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Nowruzi B, Hutarova L, Vešelenyiova D, Metcalf JS. Characterization of Neowestiellopsis persica A1387 (Hapalosiphonaceae) based on the cpcA, psbA, rpoC1, nifH and nifD gene sequences. BMC Ecol Evol 2024; 24:57. [PMID: 38711016 PMCID: PMC11075313 DOI: 10.1186/s12862-024-02244-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Complex descriptions of new strains of cyanobacteria appear very frequently. The main importance of these descriptions concerns potential new substances that they could synthesise, as well as their different properties as a result of their different ecological niches. The main gene used for these descriptions is 16 S with ITS or whole genome sequencing. Neowestiellopsis persica represents a unique example of the influence of ecology on morphological changes, with almost identical 16 S identity. Although our previously described Neowestiellopsis persica strain A1387 was characterized by 16 S analysis, we used different molecular markers to provide a way to separate strains of this genus that are closely related at the genetic level. MATERIALS AND METHODS In order to conduct an in-depth study, several molecular markers, namely psbA, rpoC1, nifD, nifH and cpcA were sequenced and studied in Neowestiellopsis persica strain A1387. RESULTS The results of the phylogenetic analysis, based on cpcA, showed that the studied strain A 1387 falls into a separate clade than N. persica, indicating that this signature sequence could be a useful molecular marker for phylogenetic separation of similar strains isolated in the future. CONCLUSIONS Analysis of strain A1387 based on gene differences confirmed that it is a Neowestiellopsis strain. The morphological changes observed in the previous study could be due to different ecological and cultivation conditions compared to the type species. At the same time, the sequences obtained have increased our understanding of this species and will help in the future to better identify strains belonging to the genus Neowestiellopsis.
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Affiliation(s)
- Bahareh Nowruzi
- Department of Biotechnology, Science and Research Branch, Islamic Azad University, Daneshgah Blvd, Simon Bulivar Blvd, Tehran, Iran.
| | - Lenka Hutarova
- Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Dominika Vešelenyiova
- Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - James S Metcalf
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
- Brain Chemistry Labs, Box 3464, Jackson, WY, 83001, USA
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Grim SL, Stuart DG, Aron P, Levin NE, Kinsman-Costello L, Waldbauer JR, Dick GJ. Seasonal shifts in community composition and proteome expression in a sulphur-cycling cyanobacterial mat. Environ Microbiol 2023; 25:2516-2533. [PMID: 37596970 DOI: 10.1111/1462-2920.16480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/29/2023] [Indexed: 08/21/2023]
Abstract
Seasonal changes in light and physicochemical conditions have strong impacts on cyanobacteria, but how they affect community structure, metabolism, and biogeochemistry of cyanobacterial mats remains unclear. Light may be particularly influential for cyanobacterial mats exposed to sulphide by altering the balance of oxygenic photosynthesis and sulphide-driven anoxygenic photosynthesis. We studied temporal shifts in irradiance, water chemistry, and community structure and function of microbial mats in the Middle Island Sinkhole (MIS), where anoxic and sulphate-rich groundwater provides habitat for cyanobacteria that conduct both oxygenic and anoxygenic photosynthesis. Seasonal changes in light and groundwater chemistry were accompanied by shifts in bacterial community composition, with a succession of dominant cyanobacteria from Phormidium to Planktothrix, and an increase in diatoms, sulphur-oxidizing bacteria, and sulphate-reducing bacteria from summer to autumn. Differential abundance of cyanobacterial light-harvesting proteins likely reflects a physiological response of cyanobacteria to light level. Beggiatoa sulphur oxidation proteins were more abundant in autumn. Correlated abundances of taxa through time suggest interactions between sulphur oxidizers and sulphate reducers, sulphate reducers and heterotrophs, and cyanobacteria and heterotrophs. These results support the conclusion that seasonal change, including light availability, has a strong influence on community composition and biogeochemical cycling of sulphur and O2 in cyanobacterial mats.
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Affiliation(s)
- Sharon L Grim
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Dack G Stuart
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Phoebe Aron
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Naomi E Levin
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, Michigan, USA
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3
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Almela P, Velázquez D, Rico E, Justel A, Quesada A. Marine Vertebrates Impact the Bacterial Community Composition and Food Webs of Antarctic Microbial Mats. Front Microbiol 2022; 13:841175. [PMID: 35464973 PMCID: PMC9023888 DOI: 10.3389/fmicb.2022.841175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/28/2022] [Indexed: 01/04/2023] Open
Abstract
The biological activity of marine vertebrates represents an input of nutrients for Antarctic terrestrial biota, with relevant consequences for the entire ecosystem. Even though microbial mats assemble most of the biological diversity of the non-marine Antarctica, the effects of the local macrofauna on these microecosystems remain understudied. Using 16S rRNA gene sequencing, 13C and 15N stable isotopes, and by characterizing the P and N-derived nutrient levels, we evaluated the effects of penguins and other marine vertebrates on four microbial mats located along the Antarctic Peninsula. Our results show that P concentrations, C/N and N/P ratios, and δ15N values of "penguin-impacted" microbial mats were significantly higher than values obtained for "macrofauna-free" sample. Nutrients derived from penguin colonies and other marine vertebrates altered the trophic interactions of communities within microbial mats, as well as the relative abundance and trophic position of meiofaunal groups. Twenty-nine bacterial families from eight different phyla significantly changed with the presence of penguins, with inorganic nitrogen (NH4 + and NO3 -) and δ15N appearing as key factors in driving bacterial community composition. An apparent change in richness, diversity, and dominance of prokaryotes was also related to penguin-derived nutrients, affecting N utilization strategies of microbial mats and relating oligotrophic systems to communities with a higher metabolic versatility. The interdisciplinary approach of this study makes these results advance our understanding of interactions and composition of communities inhabiting microbial mats from Antarctica, revealing how they are deeply associated with marine animals.
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Affiliation(s)
- Pablo Almela
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - David Velázquez
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Eugenio Rico
- Department of Ecology, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Justel
- UC3M-Santander Big Data Institute (IBiDat), Universidad Carlos III de Madrid, Madrid, Spain
- Department of Mathematics, Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Quesada
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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4
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Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O 2 Cyanobacterial Mat Community. mSystems 2021; 6:e0104221. [PMID: 34874776 PMCID: PMC8651085 DOI: 10.1128/msystems.01042-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacterial mats profoundly influenced Earth’s biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth’s biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.
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Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014. Genes (Basel) 2021; 12:genes12030389. [PMID: 33803228 PMCID: PMC8001431 DOI: 10.3390/genes12030389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022] Open
Abstract
Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.
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6
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Klatt JM, Gomez-Saez GV, Meyer S, Ristova PP, Yilmaz P, Granitsiotis MS, Macalady JL, Lavik G, Polerecky L, Bühring SI. Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat. THE ISME JOURNAL 2020; 14:3024-3037. [PMID: 32770117 PMCID: PMC7784965 DOI: 10.1038/s41396-020-0734-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/16/2020] [Accepted: 07/28/2020] [Indexed: 11/15/2022]
Abstract
Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O2 release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and AP) in versatile cyanobacteria, and interactions with sulfur reducing bacteria (SRB). Using microsensors and stable isotope probing we found that dissolved organic carbon (DOC) released by OP fuels sulfide production, likely by a specialized SRB population. Increased sulfide fluxes were only stimulated after the cyanobacteria switched from AP to OP. O2 production triggered migration of large sulfur-oxidizing bacteria from the surface to underneath the cyanobacterial layer. The resultant sulfide shield tempered AP and allowed OP to occur for a longer duration over a diel cycle. The lack of cyanobacterial DOC supply to SRB during AP therefore maximized O2 export. This mechanism is unique to benthic ecosystems because transitions between metabolisms occur on the same time scale as solute transport to functionally distinct layers, with the rearrangement of the system by migration of microorganisms exaggerating the effect. Overall, cyanobacterial versatility disrupts the synergistic relationship between sulfide production and AP, and thus enhances diel O2 production.
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Affiliation(s)
- Judith M Klatt
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Gonzalo V Gomez-Saez
- Hydrothermal Geomicrobiology, MARUM, University of Bremen, Bremen, Germany
- Alfred Wegener Institute-Helmholtz Centre for Polar and Marine Sciences, Bremerhaven, Germany
| | - Steffi Meyer
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Thünen Institute of Baltic Sea Fisheries, Thünen Institute, Rostock, Germany
| | - Petra Pop Ristova
- Hydrothermal Geomicrobiology, MARUM, University of Bremen, Bremen, Germany
| | - Pelin Yilmaz
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Michael S Granitsiotis
- Research Unit Environmental Genomics, Helmholtz Zentrum Munich, Munich, Germany
- Department of Environmental Engineering, University of Patras, Agrinio, Greece
- DOE, Joint Genome Institute, Lawerence Berkeley National Lab, Berkeley, CA, USA
| | | | - Gaute Lavik
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lubos Polerecky
- Microsensor Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
- Department of Earth Sciences-Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology, MARUM, University of Bremen, Bremen, Germany
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7
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Zilius M, Bonaglia S, Broman E, Chiozzini VG, Samuiloviene A, Nascimento FJA, Cardini U, Bartoli M. N 2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont. Sci Rep 2020; 10:13966. [PMID: 32811860 PMCID: PMC7435186 DOI: 10.1038/s41598-020-70834-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.
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Affiliation(s)
- Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | | | | | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Ulisse Cardini
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Napoli, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Italy
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8
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Sheridan KJ, Duncan EJ, Eaton-Rye JJ, Summerfield TC. The diversity and distribution of D1 proteins in cyanobacteria. PHOTOSYNTHESIS RESEARCH 2020; 145:111-128. [PMID: 32556852 DOI: 10.1007/s11120-020-00762-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
The psbA gene family in cyanobacteria encodes different forms of the D1 protein that is part of the Photosystem II reaction centre. We have identified a phylogenetically distinct D1 group that is intermediate between previously identified G3-D1 and G4-D1 proteins (Cardona et al. Mol Biol Evol 32:1310-1328, 2015). This new group contained two subgroups: D1INT, which was frequently in the genomes of heterocystous cyanobacteria and D1FR that was part of the far-red light photoacclimation gene cluster of cyanobacteria. In addition, we have identified subgroups within G3, the micro-aerobically expressed D1 protein. There are amino acid changes associated with each of the subgroups that might affect the function of Photosystem II. We show a phylogenetically broad range of cyanobacteria have these D1 types, as well as the genes encoding the G2 protein and chlorophyll f synthase. We suggest identification of additional D1 isoforms and the presence of multiple D1 isoforms in phylogenetically diverse cyanobacteria supports the role of these proteins in conferring a selective advantage under specific conditions.
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Affiliation(s)
- Kevin J Sheridan
- Department of Botany, University of Otago, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Elizabeth J Duncan
- Department of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
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9
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Zhao D, Zhang S, Xue Q, Chen J, Zhou J, Cheng F, Li M, Zhu Y, Yu H, Hu S, Zheng Y, Liu S, Xiang H. Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia. Front Microbiol 2020; 11:1740. [PMID: 32793172 PMCID: PMC7393216 DOI: 10.3389/fmicb.2020.01740] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Soda-saline lakes are a special type of alkaline lake in which the chloride concentration is greater than the carbonate/bicarbonate concentration. Due to the high pH and a usually higher osmotic pressure than that of a normal soda lake, the microbes may need more energy to thrive in such a double-extreme environment. In this study, we systematically investigated the microbiome of the brine and sediment samples of nine artificially separated ponds (salinities from 5.5% to saturation) within two soda-saline lakes in Inner Mongolia of China, assisted by deep metagenomic sequencing. The main inorganic ions shaped the microbial community in both the brines and sediments, and the chloride concentration exhibited the most significant effect. A total of 385 metagenome-assembled genomes (MAGs) were generated, in which 38 MAGs were revealed as the abundant species in at least one of the eighteen different samples. Interestingly, these abundant species also represented the most branches of the microbiome of the soda-saline lakes at the phylum level. These abundant taxa were close relatives of microorganisms from classic soda lakes and neutral saline environments, but forming a combination of both habitats. Notably, approximately half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling. These MAGs included four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with the potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration. The possible reason is that reductive sulfur compounds could provide additional energy for the related species, and reductions of oxidative sulfur compounds are more prone to occur under alkaline conditions which support the sulfur cycling. In addition, a unique 1,4-alpha-glucan phosphorylation pathway, but not a normal hydrolysis one, was found in the abundant Candidatus Nanohaloarchaeota MAG NHA-1, which would produce more energy in polysaccharide degradation. In summary, this work has revealed the abundant taxa and favorable pathways in the soda-saline lakes, indicating that efficient energy regeneration pathway may increase the capacity for environmental adaptation in such saline-alkaline environments. These findings may help to elucidate the relationship between microbial metabolism and adaptation to extreme environments.
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Affiliation(s)
- Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feiyue Cheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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10
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Yoshimura KM, Todorova S, Biddle JF. Mercury geochemistry and microbial diversity in meromictic Glacier Lake, Jamesville, NY. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:195-202. [PMID: 32036624 DOI: 10.1111/1758-2229.12823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/06/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Meromictic lakes are stratified lakes that typically stimulate phototrophic anoxic microbial metabolism, including the transformation of sulphur. Less studied are the transformations of mercury in these environments, and the microorganisms, which mediate these reactions. In order to further an understanding of redox species, mercury and microbial populations in meromictic lakes, we examined the geochemistry and microbiology of Glacier Lake in Jamesville, NY. We found an anoxic transition at a depth of 6 m, followed by active nitrate and sulphate utilization. A chlorophyll a maximum was located at 11 m, coinciding with peaks of several photoautotrophic microbial lineages and total mercury and methyl mercury. Via amplicon sequencing, the microbial population showed pronounced peaks of cyanobacteria at 10 m, Chlorobi at 12 m and Chloroflexi at 14 m. Sulphate-reducing bacteria were also most abundant between 10 and 14 m depth. A functional gene indicating the potential for the production of methyl mercury, hgcA, was detected at several depths in the lake. Our work suggests that in addition to the sulphur cycle, the cycling of mercury may be indirectly coupled with phototrophic processes in Glacier Lake.
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Affiliation(s)
| | - Svetoslava Todorova
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
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11
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Liu D, Zhang J, Lü C, Xia Y, Liu H, Jiao N, Xun L, Liu J. Synechococcus sp. Strain PCC7002 Uses Sulfide:Quinone Oxidoreductase To Detoxify Exogenous Sulfide and To Convert Endogenous Sulfide to Cellular Sulfane Sulfur. mBio 2020; 11:e03420-19. [PMID: 32098824 PMCID: PMC7042703 DOI: 10.1128/mbio.03420-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/17/2020] [Indexed: 12/19/2022] Open
Abstract
Eutrophication and deoxygenation possibly occur in coastal waters due to excessive nutrients from agricultural and aquacultural activities, leading to sulfide accumulation. Cyanobacteria, as photosynthetic prokaryotes, play significant roles in carbon fixation in the ocean. Although some cyanobacteria can use sulfide as the electron donor for photosynthesis under anaerobic conditions, little is known on how they interact with sulfide under aerobic conditions. In this study, we report that Synechococcus sp. strain PCC7002 (PCC7002), harboring an sqr gene encoding sulfide:quinone oxidoreductase (SQR), oxidized self-produced sulfide to S0, present as persulfide and polysulfide in the cell. The Δsqr mutant contained less cellular S0 and had increased expression of key genes involved in photosynthesis, but it was less competitive than the wild type in cocultures. Further, PCC7002 with SQR and persulfide dioxygenase (PDO) oxidized exogenous sulfide to tolerate high sulfide levels. Thus, SQR offers some benefits to cyanobacteria even under aerobic conditions, explaining the common presence of SQR in cyanobacteria.IMPORTANCE Cyanobacteria are a major force for primary production via oxygenic photosynthesis in the ocean. A marine cyanobacterium, PCC7002, is actively involved in sulfide metabolism. It uses SQR to detoxify exogenous sulfide, enabling it to survive better than its Δsqr mutant in sulfide-rich environments. PCC7002 also uses SQR to oxidize endogenously generated sulfide to S0, which is required for the proper expression of key genes involved in photosynthesis. Thus, SQR has at least two physiological functions in PCC7002. The observation provides a new perspective for the interplays of C and S cycles.
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Affiliation(s)
- Daixi Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Jiajie Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
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12
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Allen JF, Thake B, Martin WF. Nitrogenase Inhibition Limited Oxygenation of Earth's Proterozoic Atmosphere. TRENDS IN PLANT SCIENCE 2019; 24:1022-1031. [PMID: 31447302 DOI: 10.1016/j.tplants.2019.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 05/24/2023]
Abstract
Cyanobacteria produced the oxygen that began to accumulate on Earth 2.5 billion years ago, at the dawn of the Proterozoic Eon. By 2.4 billion years ago, the Great Oxidation Event (GOE) marked the onset of an atmosphere containing oxygen. The oxygen content of the atmosphere then remained low for almost 2 billion years. Why? Nitrogenase, the sole nitrogen-fixing enzyme on Earth, controls the entry of molecular nitrogen into the biosphere. Nitrogenase is inhibited in air containing more than 2% oxygen: the concentration of oxygen in the Proterozoic atmosphere. We propose that oxygen inhibition of nitrogenase limited Proterozoic global primary production. Oxygen levels increased when upright terrestrial plants isolated nitrogen fixation in soil from photosynthetic oxygen production in shoots and leaves.
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Affiliation(s)
- John F Allen
- Research Department of Genetics, Evolution and Environment, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK.
| | - Brenda Thake
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
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13
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Robust Archaeal and Bacterial Communities Inhabit Shallow Subsurface Sediments of the Bonneville Salt Flats. mSphere 2019; 4:4/4/e00378-19. [PMID: 31462415 PMCID: PMC6714890 DOI: 10.1128/msphere.00378-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah-Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers collected from the upper 30 cm of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse halobacteria and Salinibacter species. Sequences identical to Geitlerinema sp. strain PCC 9228, an anoxygenic cyanobacterium that uses sulfide as the electron donor for photosynthesis, are also abundant in many samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. In these sediments, we found an increased presence of Thermoplasmatales, Hadesarchaeota, Nanoarchaeaeota, Acetothermia, Desulfovermiculus, Halanaerobiales, Bacteroidetes, and Rhodovibrio This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically sterile landscape.IMPORTANCE Pleistocene Lake Bonneville, which covered a third of Utah, desiccated approximately 13,000 years ago, leaving behind the Bonneville Salt Flats (BSF) in the Utah West Desert. The potash salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the biological interactions with the salt crust have not been studied. This study is the first geospatial analysis of microbially diverse populations at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.
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14
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Hamilton TL. The trouble with oxygen: The ecophysiology of extant phototrophs and implications for the evolution of oxygenic photosynthesis. Free Radic Biol Med 2019; 140:233-249. [PMID: 31078729 DOI: 10.1016/j.freeradbiomed.2019.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/03/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022]
Abstract
The ability to harvest light to drive chemical reactions and gain energy provided microbes access to high energy electron donors which fueled primary productivity, biogeochemical cycles, and microbial evolution. Oxygenic photosynthesis is often cited as the most important microbial innovation-the emergence of oxygen-evolving photosynthesis, aided by geologic events, is credited with tipping the scale from a reducing early Earth to an oxygenated world that eventually lead to complex life. Anoxygenic photosynthesis predates oxygen-evolving photosynthesis and played a key role in developing and fine-tuning the photosystem architecture of modern oxygenic phototrophs. The release of oxygen as a by-product of metabolic activity would have caused oxidative damage to anaerobic microbiota that evolved under the anoxic, reducing conditions of early Earth. Photosynthetic machinery is particularly susceptible to the adverse effects of oxygen and reactive oxygen species and these effects are compounded by light. As a result, phototrophs employ additional detoxification mechanisms to mitigate oxidative stress and have evolved alternative oxygen-dependent enzymes for chlorophyll biosynthesis. Phylogenetic reconstruction studies and biochemical characterization suggest photosynthetic reactions centers, particularly in Cyanobacteria, evolved to both increase efficiency of electron transfer and avoid photodamage caused by chlorophyll radicals that is acute in the presence of oxygen. Here we review the oxygen and reactive oxygen species detoxification mechanisms observed in extant anoxygenic and oxygenic photosynthetic bacteria as well as the emergence of these mechanisms over evolutionary time. We examine the distribution of phototrophs in modern systems and phylogenetic reconstructions to evaluate the emergence of mechanisms to mediate oxidative damage and highlight changes in photosystems and reaction centers, chlorophyll biosynthesis, and niche space in response to oxygen production. This synthesis supports an emergence of H2S-driven anoxygenic photosynthesis in Cyanobacteria prior to the evolution of oxygenic photosynthesis and underscores a role for the former metabolism in fueling fine-tuning of the oxygen evolving complex and mechanisms to repair oxidative damage. In contrast, we note the lack of elaborate mechanisms to deal with oxygen in non-cyanobacterial anoxygenic phototrophs suggesting these microbes have occupied similar niche space throughout Earth's history.
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Affiliation(s)
- Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA; Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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15
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Momper L, Hu E, Moore KR, Skoog EJ, Tyler M, Evans AJ, Bosak T. Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs. Free Radic Biol Med 2019; 140:224-232. [PMID: 31163257 DOI: 10.1016/j.freeradbiomed.2019.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 01/23/2023]
Abstract
The extent of oxygenated environments on the early Earth was much lower than today, and cyanobacteria were critical players in Earth's shift from widespread anoxia to oxygenated surface environments. Extant cyanobacteria that aggregate into cones, tufts and ridges are used to understand the long record of photosynthesis and microbe-mineral interactions during times when oxygen was much lower, i.e., the Archean and the Proterozoic. To better understand the metabolic versatility and physiological properties of these organisms, we examined publicly available genomes of cyanobacteria from modern terrestrial hydrothermal systems and a newly sequenced genome of a cyanobacterium isolated from conical and ridged microbialites that grow in occasionally sulfidic hydrothermal springs in Yellowstone National Park, USA. Phylogenomic analyses reveal that cyanobacteria from globally distributed terrestrial and shallow marine hydrothermal systems form a monophyletic clade within the Cyanobacteria phylum. Comparative genomics of this clade reveals the genetic capacity for oxygenic photosynthesis that uses photosystems I and II, and anoxygenic photosynthesis that uses a putative sulfide quinone reductase to oxidize sulfide and bypass photosystem II. Surprisingly large proportions of the newly sequenced genome from Yellowstone National Park are also dedicated to secondary metabolite production (15.1-15.6%), of which ∼6% can be attributed to antibiotic production and resistance genes. All this may be advantageous to benthic, mat-forming photosynthesizers that have to compete for light and nutrients in sporadically or permanently sulfidic environments, and may have also improved the tolerance of ancient counterparts of these cyanobacteria to sulfidic conditions in benthic communities that colonized the coastal margins in the Archean and the Proterozoic.
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Affiliation(s)
- Lily Momper
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eileen Hu
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kelsey R Moore
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Emilie J Skoog
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Madeline Tyler
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Alexander J Evans
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
| | - Tanja Bosak
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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16
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Batchu NK, Khater S, Patil S, Nagle V, Das G, Bhadra B, Sapre A, Dasgupta S. Whole genome sequence analysis of Geitlerinema sp. FC II unveils competitive edge of the strain in marine cultivation system for biofuel production. Genomics 2019. [DOI: 10.1016/j.ygeno.2018.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Functional shifts in microbial mats recapitulate early Earth metabolic transitions. Nat Ecol Evol 2018; 2:1700-1708. [PMID: 30297749 PMCID: PMC6217971 DOI: 10.1038/s41559-018-0683-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/31/2018] [Indexed: 11/09/2022]
Abstract
Phototrophic microbial mats dominated terrestrial ecosystems for billions of years, largely causing, through cyanobacterial oxygenic photosynthesis, but also undergoing, the Great Oxidation Event approximately 2.5 billion years ago. Taking a space-for-time approach based on the universality of core metabolic pathways expressed at ecosystem level, we studied gene content and co-occurrence networks in high-diversity metagenomes from spatially close microbial mats along a steep redox gradient. The observed functional shifts suggest that anoxygenic photosynthesis was present but not predominant under early Precambrian conditions, being accompanied by other autotrophic processes. Our data also suggest that, in contrast to general assumptions, anoxygenic photosynthesis largely expanded in parallel with the subsequent evolution of oxygenic photosynthesis and aerobic respiration. Finally, our observations might represent space-for-time evidence that the Wood-Ljungdahl carbon fixation pathway dominated phototrophic mats in early ecosystems, whereas the Calvin cycle probably evolved from pre-existing variants before becoming the dominant contemporary form of carbon fixation.
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18
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Martin WF, Bryant DA, Beatty JT. A physiological perspective on the origin and evolution of photosynthesis. FEMS Microbiol Rev 2018; 42:205-231. [PMID: 29177446 PMCID: PMC5972617 DOI: 10.1093/femsre/fux056] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
The origin and early evolution of photosynthesis are reviewed from an ecophysiological perspective. Earth's first ecosystems were chemotrophic, fueled by geological H2 at hydrothermal vents and, required flavin-based electron bifurcation to reduce ferredoxin for CO2 fixation. Chlorophyll-based phototrophy (chlorophototrophy) allowed autotrophs to generate reduced ferredoxin without electron bifurcation, providing them access to reductants other than H2. Because high-intensity, short-wavelength electromagnetic radiation at Earth's surface would have been damaging for the first chlorophyll (Chl)-containing cells, photosynthesis probably arose at hydrothermal vents under low-intensity, long-wavelength geothermal light. The first photochemically active pigments were possibly Zn-tetrapyrroles. We suggest that (i) after the evolution of red-absorbing Chl-like pigments, the first light-driven electron transport chains reduced ferredoxin via a type-1 reaction center (RC) progenitor with electrons from H2S; (ii) photothioautotrophy, first with one RC and then with two, was the bridge between H2-dependent chemolithoautotrophy and water-splitting photosynthesis; (iii) photothiotrophy sustained primary production in the photic zone of Archean oceans; (iv) photosynthesis arose in an anoxygenic cyanobacterial progenitor; (v) Chl a is the ancestral Chl; and (vi), anoxygenic chlorophototrophic lineages characterized so far acquired, by horizontal gene transfer, RCs and Chl biosynthesis with or without autotrophy, from the architects of chlorophototrophy-the cyanobacterial lineage.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, University of Düsseldorf, D-40225 Düsseldorf, Germany
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
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Cyanobacterial photosynthesis under sulfidic conditions: insights from the isolate Leptolyngbya sp. strain hensonii. ISME JOURNAL 2018; 12:568-584. [PMID: 29328062 PMCID: PMC5776472 DOI: 10.1038/ismej.2017.193] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 09/01/2017] [Accepted: 10/09/2017] [Indexed: 01/10/2023]
Abstract
We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring—a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H2S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H2S and irradiance; (iii) O2 production is inhibited by H2S concentrations as low as 1 μM and the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis. We hypothesize that the specific adaptation mechanisms of the isolate to H2S emerged from a close spatial interaction with sulfate-reducing bacteria. The new isolate, Leptolyngbya sp. strain hensonii, is not closely related to other well-characterized Cyanobacteria that can perform anoxygenic photosynthesis, which further highlights the need to characterize the diversity and biogeography of metabolically versatile Cyanobacteria. The isolate will be an ideal model organism for exploring the adaptation of Cyanobacteria to sulfidic conditions.
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20
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Alvarenga DO, Fiore MF, Varani AM. A Metagenomic Approach to Cyanobacterial Genomics. Front Microbiol 2017; 8:809. [PMID: 28536564 PMCID: PMC5422444 DOI: 10.3389/fmicb.2017.00809] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/20/2017] [Indexed: 01/08/2023] Open
Abstract
Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium. With rising numbers of cyanobacterial blooms due to climate change, demand for genomic evaluations of these microorganisms is increasing. However, standard genomic techniques call for the sequencing of axenic cultures, an approach that not only adds months or even years for culture purification, but also appears to be impossible for some cyanobacteria, which is reflected in the relatively low number of publicly available genomic sequences of this phylum. Under the framework of metagenomics, on the other hand, cumbersome techniques for achieving axenic growth can be circumvented and individual genomes can be successfully obtained from microbial consortia. This review focuses on approaches for the genomic and metagenomic assessment of non-axenic cyanobacterial cultures that bypass requirements for axenity. These methods enable researchers to achieve faster and less costly genomic characterizations of cyanobacterial strains and raise additional information about their associated microorganisms. While non-axenic cultures may have been previously frowned upon in cyanobacteriology, latest advancements in metagenomics have provided new possibilities for in vitro studies of oxyphotobacteria, renewing the value of microbial consortia as a reliable and functional resource for the rapid assessment of bloom-forming cyanobacteria.
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Affiliation(s)
- Danillo O. Alvarenga
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP)Jaboticabal, Brazil
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo (USP)Piracicaba, Brazil
| | - Marli F. Fiore
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo (USP)Piracicaba, Brazil
| | - Alessandro M. Varani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP)Jaboticabal, Brazil
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21
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Meyer JL, Paul VJ, Raymundo LJ, Teplitski M. Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals. Front Microbiol 2017; 8:618. [PMID: 28458657 PMCID: PMC5394123 DOI: 10.3389/fmicb.2017.00618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/27/2017] [Indexed: 12/16/2022] Open
Abstract
Black Band Disease (BBD), the destructive microbial consortium dominated by the cyanobacterium Roseofilum reptotaenium, affects corals worldwide. While the taxonomic composition of BBD consortia has been well-characterized, substantially less is known about its functional repertoire. We sequenced the metagenomes of Caribbean and Pacific black band mats and cultured Roseofilum and obtained five metagenome-assembled genomes (MAGs) of Roseofilum, nine of Proteobacteria, and 12 of Bacteroidetes. Genomic content analysis suggests that Roseofilum is a source of organic carbon and nitrogen, as well as natural products that may influence interactions between microbes. Proteobacteria and Bacteroidetes members of the disease consortium are suited to the degradation of amino acids, proteins, and carbohydrates. The accumulation of sulfide underneath the black band mat, in part due to a lack of sulfur oxidizers, contributes to the lethality of the disease. The presence of sulfide:quinone oxidoreductase genes in all five Roseofilum MAGs and in the MAGs of several heterotrophs demonstrates that resistance to sulfide is an important characteristic for members of the BBD consortium.
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Affiliation(s)
- Julie L Meyer
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural SciencesGainesville, FL, USA
| | | | | | - Max Teplitski
- Soil and Water Science Department, University of Florida-Institute of Food and Agricultural SciencesGainesville, FL, USA.,Smithsonian Marine StationFort Pierce, FL, USA
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Klatt JM, de Beer D, Häusler S, Polerecky L. Cyanobacteria in Sulfidic Spring Microbial Mats Can Perform Oxygenic and Anoxygenic Photosynthesis Simultaneously during an Entire Diurnal Period. Front Microbiol 2016; 7:1973. [PMID: 28018309 PMCID: PMC5156726 DOI: 10.3389/fmicb.2016.01973] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/24/2016] [Indexed: 12/04/2022] Open
Abstract
We used microsensors to study the regulation of anoxygenic and oxygenic photosynthesis (AP and OP, respectively) by light and sulfide in a cyanobacterium dominating microbial mats from cold sulfidic springs. Both photosynthetic modes were performed simultaneously over all H2S concentrations (1–2200 μM) and irradiances (4–52 μmol photons m-2 s-1) tested. AP increased with H2S concentration while the sum of oxygenic and anoxygenic photosynthetic rates was constant at each light intensity. Thus, the total photosynthetically driven electron transport rate was solely controlled by the irradiance level. The partitioning between the rates of these two photosynthetic modes was regulated by both light and H2S concentration. The plastoquinone pool (PQ) receives electrons from sulfide:quinone:reductase (SQR) in AP and from photosystem II (PSII) in OP. It is thus the link in the electron transport chain where both pathways intersect, and the compound that controls their partitioning. We fitted our data with a model of the photosynthetic electron transport that includes the kinetics of plastoquinone reduction and oxidation. The model results confirmed that the observed partitioning between photosynthetic modes can be explained by a simple kinetic control based on the affinity of SQR and PSII toward PQ. The SQR enzyme and PSII have similar affinities toward PQ, which explains the concurrent OP and AP over an astonishingly wide range of H2S concentrations and irradiances. The elegant kinetic control of activity makes the cyanobacterium successful in the fluctuating spring environment. We discuss how these specific regulation mechanisms may have played a role in ancient H2S-rich oceans.
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Affiliation(s)
- Judith M Klatt
- Microsensor Group, Max-Planck-Institute for Marine MicrobiologyBremen, Germany; Geomicrobiology Lab, Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
| | - Dirk de Beer
- Microsensor Group, Max-Planck-Institute for Marine Microbiology Bremen, Germany
| | - Stefan Häusler
- Microsensor Group, Max-Planck-Institute for Marine Microbiology Bremen, Germany
| | - Lubos Polerecky
- Microsensor Group, Max-Planck-Institute for Marine MicrobiologyBremen, Germany; Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
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