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Hesketh-Best PJ, Bosco-Santos A, Garcia SL, O’Beirne MD, Werne JP, Gilhooly WP, Silveira CB. Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:126. [PMID: 38665202 PMCID: PMC11041744 DOI: 10.1038/s43247-023-00796-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/05/2023] [Indexed: 04/28/2024]
Abstract
Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.
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Affiliation(s)
| | - Alice Bosco-Santos
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Sofia L. Garcia
- Department of Biology, University of Miami, Coral Gables, FL USA
| | - Molly D. O’Beirne
- Department of Geology & Environmental Science, University of Pittsburgh, Pittsburgh, PA USA
| | - Josef P. Werne
- Department of Geology & Environmental Science, University of Pittsburgh, Pittsburgh, PA USA
| | - William P. Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN USA
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Bhatnagar S, Cowley ES, Kopf SH, Castro SP, Kearney S, Dawson SC, Hanselmann K, Ruff SE. Author Correction: Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. ENVIRONMENTAL MICROBIOME 2023; 18:27. [PMID: 36997980 PMCID: PMC10064758 DOI: 10.1186/s40793-023-00472-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Affiliation(s)
- Srijak Bhatnagar
- Faculty of Science and Technology, Athabasca University, Athabasca, AB Canada
| | - Elise S. Cowley
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado, Boulder, CO USA
| | - Sherlynette Pérez Castro
- Ecosystems Center and J. Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
| | - Sean Kearney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Scott C. Dawson
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA USA
| | | | - S. Emil Ruff
- Ecosystems Center and J. Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
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Fuchsman CA, Garcia Prieto D, Hays MD, Cram JA. Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth. PeerJ 2023; 11:e14924. [PMID: 36874978 PMCID: PMC9983427 DOI: 10.7717/peerj.14924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Background Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans. Methodology We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes. Results Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition. Conclusions Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.
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Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - David Garcia Prieto
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Matthew D Hays
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
| | - Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, United States of America
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Grouzdev D, Gaisin V, Lunina O, Krutkina M, Krasnova E, Voronov D, Baslerov R, Sigalevich P, Savvichev A, Gorlenko V. Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota. FEMS Microbiol Ecol 2022; 98:6693937. [PMID: 36073352 DOI: 10.1093/femsec/fiac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022] Open
Abstract
Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column. In the present work, metagenomic sequencing was used to investigate the natural population of brown Chl. phaeovibrioides ZM in a marine stratified Zeleny Mys lagoon in the Kandalaksha Bay (the White Sea) to supplement the previously obtained genomes of brown Chlorobiaceae. The genomes of brown and green Chlorobiaceae were investigated using comparative genome analysis and phylogenetic and reconciliation analysis to reconstruct the evolution of these ecological forms. Our results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination. However, despite the vertical inheritance of these characteristics, among modern Chlorobiaceae populations, the genes responsible for synthesizing the pigments of the brown form are subject to active horizontal transfer.
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Affiliation(s)
- Denis Grouzdev
- SciBear OU, 10115 Tallinn, Estonia.,School of Marine and Atmospheric Sciences, Stony Brook University, 11794, Stony Brook, USA
| | - Vasil Gaisin
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.,Current affiliation: Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Olga Lunina
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | | | - Elena Krasnova
- Pertsov White Sea Biological Station, 184042, Republic Karelia, Russia
| | - Dmitry Voronov
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia
| | - Roman Baslerov
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Pavel Sigalevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Alexander Savvichev
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Vladimir Gorlenko
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
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Panwar P, Allen MA, Williams TJ, Haque S, Brazendale S, Hancock AM, Paez-Espino D, Cavicchioli R. Remarkably coherent population structure for a dominant Antarctic Chlorobium species. MICROBIOME 2021; 9:231. [PMID: 34823595 PMCID: PMC8620254 DOI: 10.1186/s40168-021-01173-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/09/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. RESULTS A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml-1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. CONCLUSION The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. Video abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Sabrina Haque
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , Present address: Pegarah, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Present address: Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Present address: Mammoth Biosciences, Inc., 1000 Marina Blvd. Suite 600, Brisbane, CA, USA
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics. Genes (Basel) 2021; 12:genes12060886. [PMID: 34201311 PMCID: PMC8226683 DOI: 10.3390/genes12060886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus–host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.
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Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions. THE ISME JOURNAL 2021; 15:1569-1584. [PMID: 33452481 PMCID: PMC8163819 DOI: 10.1038/s41396-020-00870-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/29/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023]
Abstract
Temperate phages are viruses of bacteria that can establish two types of infection: a lysogenic infection in which the virus replicates with the host cell without producing virions, and a lytic infection where the host cell is eventually destroyed, and new virions are released. While both lytic and lysogenic infections are routinely observed in the environment, the ecological and evolutionary processes regulating these viral dynamics are still not well understood, especially for uncultivated virus-host pairs. Here, we characterized the long-term dynamics of uncultivated viruses infecting green sulfur bacteria (GSB) in a model freshwater lake (Trout Bog Lake, TBL). As no GSB virus has been formally described yet, we first used two complementary approaches to identify new GSB viruses from TBL; one in vitro based on flow cytometry cell sorting, the other in silico based on CRISPR spacer sequences. We then took advantage of existing TBL metagenomes covering the 2005-2018 period to examine the interactions between GSB and their viruses across years and seasons. From our data, GSB populations in TBL were constantly associated with at least 2-8 viruses each, including both lytic and temperate phages. The dominant GSB population in particular was consistently associated with two prophages with a nearly 100% infection rate for >10 years. We illustrate with a theoretical model that such an interaction can be stable given a low, but persistent, level of prophage induction in low-diversity host populations. Overall, our data suggest that lytic and lysogenic viruses can readily co-infect the same host population, and that host strain-level diversity might be an important factor controlling virus-host dynamics including lytic/lysogeny switch.
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Li M, Fang A, Yu X, Zhang K, He Z, Wang C, Peng Y, Xiao F, Yang T, Zhang W, Zheng X, Zhong Q, Liu X, Yan Q. Microbially-driven sulfur cycling microbial communities in different mangrove sediments. CHEMOSPHERE 2021; 273:128597. [PMID: 33077194 DOI: 10.1016/j.chemosphere.2020.128597] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 05/13/2023]
Abstract
Microbially-driven sulfur cycling is a vital biogeochemical process in the sulfur-rich mangrove ecosystem. It is critical to evaluate the potential impact of sulfur transformation in mangrove ecosystems. To reveal the diversity, composition, and structure of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) and underlying mechanisms, we analyzed the physicochemical properties and sediment microbial communities from an introduced mangrove species (Sonneratia apetala), a native mangrove species (Kandelia obovata) and the mudflat in Hanjiang River Estuary in Guangdong (23.27°N, 116.52°E), China. The results indicated that SOB was dominated by autotrophic Thiohalophilus and chemoautotrophy Chromatium in S. apetala and K. obovata, respectively, while Desulfatibacillum was the dominant genus of SRB in K. obovata sediments. Also, the redundancy analysis indicated that temperature, redox potential (ORP), and SO42- were the significant factors influencing the sulfur cycling microbial communities with elemental sulfur (ES) as the key factor driver for SOB and total carbon (TC) for SRB in mangrove sediments. Additionally, the morphological transformation of ES, acid volatile sulfide (AVS) and SO42- explained the variation of sulfur cycling microbial communities under sulfur-rich conditions, and we found mangrove species-specific dominant Thiohalobacter, Chromatium and Desulfatibacillum, which could well use ES and SO42-, thus promoting the sulfur cycling in mangrove sediments. Meanwhile, the change of nutrient substances (TN, TC) explained why SOB were more susceptible to environmental changes than SRB. Sulfate reducing bacteria produces sulfide in anoxic sediments at depth that then migrate upward, toward fewer reducing conditions, where it's oxidized by sulfur oxidizing bacteria. This study indicates the high ability of SOB and SRB in ES, SO42-,S2- and S2- generation and transformation in sulfur-rich mangrove ecosystems, and provides novel insights into sulfur cycling in other wetland ecosystems from a microbial perspective.
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Affiliation(s)
- Mingyue Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Anqi Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Keke Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
| | - Tony Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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Panwar P, Allen MA, Williams TJ, Hancock AM, Brazendale S, Bevington J, Roux S, Páez-Espino D, Nayfach S, Berg M, Schulz F, Chen IMA, Huntemann M, Shapiro N, Kyrpides NC, Woyke T, Eloe-Fadrosh EA, Cavicchioli R. Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community. MICROBIOME 2020; 8:116. [PMID: 32772914 PMCID: PMC7416419 DOI: 10.1186/s40168-020-00889-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/30/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Cold environments dominate the Earth's biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000-7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. RESULTS The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. CONCLUSION Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract.
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Affiliation(s)
- Pratibha Panwar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Alyce M Hancock
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Tasmania, Australia
| | - Sarah Brazendale
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
- , 476 Lancaster Rd, Pegarah, Australia
| | - James Bevington
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia
| | - Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - David Páez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Mammoth BioSciences, 279 East Grand Ave, South San Francisco, CA, USA
| | - Stephen Nayfach
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Maureen Berg
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - I-Min A Chen
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, 2052, Australia.
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Abstract
Modified tetrapyrroles are large macrocyclic compounds, consisting of diverse conjugation and metal chelation systems and imparting an array of colors to the biological structures that contain them. Tetrapyrroles represent some of the most complex small molecules synthesized by cells and are involved in many essential processes that are fundamental to life on Earth, including photosynthesis, respiration, and catalysis. These molecules are all derived from a common template through a series of enzyme-mediated transformations that alter the oxidation state of the macrocycle and also modify its size, its side-chain composition, and the nature of the centrally chelated metal ion. The different modified tetrapyrroles include chlorophylls, hemes, siroheme, corrins (including vitamin B12), coenzyme F430, heme d1, and bilins. After nearly a century of study, almost all of the more than 90 different enzymes that synthesize this family of compounds are now known, and expression of reconstructed operons in heterologous hosts has confirmed that most pathways are complete. Aside from the highly diverse nature of the chemical reactions catalyzed, an interesting aspect of comparative biochemistry is to see how different enzymes and even entire pathways have evolved to perform alternative chemical reactions to produce the same end products in the presence and absence of oxygen. Although there is still much to learn, our current understanding of tetrapyrrole biogenesis represents a remarkable biochemical milestone that is summarized in this review.
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Affiliation(s)
- Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
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11
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Bhatnagar S, Cowley ES, Kopf SH, Pérez Castro S, Kearney S, Dawson SC, Hanselmann K, Ruff SE. Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. ENVIRONMENTAL MICROBIOME 2020; 15:3. [PMID: 33902727 PMCID: PMC8066431 DOI: 10.1186/s40793-019-0348-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/25/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. RESULTS Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp. CONCLUSIONS The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.
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Affiliation(s)
- Srijak Bhatnagar
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - Elise S. Cowley
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI USA
| | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado, Boulder, CO USA
| | - Sherlynette Pérez Castro
- Ecosystems Center and J. Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
| | - Sean Kearney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Scott C. Dawson
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA USA
| | | | - S. Emil Ruff
- Ecosystems Center and J. Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
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12
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Genome Sequences of a Green-Colored Chlorobium phaeovibrioides Strain Containing Two Plasmids and a Closely Related Plasmid-Free Brown-Colored Strain. Microbiol Resour Announc 2020; 9:9/2/e01172-19. [PMID: 31919163 PMCID: PMC6952649 DOI: 10.1128/mra.01172-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequences of the green sulfur bacterium Chlorobium phaeovibrioides strains GrTcv12 and PhvTcv-s14, isolated from the chemocline zone from meromictic Lake Trekhtzvetnoe, separated from the White Sea, in Russia. This is the first report showing the presence of plasmids containing antiphage systems in the Chlorobium sp. genome. Here, we report the draft genome sequences of the green sulfur bacterium Chlorobium phaeovibrioides strains GrTcv12 and PhvTcv-s14, isolated from the chemocline zone from meromictic Lake Trekhtzvetnoe, separated from the White Sea, in Russia. This is the first report showing the presence of plasmids containing antiphage systems in the Chlorobium sp. genome.
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13
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Ward BA, Collins S, Dutkiewicz S, Gibbs S, Bown P, Ridgwell A, Sauterey B, Wilson JD, Oschlies A. Considering the Role of Adaptive Evolution in Models of the Ocean and Climate System. JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS 2019; 11:3343-3361. [PMID: 32025278 PMCID: PMC6988444 DOI: 10.1029/2018ms001452] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 05/24/2023]
Abstract
Numerical models have been highly successful in simulating global carbon and nutrient cycles in today's ocean, together with observed spatial and temporal patterns of chlorophyll and plankton biomass at the surface. With this success has come some confidence in projecting the century-scale response to continuing anthropogenic warming. There is also increasing interest in using such models to understand the role of plankton ecosystems in past oceans. However, today's marine environment is the product of billions of years of continual evolution-a process that continues today. In this paper, we address the questions of whether an assumption of species invariance is sufficient, and if not, under what circumstances current model projections might break down. To do this, we first identify the key timescales and questions asked of models. We then review how current marine ecosystem models work and what alternative approaches are available to account for evolution. We argue that for timescales of climate change overlapping with evolutionary timescales, accounting for evolution may to lead to very different projected outcomes regarding the timescales of ecosystem response and associated global biogeochemical cycling. This is particularly the case for past extinction events but may also be true in the future, depending on the eventual degree of anthropogenic disruption. The discipline of building new numerical models that incorporate evolution is also hugely beneficial in itself, as it forces us to question what we know about adaptive evolution, irrespective of its quantitative role in any specific event or environmental changes.
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Affiliation(s)
- B. A. Ward
- Ocean and Earth ScienceUniversity of SouthamptonSouthamptonUK
| | - S. Collins
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - S. Dutkiewicz
- Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
| | - S. Gibbs
- Ocean and Earth ScienceUniversity of SouthamptonSouthamptonUK
| | - P. Bown
- Department of GeologyUniversity College LondonLondonUK
| | - A. Ridgwell
- Department of Earth SciencesUniversity of CaliforniaRiversideCAUSA
- School of Geographical SciencesUniversity of BristolBristolUK
| | - B. Sauterey
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS)ParisFrance
| | - J. D. Wilson
- School of Geographical SciencesUniversity of BristolBristolUK
| | - A. Oschlies
- GEOMAR Helmholtz Centre for Ocean ResearchKielGermany
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14
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Douglas GM, Langille MGI. Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes. Genome Biol Evol 2019; 11:2750-2766. [PMID: 31504488 PMCID: PMC6777429 DOI: 10.1093/gbe/evz184] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.
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Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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15
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Genome Sequences of Green- and Brown-Colored Strains of Chlorobium phaeovibrioides with Gas Vesicles. Microbiol Resour Announc 2019; 8:8/29/e00711-19. [PMID: 31320438 PMCID: PMC6639628 DOI: 10.1128/mra.00711-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The draft genomes of green-colored Chlorobium phaeovibrioidesGrKhr17 and brown-colored Chlorobium phaeovibrioidesBrKhr17, green sulfur bacteria with gas vesicles isolated from Lake Bolshye Khruslomeny, are presented. These sequences contribute to genomic analyses of the Chlorobiaceae family that are part of ongoing research seeking to better understand their ecosystem-specific adaptations. The draft genomes of green-colored Chlorobium phaeovibrioidesGrKhr17 and brown-colored Chlorobium phaeovibrioidesBrKhr17, green sulfur bacteria with gas vesicles isolated from Lake Bolshye Khruslomeny, are presented. These sequences contribute to genomic analyses of the Chlorobiaceae family that are part of ongoing research seeking to better understand their ecosystem-specific adaptations.
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16
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Diao M, Huisman J, Muyzer G. Spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in a seasonally stratified lake. FEMS Microbiol Ecol 2019. [PMID: 29528404 PMCID: PMC5939864 DOI: 10.1093/femsec/fiy040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria drive major transformations in the sulfur cycle, and play vital roles in oxic--anoxic transitions in lakes and coastal waters. However, information on the succession of these sulfur bacteria in seasonally stratified lakes using molecular biological techniques is scarce. Here, we used 16S rRNA gene amplicon sequencing to study the spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in Lake Vechten. Oxygen and sulfate were mixed throughout the water column in winter and early spring. Meanwhile, SRB, green sulfur bacteria (GSB), purple sulfur bacteria (PSB), and colorless sulfur bacteria (CSB) exclusively inhabited the sediment. After the water column stratified, oxygen and nitrate concentrations decreased in the hypolimnion and various SRB species expanded into the anoxic hypolimnion. Consequently, sulfate was reduced to sulfide, stimulating the growth of PSB and GSB in the metalimnion and hypolimnion during summer stratification. When hypoxia spread throughout the water column during fall turnover, SRB and GSB vanished from the water column, whereas CSB (mainly Arcobacter) and PSB (Lamprocystis) became dominant and oxidized the accumulated sulfide under micro-aerobic conditions. Our results support the view that, once ecosystems have become anoxic and sulfidic, a large oxygen influx is needed to overcome the anaerobic sulfur cycle and bring the ecosystems back into their oxic state.
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Affiliation(s)
- Muhe Diao
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
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17
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Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, Boyd ES, Ward DM, Hanada S, Bryant DA. " Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities. Front Microbiol 2019; 9:3159. [PMID: 30687241 PMCID: PMC6338057 DOI: 10.3389/fmicb.2018.03159] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Nathaniel W Fortney
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Joval N Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Natural Sciences, University of St. La Salle, Bacolod, Philippines
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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18
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Xu P, Lu B, Liu J, Chao J, Donkersley P, Holdbrook R, Lu Y. Duplication and expression of horizontally transferred polygalacturonase genes is associated with host range expansion of mirid bugs. BMC Evol Biol 2019; 19:12. [PMID: 30626314 PMCID: PMC6327464 DOI: 10.1186/s12862-019-1351-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUD Horizontal gene transfer and gene duplication are two major mechanisms contributing to the evolutionary adaptation of organisms. Previously, polygalacturonase genes (PGs) were independently horizontally transferred and underwent multiple duplications in insects (e.g., mirid bugs and beetles). Here, we chose three phytozoophagous mirid bugs (Adelphocoris suturalis, A. fasciaticollis, A. lineolatus) and one zoophytophagous mirid bug (Nesidiocoris tenuis) to detect whether the duplication, molecular evolution, and expression levels of PGs were related to host range expansion in mirid bugs. RESULTS By RNA-seq, we reported 30, 20, 19 and 8 PGs in A. suturalis, A. fasciaticollis, A. lineolatus and N. tenuis, respectively. Interestingly, the number of PGs was significantly positive correlation to the number of host plants (P = 0.0339) in mirid bugs. Most PGs (> 17) were highly expressed in the three phytozoophagous mirid bugs, while only one PG was relatively highly expressed in the zoophytophagous mirid bug. Natural selection analysis clearly showed that a significant relaxation of selection pressure acted on the PGs in zoophytophagous mirid bugs (K = 0.546, P = 0.0158) rather than in phytozoophagous mirid bugs (K = 1, P = 0.92), suggesting a function constraint of PGs in phytozoophagous mirid bugs. CONCLUSION Taken together with gene duplication, molecular evolution, and expression levels, our results suggest that PGs are more strictly required by phytozoophagous than by zoophytophagous mirid bugs and that the duplication of PGs is associated with the expansion of host plant ranges in mirid bugs.
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Affiliation(s)
- Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ UK
| | - Bin Lu
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041 People’s Republic of China
| | - Jinyan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 People’s Republic of China
| | - Philip Donkersley
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ UK
| | - Robert Holdbrook
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ UK
| | - Yanhui Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
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19
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Savvichev AS, Babenko VV, Lunina ON, Letarova MA, Boldyreva DI, Veslopolova EF, Demidenko NA, Kokryatskaya NM, Krasnova ED, Gaisin VA, Kostryukova ES, Gorlenko VM, Letarov AV. Sharp water column stratification with an extremely dense microbial population in a small meromictic lake, Trekhtzvetnoe. Environ Microbiol 2018; 20:3784-3797. [PMID: 30117254 DOI: 10.1111/1462-2920.14384] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 07/27/2018] [Accepted: 08/09/2018] [Indexed: 11/28/2022]
Abstract
Located on the shore of Kandalaksha Bay (the White Sea, Russia) and previously separated from it, Trekhtzvetnoe Lake (average depth 3.5 m) is one of the shallowest meromictic lakes known. Despite its shallowness, it features completely developed water column stratification with high-density microbial chemocline community (bacterial plate) and high rates of major biogeochemical processes. A sharp halocline stabilizes the stratification. Chlorobium phaeovibrioides dominated the bacterial plate, which reached a density of 2 × 108 cell ml-1 and almost completely intercepts H2 S diffusion from the anoxic monimolimnion. The resulting anoxygenic photosynthesis rate reached 240 μmol C l-1 day-1 , exceeding the oxygenic photosynthesis rate in the mixolimnion. The rates of other processes are also high, reaching 4.5 μmol CH4 l-1 day-1 for methane oxidation and 35 μmol S l-1 day-1 for sulfate reduction. Metagenomic analysis demonstrated that the Chl. phaeovibrioides population in the bacterial plate layer had nearly clonal homogeneity, although some fraction of these cells harbour a plasmid. The Chlorobium population was associated with bacteriophages that share homology with CRISPR spacers in the host. These features make the ecosystem of the Trekhtzvetnoe Lake a valuable model for studying regulation and evolution processes in natural high-density microbial systems.
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Affiliation(s)
- Alexander S Savvichev
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Vladislav V Babenko
- Federal Medical Biological Agency, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Olga N Lunina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maria A Letarova
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Daria I Boldyreva
- Federal Medical Biological Agency, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Elena F Veslopolova
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Natalia M Kokryatskaya
- Federal Research Centre for Integrated Studies of the Arctic, Arkhangelsk, 163000, Russia
| | - Elena D Krasnova
- Nikolay Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vasil A Gaisin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Elena S Kostryukova
- Federal Medical Biological Agency, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Vladimir M Gorlenko
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Letarov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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20
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Zhang S, Merino N, Okamoto A, Gedalanga P. Interkingdom microbial consortia mechanisms to guide biotechnological applications. Microb Biotechnol 2018; 11:833-847. [PMID: 30014573 PMCID: PMC6116752 DOI: 10.1111/1751-7915.13300] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/01/2023] Open
Abstract
Microbial consortia are capable of surviving diverse conditions through the formation of synergistic population-level structures, such as stromatolites, microbial mats and biofilms. Biotechnological applications are poised to capitalize on these unique interactions. However, current artificial co-cultures constructed for societal benefits, including biosynthesis, agriculture and bioremediation, face many challenges to perform as well as natural consortia. Interkingdom microbial consortia tend to be more robust and have higher productivity compared with monocultures and intrakingdom consortia, but the control and design of these diverse artificial consortia have received limited attention. Further, feasible research techniques and instrumentation for comprehensive mechanistic insights have only recently been established for interkingdom microbial communities. Here, we review these recent advances in technology and our current understanding of microbial interaction mechanisms involved in sustaining or developing interkingdom consortia for biotechnological applications. Some of the interactions among members from different kingdoms follow similar mechanisms observed for intrakingdom microbial consortia. However, unique interactions in interkingdom consortia, including endosymbiosis or interkingdom-specific cell-cell interactions, provide improved mitigation to external stresses and inhibitory compounds. Furthermore, antagonistic interactions among interkingdom species can promote fitness, diversification and adaptation, along with the production of beneficial metabolites and enzymes for society. Lastly, we shed light on future research directions to develop study methods at the level of metabolites, genes and meta-omics. These potential research methods could lead to the control and utilization of highly diverse microbial communities.
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Affiliation(s)
- Shu Zhang
- Global Research Center for Environment and Energy based on Nanomaterials ScienceNational Institute for Material Science1‐1 NamikiTsukubaIbarakiJapan
- Department of Molecular Microbiology and ImmunologyNorris Comprehensive Cancer CenterUniversity of Southern California1441 Eastlake StreetLos AngelesCA90033USA
- Present address:
Section of Infection and ImmunityHerman Ostrow School of DentistryUniversity of Southern CaliforniaCA90089‐0641USA
| | - Nancy Merino
- Earth‐Life Science InstituteTokyo Institute of Technology, 2‐12‐1‐I7E‐323Ookayama, Meguro‐kuTokyo 152‐8550Japan
- Department of Earth SciencesUniversity of Southern California, 835 Bloom Walk, SHS 562Los AngelesCA 90089‐0740USA
| | - Akihiro Okamoto
- Global Research Center for Environment and Energy based on Nanomaterials ScienceNational Institute for Material Science1‐1 NamikiTsukubaIbarakiJapan
| | - Phillip Gedalanga
- Department of Health ScienceCalifornia State University Fullerton, 800 North State College BoulevardFullertonCA 92831‐3599USA
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21
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Thiel V, Tank M, Bryant DA. Diversity of Chlorophototrophic Bacteria Revealed in the Omics Era. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:21-49. [PMID: 29505738 DOI: 10.1146/annurev-arplant-042817-040500] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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22
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Nguyen TA, Greig J, Khan A, Goh C, Jedd G. Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly. PLoS Biol 2018; 16:e2004920. [PMID: 29689046 PMCID: PMC5915273 DOI: 10.1371/journal.pbio.2004920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/19/2018] [Indexed: 12/31/2022] Open
Abstract
Horizontal gene transfer (HGT) can promote evolutionary adaptation by transforming a species' relationship to the environment. In most well-understood cases of HGT, acquired and donor functions appear to remain closely related. Thus, the degree to which HGT can lead to evolutionary novelties remains unclear. Mucorales fungi sense gravity through the sedimentation of vacuolar protein crystals. Here, we identify the octahedral crystal matrix protein (OCTIN). Phylogenetic analysis strongly supports acquisition of octin by HGT from bacteria. A bacterial OCTIN forms high-order periplasmic oligomers, and inter-molecular disulphide bonds are formed by both fungal and bacterial OCTINs, suggesting that they share elements of a conserved assembly mechanism. However, estimated sedimentation velocities preclude a gravity-sensing function for the bacterial structures. Together, our data suggest that HGT from bacteria into the Mucorales allowed a dramatic increase in assembly scale and emergence of the gravity-sensing function. We conclude that HGT can lead to evolutionary novelties that emerge depending on the physiological and cellular context of protein assembly.
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Affiliation(s)
- Tu Anh Nguyen
- Temasek Life Sciences Laboratory & Department of Biological Sciences, The National University of Singapore, Singapore
| | - Jamie Greig
- Temasek Life Sciences Laboratory & Department of Biological Sciences, The National University of Singapore, Singapore
| | - Asif Khan
- Temasek Life Sciences Laboratory & Department of Biological Sciences, The National University of Singapore, Singapore
| | - Cara Goh
- Temasek Life Sciences Laboratory & Department of Biological Sciences, The National University of Singapore, Singapore
| | - Gregory Jedd
- Temasek Life Sciences Laboratory & Department of Biological Sciences, The National University of Singapore, Singapore
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Fernandez-Lopez R, Redondo S, Garcillan-Barcia MP, de la Cruz F. Towards a taxonomy of conjugative plasmids. Curr Opin Microbiol 2017; 38:106-113. [PMID: 28586714 DOI: 10.1016/j.mib.2017.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/10/2017] [Accepted: 05/17/2017] [Indexed: 01/14/2023]
Abstract
Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage plasmid studies.
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Affiliation(s)
- Raul Fernandez-Lopez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain
| | - Santiago Redondo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain
| | - M Pilar Garcillan-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria, Santander, Spain.
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24
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Thweatt JL, Ferlez BH, Golbeck JH, Bryant DA. BciD Is a Radical S-Adenosyl-l-methionine (SAM) Enzyme That Completes Bacteriochlorophyllide e Biosynthesis by Oxidizing a Methyl Group into a Formyl Group at C-7. J Biol Chem 2016; 292:1361-1373. [PMID: 27994052 DOI: 10.1074/jbc.m116.767665] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/12/2016] [Indexed: 01/05/2023] Open
Abstract
Green bacteria are chlorophotorophs that synthesize bacteriochlorophyll (BChl) c, d, or e, which assemble into supramolecular, nanotubular structures in large light-harvesting structures called chlorosomes. The biosynthetic pathways of these chlorophylls are known except for one reaction. Null mutants of bciD, which encodes a putative radical S-adenosyl-l-methionine (SAM) protein, are unable to synthesize BChl e but accumulate BChl c; however, it is unknown whether BciD is sufficient to convert BChl c (or its precursor, bacteriochlorophyllide (BChlide) c) into BChl e (or BChlide e). To determine the function of BciD, we expressed the bciD gene of Chlorobaculum limnaeum strain DSMZ 1677T in Escherichia coli and purified the enzyme under anoxic conditions. Electron paramagnetic resonance spectroscopy of BciD indicated that it contains a single [4Fe-4S] cluster. In assays containing SAM, BChlide c or d, and sodium dithionite, BciD catalyzed the conversion of SAM into 5'-deoxyadenosine and BChlide c or d into BChlide e or f, respectively. Our analyses also identified intermediates that are proposed to be 71-OH-BChlide c and d Thus, BciD is a radical SAM enzyme that converts the methyl group of BChlide c or d into the formyl group of BChlide e or f This probably occurs by a mechanism involving consecutive hydroxylation reactions of the C-7 methyl group to form a geminal diol intermediate, which spontaneously dehydrates to produce the final products, BChlide e or BChlide f The demonstration that BciD is sufficient to catalyze the conversion of BChlide c into BChlide e completes the biosynthetic pathways for all "Chlorobium chlorophylls."
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Affiliation(s)
| | - Bryan H Ferlez
- From the Departments of Biochemistry and Molecular Biology and
| | - John H Golbeck
- From the Departments of Biochemistry and Molecular Biology and.,Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - Donald A Bryant
- From the Departments of Biochemistry and Molecular Biology and .,the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
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