean water column structures the viral community, which can be used to guide models of the viral impact on marine and global biogeochemical cycling.
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31
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Yoshizawa S, Azuma T, Kojima K, Inomura K, Hasegawa M, Nishimura Y, Kikuchi M, Armin G, Tsukamoto Y, Miyashita H, Ifuku K, Yamano T, Marchetti A, Fukuzawa H, Sudo Y, Kamikawa R. Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms. Microbes Environ 2023; 38:n/a. [PMID: 37344444 DOI: 10.1264/jsme2.me23015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Diatoms are a major phytoplankton group responsible for approximately 20% of carbon fixation on Earth. They perform photosynthesis using light-harvesting chlo-rophylls located in plastids, an organelle obtained through eukaryote-eukaryote endosymbiosis. Microbial rhodopsin, a photoreceptor distinct from chlo-rophyll-based photosystems, was recently identified in some diatoms. However, the physiological function of diatom rhodopsin remains unclear. Heterologous expression techniques were herein used to investigate the protein function and subcellular localization of diatom rhodopsin. We demonstrated that diatom rhodopsin acts as a light-driven proton pump and localizes primarily to the outermost membrane of four membrane-bound complex plastids. Using model simulations, we also examined the effects of pH changes inside the plastid due to rhodopsin-mediated proton transport on photosynthesis. The results obtained suggested the involvement of rhodopsin-mediated local pH changes in a photosynthetic CO2-concentrating mechanism in rhodopsin-possessing diatoms.
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Affiliation(s)
- Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo
- Graduate School of Frontier Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University
| | - Keiichi Kojima
- School of Pharmaceutical Sciences, Okayama University
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | | | - Masumi Hasegawa
- Atmosphere and Ocean Research Institute, The University of Tokyo
- Graduate School of Frontier Sciences, The University of Tokyo
| | - Yosuke Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | | | | | - Yuya Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University
| | | | | | - Adrian Marchetti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill
| | | | - Yuki Sudo
- School of Pharmaceutical Sciences, Okayama University
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
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Ding S, Henkel JV, Hopmans EC, Bale NJ, Koenen M, Villanueva L, Sinninghe Damsté JS. Changes in the membrane lipid composition of a Sulfurimonas species depend on the electron acceptor used for sulfur oxidation. ISME Commun 2022; 2:121. [PMID: 37938789 PMCID: PMC9789136 DOI: 10.1038/s43705-022-00207-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 11/09/2023]
Abstract
Sulfurimonas species are among the most abundant sulfur-oxidizing bacteria in the marine environment. They are capable of using different electron acceptors, this metabolic flexibility is favorable for their niche adaptation in redoxclines. When oxygen is depleted, most Sulfurimonas spp. (e.g., Sulfurimonas gotlandica) use nitrate ([Formula: see text]) as an electron acceptor to oxidize sulfur, including sulfide (HS-), S0 and thiosulfate, for energy production. Candidatus Sulfurimonas marisnigri SoZ1 and Candidatus Sulfurimonas baltica GD2, recently isolated from the redoxclines of the Black Sea and Baltic Sea respectively, have been shown to use manganese dioxide (MnO2) rather than [Formula: see text] for sulfur oxidation. The use of different electron acceptors is also dependent on differences in the electron transport chains embedded in the cellular membrane, therefore changes in the membrane, including its lipid composition, are expected but are so far unexplored. Here, we used untargeted lipidomic analysis to reveal changes in the composition of the lipidomes of three representative Sulfurimonas species grown using either [Formula: see text] and MnO2. We found that all Sulfurimonas spp. produce a series of novel phosphatidyldiazoalkyl-diacylglycerol lipids. Ca. Sulfurimonas baltica GD2 adapts its membrane lipid composition depending on the electron acceptors it utilizes for growth and survival. When carrying out MnO2-dependent sulfur oxidation, the novel phosphatidyldiazoalkyl-diacylglycerol headgroup comprises shorter alkyl moieties than when sulfur oxidation is [Formula: see text]-dependent. This is the first report of membrane lipid adaptation when an organism is grown with different electron acceptors. We suggest novel diazoalkyl lipids have the potential to be used as a biomarker for different conditions in redox-stratified systems.
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Affiliation(s)
- Su Ding
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands.
| | - Jan V Henkel
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Ellen C Hopmans
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Nicole J Bale
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Michel Koenen
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
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Abstract
Chemists have studied marine animals for the better part of a century because they contain a diverse array of bioactive compounds. Tens of thousands of compounds have been reported, many with elaborate structural motifs and biological mechanisms of action found nowhere else. The challenge holding back the field has long been that of supply. Compounds are sometimes obtained by cultivating marine animals or by wild harvest, but this often presents logistical and environmental challenges. Some of the most medically important marine animal compounds are supplied by synthesis, often through multistep procedures that delay drug development. A relatively small number of such agents have been approved by the U.S. Food and Drug Administration, often after a heroic effort. In a recent mBio paper, Uppal and coworkers (https://doi.org/10.1128/mBio.01524-22) address key hurdles underlying the supply issue, discovering an uncultivated new bacterial genus from a marine sponge and reconstituting the biosynthetic pathway for expression.
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Shulga N, Abramov S, Klyukina A, Ryazantsev K, Gavrilov S. Fast-growing Arctic Fe-Mn deposits from the Kara Sea as the refuges for cosmopolitan marine microorganisms. Sci Rep 2022; 12:21967. [PMID: 36539439 PMCID: PMC9768204 DOI: 10.1038/s41598-022-23449-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022] Open
Abstract
The impact of biomineralization and redox processes on the formation and growth of ferromanganese deposits in the World Ocean remains understudied. This problem is particularly relevant for the Arctic marine environment where sharp seasonal variations of temperature, redox conditions, and organic matter inflow significantly impact the biogenic and abiotic pathways of ferromanganese deposits formation. The microbial communities of the fast-growing Arctic Fe-Mn deposits have not been reported so far. Here, we describe the microbial diversity, structure and chemical composition of nodules, crust and their underlying sediments collected from three different sites of the Kara Sea. Scanning electron microscopy revealed a high abundance of microfossils and biofilm-like structures within the nodules. Phylogenetic profiling together with redundancy and correlation analyses revealed a positive selection for putative metal-reducers (Thermodesulfobacteriota), iron oxidizers (Hyphomicrobiaceae and Scalinduaceae), and Fe-scavenging Nitrosopumilaceae or Magnetospiraceae in the microenvironments of the Fe-Mn deposits from their surrounding benthic microbial populations. We hypothesize that in the Kara Sea, the nodules provide unique redox-stable microniches for cosmopolitan benthic marine metal-cycling microorganisms in an unsteady environment, thus focusing the overall geochemical activity of nodule-associated microbial communities and accelerating processes of ferromanganese deposits formation to uniquely high rates.
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Affiliation(s)
- Natalia Shulga
- grid.426292.90000 0001 2295 4196Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Abramov
- grid.5719.a0000 0004 1936 9713Department of Environmental Microbiology, Institute of Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Stuttgart, Germany
| | - Alexandra Klyukina
- grid.4886.20000 0001 2192 9124Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Ryazantsev
- grid.4886.20000 0001 2192 9124Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Gavrilov
- grid.4886.20000 0001 2192 9124Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Gong X, Del Río ÁR, Xu L, Chen Z, Langwig MV, Su L, Sun M, Huerta-Cepas J, De Anda V, Baker BJ. New globally distributed bacterial phyla within the FCB superphylum. Nat Commun 2022; 13:7516. [PMID: 36473838 PMCID: PMC9727166 DOI: 10.1038/s41467-022-34388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China.
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Mingxue Sun
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78701, USA.
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Munson-McGee JH, Lindsay MR, Sintes E, Brown JM, D'Angelo T, Brown J, Lubelczyk LC, Tomko P, Emerson D, Orcutt BN, Poulton NJ, Herndl GJ, Stepanauskas R. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 2022; 612:764-770. [PMID: 36477536 PMCID: PMC9771814 DOI: 10.1038/s41586-022-05505-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.
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Affiliation(s)
| | | | - Eva Sintes
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Instituto Español de Oceanografía-CSIC, Centro Oceanográfico de Baleares, Palma, Spain
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Joe Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
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Harding KJ, Turk-Kubo KA, Mak EWK, Weber PK, Mayali X, Zehr JP. Cell-specific measurements show nitrogen fixation by particle-attached putative non-cyanobacterial diazotrophs in the North Pacific Subtropical Gyre. Nat Commun 2022; 13:6979. [PMID: 36379938 PMCID: PMC9666432 DOI: 10.1038/s41467-022-34585-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
Biological nitrogen fixation is a major important source of nitrogen for low-nutrient surface oceanic waters. Nitrogen-fixing (diazotrophic) cyanobacteria are believed to be the primary contributors to this process, but the contribution of non-cyanobacterial diazotrophic organisms in oxygenated surface water, while hypothesized to be important, has yet to be demonstrated. In this study, we used simultaneous 15N-dinitrogen and 13C-bicarbonate incubations combined with nanoscale secondary ion mass spectrometry analysis to screen tens of thousands of mostly particle-associated, cell-like regions of interest collected from the North Pacific Subtropical Gyre. These dual isotope incubations allow us to distinguish between non-cyanobacterial and cyanobacterial nitrogen-fixing microorganisms and to measure putative cell-specific nitrogen fixation rates. With this approach, we detect nitrogen fixation by putative non-cyanobacterial diazotrophs in the oxygenated surface ocean, which are associated with organic-rich particles (<210 µm size fraction) at two out of seven locations sampled. When present, up to 4.1% of the analyzed particles contain at least one active putative non-cyanobacterial diazotroph. The putative non-cyanobacterial diazotroph nitrogen fixation rates (0.76 ± 1.60 fmol N cell-1 d-1) suggest that these organisms are capable of fixing dinitrogen in oxygenated surface water, at least when attached to particles, and may contribute to oceanic nitrogen fixation.
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Affiliation(s)
- Katie J Harding
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | | | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA.
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Miranda K, Weigel BL, Fogarty EC, Veseli IA, Giblin AE, Eren AM, Pfister CA. The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes. mSystems 2022; 7:e0059222. [PMID: 35993708 DOI: 10.1128/msystems.00592-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems. IMPORTANCE Kelps, seagrasses, and surfgrasses are ecosystem engineers on rocky shorelines, where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms, sulfur oxidation, and the production of B vitamins. In turn, these microbes have the genetic capabilities to assimilate the dissolved organic compounds released by their macrophyte hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal seaweeds and seagrasses is likely due in part to the activities of associated microbes, and an increased understanding of these associations is needed.
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Andrew S, Wilson T, Smith S, Marchetti A, Septer AN. A tripartite model system for Southern Ocean diatom-bacterial interactions reveals the coexistence of competing symbiotic strategies. ISME Commun 2022; 2:97. [PMID: 37938401 PMCID: PMC9723598 DOI: 10.1038/s43705-022-00181-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 09/24/2023]
Abstract
Southern Ocean (SO) diatoms play an important role in global carbon flux, and their influence on carbon export is directly linked to interactions with epiphytic bacteria. Bacterial symbionts that increase diatom growth promote atmospheric carbon uptake, while bacterial degraders divert diatom biomass into the microbial loop where it can then be released as carbon dioxide through respiration. To further explore SO diatom-bacterial associations, a natural model system is needed that is representative of these diverse and important interactions. Here, we use concurrent cultivation to isolate a species of the ecologically-important SO diatom, Pseudo-nitzschia subcurvata, and its co-occurring bacteria. Although vitamin-depleted, axenic Pseudo-nitzschia grew poorly in culture, addition of a co-isolated Roseobacter promoted diatom growth, while addition of a co-isolated Flavobacterium negatively impacted diatom growth. Microscopy revealed both bacterial isolates are physically associated with diatom cells and genome sequencing identified important predicted functions including vitamin synthesis, motility, cell attachment mechanisms, and diverse antimicrobial weapons that could be used for interbacterial competition. These findings revealed the natural coexistence of competing symbiotic strategies of diatom-associated bacteria in the SO, and the utility of this tripartite system, composed of a diatom and two bacterial strains, as a co-culture model to probe ecological-relevant interactions between diatoms and the bacteria that compete for access to the phycosphere.
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Affiliation(s)
- Sarah Andrew
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Travis Wilson
- Environment, Ecology & Energy Program, University of North Carolina, Chapel Hill, NC, USA
| | - Stephanie Smith
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Adrian Marchetti
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Alecia N Septer
- Department of Earth, Marine & Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA.
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Engelberts JP, Abdul Wahab MA, Maldonado M, Rix L, Marangon E, Robbins SJ, Wagner M, Webster NS. Microbes from Mum: symbiont transmission in the tropical reef sponge Ianthella basta. ISME Commun 2022; 2:90. [PMID: 37938734 PMCID: PMC9723589 DOI: 10.1038/s43705-022-00173-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 05/28/2023]
Abstract
Most marine sponge species harbour distinct communities of microorganisms which contribute to various aspects of their host's health and physiology. In addition to their key roles in nutrient transformations and chemical defence, these symbiotic microbes can shape sponge phenotype by mediating important developmental stages and influencing the environmental tolerance of the host. However, the characterisation of each microbial taxon throughout a sponge's life cycle remains challenging, with several sponge species hosting up to 3000 distinct microbial species. Ianthella basta, an abundant broadcast spawning species in the Indo-Pacific, is an emerging model for sponge symbiosis research as it harbours only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium. Here, we successfully spawned Ianthella basta, characterised its mode of reproduction, and used 16S rRNA gene amplicon sequencing, fluorescence in situ hybridisation, and transmission electron microscopy to characterise the microbial community throughout its life cycle. We confirmed I. basta as being gonochoric and showed that the three dominant symbionts, which together make up >90% of the microbiome according to 16S rRNA gene abundance, are vertically transmitted from mother to offspring by a unique method involving encapsulation in the peri-oocytic space, suggesting an obligate relationship between these microbes and their host.
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Affiliation(s)
- J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | | | - Manuel Maldonado
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Laura Rix
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Emma Marangon
- Australian Institute of Marine Science, Townsville, QLD, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
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Downey KM, Judy KJ, Pinseel E, Alverson AJ, Lewis JA. The dynamic response to hypoosmotic stress reveals distinct stages of freshwater acclimation by a euryhaline diatom. Mol Ecol 2022; 32:2766-2783. [PMID: 36151935 DOI: 10.1111/mec.16703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022]
Abstract
The salinity gradient separating marine and freshwater environments is a major ecological divide, and the mechanisms by which most organisms adapt to new salinity environments are poorly understood. Diatoms are a lineage of ancestrally marine microalgae that have repeatedly colonized and diversified in freshwaters. Cyclotella cryptica is a euryhaline diatom found in salinities ranging from fully freshwater to fully marine, thus providing a powerful system for understanding the genomic mechanisms for mitigating and acclimating to low salinity. To understand how diatoms mitigate acute hypoosmotic stress, we abruptly shifted C. cryptica from seawater to freshwater and performed transcriptional profiling during the first 10 hours. Freshwater shock dramatically remodeled the transcriptome, with ~50% of the genome differentially expressed in at least one time point. The peak response occurred within 1 hour, with strong repression of genes involved in cell growth and osmolyte production, and strong induction of specific stress defense genes. Transcripts largely returned to baseline levels within 4-10 hours, with growth resuming shortly thereafter, suggesting that gene expression dynamics may be useful for predicting acclimation. Moreover, comparison to a transcriptomics study of C. cryptica following months-long acclimation to freshwater revealed little overlap between the genes and processes differentially expressed in cells exposed to acute stress versus fully acclimated conditions. Altogether, this study highlights the power of time-resolved transcriptomics to reveal fundamental insights into how cells dynamically respond to an acute environmental shift and provides new insights into how diatoms mitigate natural salinity fluctuations and have successfully diversified across freshwater habitats worldwide.
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Affiliation(s)
- Kala M Downey
- University of Arkansas, Department of Biological Sciences, Fayetteville, AR, USA
| | - Kathryn J Judy
- University of Arkansas, Department of Biological Sciences, Fayetteville, AR, USA
| | - Eveline Pinseel
- University of Arkansas, Department of Biological Sciences, Fayetteville, AR, USA
| | - Andrew J Alverson
- University of Arkansas, Department of Biological Sciences, Fayetteville, AR, USA
| | - Jeffrey A Lewis
- University of Arkansas, Department of Biological Sciences, Fayetteville, AR, USA
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Haney AM, Sanfilippo JE, Garczarek L, Partensky F, Kehoe DM. Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation. mBio 2022;:e0151122. [PMID: 35856560 DOI: 10.1128/mbio.01511-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine cyanobacteria depend on light for photosynthesis, restricting their growth to the photic zone. The upper part of this layer is exposed to strong UV radiation (UVR), a DNA mutagen that can harm these microorganisms. To thrive in UVR-rich waters, marine cyanobacteria employ photoprotection strategies that are still not well defined. Among these are photolyases, light-activated enzymes that repair DNA dimers generated by UVR. Our analysis of genomes of 81 strains of Synechococcus, Cyanobium, and Prochlorococcus isolated from the world’s oceans shows that they possess up to five genes encoding different members of the photolyase/cryptochrome family, including a photolyase with a novel domain arrangement encoded by either one or two separate genes. We disrupted the putative photolyase-encoding genes in Synechococcus sp. strain RS9916 and discovered that each gene contributes to the overall capacity of this organism to survive UVR. Additionally, each conferred increased survival after UVR exposure when transformed into Escherichia coli lacking its photolyase and SOS response. Our results provide the first evidence that this large set of photolyases endows Synechococcus with UVR resistance that is far superior to that of E. coli, but that, unlike for E. coli, these photolyases provide Synechococcus with the vast majority of its UVR tolerance.
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Loureiro C, Galani A, Gavriilidou A, Chaib de Mares M, van der Oost J, Medema MH, Sipkema D. Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification. mSystems 2022;:e0035722. [PMID: 35862823 DOI: 10.1128/msystems.00357-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.
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Conrad RE, Viver T, Gago JF, Hatt JK, Venter SN, Rossello-Mora R, Konstantinidis KT. Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations. ISME J 2022; 16:1222-1234. [PMID: 34887548 PMCID: PMC9039077 DOI: 10.1038/s41396-021-01149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 05/03/2023]
Abstract
Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.
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Affiliation(s)
- Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Janet K Hatt
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
| | - Konstantinos T Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria. Appl Environ Microbiol 2022;:e0025522. [PMID: 35311512 DOI: 10.1128/aem.00255-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link between marine primary production and remineralization of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here, we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range. IMPORTANCE Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The nearly identical genomes of four strains of Melnitz isolated from different marine provinces and the global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems, and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning may not be necessarily restricted to phylogenetically related hosts but is a function of shared physical and biochemical properties of the cell.
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Clark CM, Hernandez A, Mullowney MW, Fitz-Henley J, Li E, Romanowski SB, Pronzato R, Manconi R, Sanchez LM, Murphy BT. Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges. ISME Commun 2022; 2:22. [PMID: 37938725 PMCID: PMC9723699 DOI: 10.1038/s43705-022-00105-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2023]
Abstract
Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.
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Affiliation(s)
- Chase M Clark
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Antonio Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael W Mullowney
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Jhewelle Fitz-Henley
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Emma Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Sean B Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Roberto Pronzato
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
| | - Renata Manconi
- Dipartimento Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
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Karlsen C, Tzimorotas D, Robertsen EM, Kirste KH, Bogevik AS, Rud I. Feed microbiome: confounding factor affecting fish gut microbiome studies. ISME Commun 2022; 2:14. [PMID: 37938665 PMCID: PMC9723547 DOI: 10.1038/s43705-022-00096-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 06/01/2023]
Abstract
There is an increasing interest in the impact of feed on the fish gut microbiome. Most of the studies are based on sequencing the bacterial housekeeping gene 16S rRNA from extracted total DNA, including resident and non-resident live bacteria as well as dead bacteria. It has not been a common practice to include the feed as control, although it contains various nutritious ingredients that microorganisms can use before or after feed preparation. Thus, study designs using digesta as a proxy for the intestinal microbiome raise the concern that composition of the gut microbiome might be biased by carry-over of microbial DNA from the feed itself. Here we report analysis of 15 feeds and representative intestinal digesta of Atlantic salmon (Salmo salar) from five independent case studies. This allowed us to identify "feed microbiomes" that were microbially diverse and shared taxa with digesta microbiomes. Digesta-specific microbiomes were identified, though they were mainly enriched by a few taxa, such as Mycoplasma and Ruminococcaceae. Overall, findings are consistent with a model wherein gut microbial profiles are to a different degree influenced by bacterial DNA present in the feed itself through a "feed microbiome" carry-over effect.
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Affiliation(s)
| | | | - Espen Mikal Robertsen
- Centre for Bioinformatics, Faculty of Science and Technology, UiT The Arctic University of Norway, PO Box 6050 Langnes, N-9037, Tromsø, Norway
| | | | | | - Ida Rud
- Nofima, Osloveien 1, 1433, Ås, Norway
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Li J, Majzoub ME, Marzinelli EM, Dai Z, Thomas T, Egan S. Bacterial controlled mitigation of dysbiosis in a seaweed disease. ISME J 2022; 16:378-87. [PMID: 34341505 DOI: 10.1038/s41396-021-01070-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023]
Abstract
Disease in the marine environment is predicted to increase with anthropogenic stressors and already affects major habitat-formers, such as corals and seaweeds. Solutions to address this issue are urgently needed. The seaweed Delisea pulchra is prone to a bleaching disease, which is caused by opportunistic pathogens and involves bacterial dysbiosis. Bacteria that can inhibit these pathogens and/or counteract dysbiosis are therefore hypothesised to reduce disease. This study aimed to identify such disease-protective bacteria and investigate their protective action. One strain, Phaeobacter sp. BS52, isolated from healthy D. pulchra, was antagonistic towards bleaching pathogens and significantly increased the proportion of healthy individuals when applied before the pathogen challenge (pathogen-only vs. BS52 + pathogen: 41-80%), and to a level similar to the control. However, no significant negative correlations between the relative abundances of pathogens and BS52 on D. pulchra were detected. Instead, inoculation of BS52 mitigated pathogen-induced changes in the epibacterial community. These observations suggest that the protective activity of BS52 was due to its ability to prevent dysbiosis, rather than direct pathogen inhibition. This study demonstrates the feasibility of manipulating bacterial communities in seaweeds to reduce disease and that mitigation of dysbiosis can have positive health outcomes.
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Manck LE, Park J, Tully BJ, Poire AM, Bundy RM, Dupont CL, Barbeau KA. Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean. ISME J 2022; 16:358-369. [PMID: 34341506 PMCID: PMC8776838 DOI: 10.1038/s41396-021-01065-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023]
Abstract
It is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which siderophores affect the availability of iron from specific sources and the resulting significance of these processes on iron biogeochemical cycling as a whole have remained largely untested. In this study, we develop a model system for testing the effects of siderophore production on iron bioavailability using the marine copiotroph Alteromonas macleodii ATCC 27126. Through the generation of the knockout cell line ΔasbB::kmr, which lacks siderophore biosynthetic capabilities, we demonstrate that the production of the siderophore petrobactin enables the acquisition of iron from mineral sources and weaker iron-ligand complexes. Notably, the utilization of lithogenic iron, such as that from atmospheric dust, indicates a significant role for siderophores in the incorporation of new iron into marine systems. We have also detected petrobactin, a photoreactive siderophore, directly from seawater in the mid-latitudes of the North Pacific and have identified the biosynthetic pathway for petrobactin in bacterial metagenome-assembled genomes widely distributed across the global ocean. Together, these results improve our mechanistic understanding of the role of siderophore production in iron biogeochemical cycling in the marine environment wherein iron speciation, bioavailability, and residence time can be directly influenced by microbial activities.
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Affiliation(s)
- Lauren E Manck
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Jiwoon Park
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - Alfonso M Poire
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA, USA
| | - Randelle M Bundy
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Christopher L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Human Health, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Synthetic Biology, J. Craig Venter Institute, La Jolla, CA, USA
| | - Katherine A Barbeau
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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Hedlund BP, Zhang C, Wang F, Rinke C, Martin WF. Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea. Front Microbiol 2022; 12:827229. [PMID: 35126338 PMCID: PMC8816317 DOI: 10.3389/fmicb.2021.827229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai JiaoTong University, Shanghai, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - William F. Martin
- Institute for Molecular Evolution, University of Dusseldorf Medical School, Düsseldorf, Germany
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