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Tang J, Jiang Y, Hu Z, Zhou H, You D, Daroch M. Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov. Mol Phylogenet Evol 2024; 197:108094. [PMID: 38723792 DOI: 10.1016/j.ympev.2024.108094] [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: 11/02/2023] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Thermophilic unicellular cyanobacteria of the family Thermosynechococcaceae are essential primary producers and integral components of many microbial mats found in hot springs of Asia and North America. Historically, based on their simple morphology, these organisms, along with members of taxonomically unrelated thermophilic Thermostichaceae have been described with a generic term, "Synechococcus", used for elongated unicellular cyanobacteria. This has created significant misperception in the scientific literature regarding the taxonomic status of these essential thermophilic primary producers and their relationship with Synechococcus sensu stricto. In this manuscript, we attempted a genome-driven taxonomic reevaluation of the family Thermosynechococcaceae. Application of genomic analyses such as GTDB classification, ANI/AAI and phylogenomics support the delineation of eight species within genus Thermosynechococcus. Two subspecies were further identified within T. taiwanensis by dDDH and phylogenomics. Moreover, the results also suggest the presence of two putative new genera phylogenetically alongside genus Thermosynechococcus, a thermophilic genus Parathermosynechococcus represented by PCC 6715 and a non-thermophilic genus represented by PCC 6312. The proposed genospecies and new genera were further integrated with morphological and/or ecological information. Interestingly, the phylogeny of 16S-23S ITS achieved a better taxonomic relationship than that of 16S rRNA and supported the genome-based classification of Thermosynechococcus spp. Finally, the pan-genome analysis indicated a conserved pattern of genomic core among known members of Thermosynechococcus.
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Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Ying Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Zhe Hu
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Dawei You
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China.
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George C, Lim CXQ, Tong Y, Pointing SB. Community structure of thermophilic photosynthetic microbial mats and flocs at Sembawang Hot Spring, Singapore. Front Microbiol 2023; 14:1189468. [PMID: 37396374 PMCID: PMC10313338 DOI: 10.3389/fmicb.2023.1189468] [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: 03/19/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
The Sembawang Hot Spring in Singapore lies at the foot of a major regional geological feature called the Bentong-Raub Suture Zone. Amid an extensively managed surface geothermal park, an undisturbed hot spring emerges with source water at 61°C, pH 6.8, and 1 mg/L dissolved sulfide. A small main pool at the source supported orange-green benthic flocs, whereas the outflow channel with gradually less extreme environmental stress supported extensive vivid green microbial mats. Microscopy revealed that cyanobacterial morphotypes were distinct in flocs and mats at several intervals along the environmental gradient, and we describe a spiraling pattern in the oscillatorian cyanobacteria that may reflect response to poly-extreme stress. Estimation of diversity using 16S rRNA gene sequencing revealed assemblages that were dominated by phototrophic bacteria. The most abundant taxa in flocs at 61°C/1 mg/L sulfide were Roseiflexus sp. and Thermosynechococcus elongatus, whilst the mats at 45.7-55.3°C/0-0.5 mg/L sulfide were dominated by Oscillatoriales cyanobacterium MTP1 and Chloroflexus sp. Occurrence of diverse chemoautotrophs and heterotrophs reflected known thermal ranges for taxa, and of note was the high abundance of thermophilic cellulolytic bacteria that likely reflected the large allochthonous leaf input. A clear shift in ASV-defined putative ecotypes occurred along the environmental stress gradient of the hot spring and overall diversity was inversely correlated to environmental stress. Significant correlations for abiotic variables with observed biotic diversity were identified for temperature, sulfide, and carbonate. A network analysis revealed three putative modules of biotic interactions that also reflected the taxonomic composition at intervals along the environmental gradient. Overall, the data indicated that three distinct microbial communities were supported within a small spatial scale along the poly-extreme environmental gradient. The findings add to the growing inventory of hot spring microbiomes and address an important biogeographic knowledge gap for the region.
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Affiliation(s)
- Christaline George
- Yale-NUS College, National University of Singapore, Singapore, Singapore
| | - Chloe Xue Qi Lim
- Yale-NUS College, National University of Singapore, Singapore, Singapore
| | - Yan Tong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Stephen Brian Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Das S, Najar IN, Sherpa MT, Kumari A, Thakur N. Post-monsoon seasonal variation of prokaryotic diversity in solfataric soil from the North Sikkim hot spring. Int Microbiol 2022; 26:281-294. [PMID: 36478539 DOI: 10.1007/s10123-022-00298-x] [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: 04/24/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
The solfataric soil sediments of the hot springs of Sikkim located at Yume Samdung and Lachen valley were studied for deciphering the bacterial diversity. The main aim here is to present a comparative study and generate a baseline data on the post-monsoon seasonal variation for the months of October and December, analyzed through 16S rRNA V3-V4 amplicon sequencing. The results have shown that there is not much variation at phylum level in the month of October in all the three hot springs such as New Yume Samdung (NYS), Old Yume Samdung (OYS), and Tarum (TAR) hot spring. The abundant phyla mainly present were Firmicutes, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Similarly, in the month of December, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were prevalent; however, the percent relative abundance of these phyla in the month of December is relatively less. Besides this decrease in percent abundance, it was interestingly seen that relatively more phyla were found contributing towards the bacterial diversity in the month of December. Similar to phylum level, at genus level, there was not much variation seen among various prevalent genera of the three studied hot springs in both months. The major genera prevalent in both months among all the three hot springs were followed by Bacillus, Desulfotomaculum, Lactobacillus, and Paenibacillus. A similar trend was also seen at gene level that relative abundance of various genera was higher in the month of October but more genera were found to be contributing towards bacterial diversity in the month of December. Few distinct genera were found to be more abundant in the month of December such as Rhodopirellula and Blastopirellula. The results may conclude that there is not much variation in the abundance and type of bacterial communities during the post-monsoon season in the month of October and December. However, this may be assumed that there is the accumulation or increase in the bacterial communities during the winter (relatively higher temperature among hot springs) and may favor few mesophilic and more thermophilic communities as well.
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Affiliation(s)
- Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India
| | | | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, 737102, Sikkim, India.
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Twing KI, Ward LM, Kane ZK, Sanders A, Price RE, Pendleton HL, Giovannelli D, Brazelton WJ, McGlynn SE. Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland. Front Microbiol 2022; 13:960335. [PMID: 36466646 PMCID: PMC9713835 DOI: 10.3389/fmicb.2022.960335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/05/2022] [Indexed: 10/20/2023] Open
Abstract
Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.
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Affiliation(s)
- Katrina I. Twing
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - L. M. Ward
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Geosciences, Smith College, Northampton, MA, United States
| | - Zachary K. Kane
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Alexa Sanders
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Roy Edward Price
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - H. Lizethe Pendleton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - William J. Brazelton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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Proteomic Time-Course Analysis of the Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus aurantiacus, during the Transition from Respiration to Phototrophy. Microorganisms 2022; 10:microorganisms10071288. [PMID: 35889008 PMCID: PMC9316378 DOI: 10.3390/microorganisms10071288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Chloroflexus aurantiacus is a filamentous anoxygenic phototrophic bacterium that grows chemotrophically under oxic conditions and phototrophically under anoxic conditions. Because photosynthesis-related genes are scattered without any gene clusters in the genome, it is still unclear how this bacterium regulates protein expression in response to environmental changes. In this study, we performed a proteomic time-course analysis of how C. aurantiacus expresses proteins to acclimate to environmental changes, namely the transition from chemoheterotrophic respiratory to photoheterotrophic growth mode. Proteomic analysis detected a total of 2520 proteins out of 3934 coding sequences in the C. aurantiacus genome from samples collected at 13 time points. Almost all proteins for reaction centers, light-harvesting chlorosomes, and carbon fixation pathways were successfully detected during the growing phases in which optical densities and relative bacteriochlorophyll c contents increased simultaneously. Combination of proteomics and pigment analysis suggests that the self-aggregation of bacteriochlorophyllide c could precede the esterification of the hydrophobic farnesyl tail in cells. Cytoplasmic subunits of alternative complex III were interchanged between oxic and anoxic conditions, although membrane-bound subunits were used for both conditions. These data highlight the protein expression dynamics of phototrophy-related genes during the transition from respiration to phototrophy.
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Homologs of Phycobilisome Abundance Regulator PsoR Are Widespread across Cyanobacteria. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
During chromatic acclimation (CA), cyanobacteria undergo shifts in their physiology and metabolism in response to changes in their light environment. Various forms of CA, which involves the tuning of light-harvesting accessory complexes known as phycobilisomes (PBS) in response to distinct wavelengths of light, have been recognized. Recently, a negative regulator of PBS abundance, PsoR, about which little was known, was identified. We used sequence analyses and bioinformatics to predict the role of PsoR in cyanobacteria and PBS regulation and to examine its presence in a diverse range of cyanobacteria. PsoR has sequence similarities to the β-CASP family of proteins involved in DNA and RNA processing. PsoR is a putative nuclease widespread across Cyanobacteria, of which over 700 homologs have been observed. Promoter analysis suggested that psoR is co-transcribed with upstream gene tcpA. Multiple transcription factors involved in global gene regulation and stress responses were predicted to bind to the psoR-tcpA promoter. The predicted protein–protein interactions with PsoR homologs included proteins involved in DNA and RNA metabolism, as well as a phycocyanin-associated protein predicted to interact with PsoR from Fremyella diplosiphon (FdPsoR). The widespread presence of PsoR homologs in Cyanobacteria and their ties to DNA- and RNA-metabolizing proteins indicated a potentially unique role for PsoR in CA and PBS abundance regulation.
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7
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Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures. Sci Rep 2022; 12:2850. [PMID: 35181739 PMCID: PMC8857248 DOI: 10.1038/s41598-022-06943-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.
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Asamatsu K, Yoshitake K, Saito M, Prasitwuttisak W, Ishibashi JI, Tsutsumi A, Mustapha NA, Maeda T, Yanagawa K. A Novel Archaeal Lineage in Boiling Hot Springs around Oyasukyo Gorge (Akita, Japan). Microbes Environ 2021; 36. [PMID: 34819404 PMCID: PMC8674440 DOI: 10.1264/jsme2.me21048] [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: 11/12/2022] Open
Abstract
A novel deep-branching archaeal lineage was discovered at high-temperature hot springs around Oyasukyo Gorge in Akita Prefecture, Japan. Actively boiling hot spring water contained >1×104 microbes mL-1. The microbial community composition assessed by analyzing 16S rRNA gene amplicons revealed that the dominant bacterial phyla were Proteobacteria and Aquificae (>50% of the microbial composition) in samples collected in 2016 and 2019, respectively. Approximately 10% of the reads obtained in both years were not assigned to any taxonomy. The more detailed phylogenetic positions of the unassigned sequences identified using a clone library and phylogenetic tree showed that they formed a clade that was independent, distantly related to known phyla, and had low similarity (<82%) to all other sequences in available databases. The present results suggest that this novel archaeal phylum-level lineage thrives in boiling hot springs in Japan.
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Affiliation(s)
| | - Kai Yoshitake
- Faculty of Environmental Engineering, The University of Kitakyushu
| | - Makoto Saito
- Faculty of Environmental Engineering, The University of Kitakyushu
| | | | - Jun-Ichiro Ishibashi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University
| | - Akihi Tsutsumi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University
| | - Nurul Asyifah Mustapha
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
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Rozanov AS, Korzhuk AV, Shekhovtsov SV, Vasiliev GV, Peltek SE. Microorganisms of Two Thermal Pools on Kunashir Island, Russia. BIOLOGY 2021; 10:924. [PMID: 34571800 PMCID: PMC8468003 DOI: 10.3390/biology10090924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022]
Abstract
The Kuril Archipelago is a part of the Circum-Pacific Belt (Ring of Fire). These islands have numerous thermal springs. There are very few studies on these microbial communities, and none of them have been conducted by modern molecular biological methods. Here we performed the first metagenomic study on two thermophilic microbial communities of Kunashir Island. Faust Lake is hot (48 °C) and highly acidic (pH 2.0). We constructed 28 metagenome-assembled genomes as well as 17 16S ribosomal RNA sequences. We found that bottom sediments of Faust Lake are dominated by a single species of red algae belonging to the Cyanidiaceae family. Archaeans in Faust Lake are more diverse than bacteria but less abundant. The Tretyakovsky Thermal Spring is also hot (52 °C) but only weakly acidic (pH 6.0). It has much higher microbial diversity (233 metagenome-assembled genomes; 93 16S ribosomal RNAs) and is dominated by bacteria, with only several archaeans and one fungus. Despite their geographic proximity, these two thermal springs were found to not share any species. A comparison of these two lakes with other thermal springs of the Circum-Pacific Belt revealed that only a few members of the communities are shared among different locations.
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Affiliation(s)
- Aleksei S. Rozanov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Anton V. Korzhuk
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Sergei E. Peltek
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
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Mazière C, Agogué H, Cravo-Laureau C, Cagnon C, Lanneluc I, Sablé S, Fruitier-Arnaudin I, Dupuy C, Duran R. New insights in bacterial and eukaryotic diversity of microbial mats inhabiting exploited and abandoned salterns at the Ré Island (France). Microbiol Res 2021; 252:126854. [PMID: 34454310 DOI: 10.1016/j.micres.2021.126854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/09/2021] [Accepted: 08/21/2021] [Indexed: 01/04/2023]
Abstract
In order to understand the effect of human practices on microbial mats organisation, the study aimed to investigate the biodiversity within microbial mats from exploited and abandoned salterns. Despite several attempts, archaeal 16S rRNA gene fragment sequences were not obtained, indicating that microbial mats were probably dominated by Bacteria with very low abundance of Archaea (< 1%). Thus, the study compared the bacterial and meiofaunal diversity of microbial mats from abandoned and exploited salterns. The higher salinity (101 ± 3.7 psu vs. 51.1 ± 0.7 psu; Welch t-test p < 0.05) of the exploited site maintained lower bacterial diversity in comparison to the abandoned site where the salinity gradient was no longer maintained. However, the microbial mats exhibited similar bacterial class composition while the eukaryotic diversity was significantly higher in the exploited saltern. The abandoned saltern was dominated by sulfate-reducing bacteria and Nematoda, while the exploited saltern was characterized by the presence of halophilic bacteria belonging to Marinobacter, Salinivibrio and Rhodohalobacter genera, and the larger abundance of Hypotrichia (ciliates). Such bacterial and eukaryotic diversity difference might be explained by human actions for salt recovery in exploited salterns such as scraping the surface of microbial mat and increasing salinity renewing the microbial mat each year. Such action decreases the bacterial diversity changing the food web structure that favour the presence of a larger diversity of eukaryotic organisms. Our study provides new insights on microbial mat communities inhabiting salterns, especially the consequences of abandoning saltern exploitation.
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Affiliation(s)
- Camille Mazière
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France; UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Hélène Agogué
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | | | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Isabelle Lanneluc
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Sophie Sablé
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Ingrid Fruitier-Arnaudin
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Christine Dupuy
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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Kawai S, Martinez JN, Lichtenberg M, Trampe E, Kühl M, Tank M, Haruta S, Nishihara A, Hanada S, Thiel V. In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat. Microorganisms 2021; 9:microorganisms9030652. [PMID: 33801086 PMCID: PMC8004040 DOI: 10.3390/microorganisms9030652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.
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Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
- Correspondence: (S.K.); (V.T.)
| | - Joval N. Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Department of Natural Sciences, College of Arts and Sciences, University of St. La Salle, Bacolod City, Negros Occidental 6100, Philippines
| | - Mads Lichtenberg
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Erik Trampe
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Michael Kühl
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Correspondence: (S.K.); (V.T.)
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12
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Saini MK, ChihChe W, Soulier N, Sebastian A, Albert I, Thiel V, Bryant DA, Hanada S, Tank M. Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan. Int J Syst Evol Microbiol 2020; 70:5701-5710. [PMID: 32931408 DOI: 10.1099/ijsem.0.004465] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were the major pigments. Dense liquid cultures were red in colour. Strain No.7T was able to grow photoautotrophically using sulfide, thiosulfate, sulfite and hydrogen (in the presence of sulfide) as electron donors and bicarbonate as the sole carbon source. Optimum growth occurred under anaerobic conditions in the light at 50 °C (range, 40-56 °C) and pH 7.2 (range, pH 7-8). Major fatty acids were C16 : 0 (46.8 %), C16 : 1 ω7c (19.9 %), C18 : 1 ω7c (21.1 %), C14 : 0 (4.6 %) and C18 : 0 (2.4 %). The polar lipid profile showed phosphatidylglycerol and unidentified aminophospholipids to be the major lipids. The only quinone detected was ubiquinone-8. 16S rRNA gene sequence comparisons indicated that the novel bacterium is only distantly related to Thermochromatium tepidum with a nucleotide identity of 90.4 %. The phylogenetic analysis supported the high novelty of strain No.7T with a long-branching phylogenetic position within the Chromatiaceae next to Thermochromatium tepidum. The genome comprised a circular chromosome of 2.99 Mbp (2 989 870 bp), included no plasmids and had a DNA G+C content of 61.2 mol%. Polyphasic taxonomic analyses of the isolate suggested strain No.7T is a novel genus within the Chromatiaceae. The proposed genus name of the second truly thermophilic purple sulphur bacterium is Caldichromatium gen. nov. with the type species Caldichromatium japonicum sp. nov. (DSM 110881=JCM 39101).
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Affiliation(s)
- Mohit Kumar Saini
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Weng ChihChe
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Nathan Soulier
- Department of Biochemistry and Molecular Biology, Eberly College of Science, The Pennsylvania State University, PA 16802, USA
| | - Aswathy Sebastian
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Istvan Albert
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Biochemistry and Molecular Biology, Eberly College of Science, The Pennsylvania State University, PA 16802, USA
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Donald A Bryant
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.,Department of Biochemistry and Molecular Biology, Eberly College of Science, The Pennsylvania State University, PA 16802, USA
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 1920397, Japan.,DSMZ - German Culture Collection of Microorganisms and Cell Cultures, GmbH Inhoffenstraße 7B 38124 Braunschweig, Germany
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13
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Izaki K, Haruta S. Aerobic Production of Bacteriochlorophylls in the Filamentous Anoxygenic Photosynthetic Bacterium, Chloroflexus aurantiacus in the Light. Microbes Environ 2020; 35. [PMID: 32418929 PMCID: PMC7308566 DOI: 10.1264/jsme2.me20015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Filamentous anoxygenic photosynthetic bacteria grow by photosynthesis and aerobic respiration. The present study investigated the effects of light and O2 on bacteriochlorophyll contents and the transcription levels of photosynthesis-related genes in Chloroflexus aurantiacus J-10-fl T. Under aerobic conditions, C. aurantiacus produced marked amounts of bacteriochlorophylls in the presence of light, although their production was strongly suppressed in the dark. The transcription levels of genes related to the synthesis of bacteriochlorophylls, photosystems, and chlorosomes: bchM, bchU, pufL, pufBA, and csmM, were markedly increased by illumination. These results suggest that C. aurantiacus continuously synthesizes ATP by photophosphorylation even in the presence of O2.
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Affiliation(s)
- Kazaha Izaki
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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14
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Wörmer L, Gajendra N, Schubotz F, Matys ED, Evans TW, Summons RE, Hinrichs KU. A micrometer-scale snapshot on phototroph spatial distributions: mass spectrometry imaging of microbial mats in Octopus Spring, Yellowstone National Park. GEOBIOLOGY 2020; 18:742-759. [PMID: 32936514 DOI: 10.1111/gbi.12411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial mats from alkaline hot springs in the Yellowstone National Park are ideal natural laboratories to study photosynthetic life under extreme conditions, as well as the nuanced interactions of oxygenic and anoxygenic phototrophs. They represent distinctive examples of chlorophototroph (i.e., chlorophyll or bacteriochlorophyll-based phototroph) diversity, and several novel phototrophs have been first described in these systems, all confined in space, coexisting and competing for niches defined by parameters such as light, oxygen, or temperature. In a novel approach, we employed mass spectrometry imaging of chloropigments, quinones, and intact polar lipids (IPLs) to describe the spatial distribution of different groups of chlorophototrophs along the ~ 1 cm thick microbial mat at 75 µm resolution and in the top ~ 1.5 mm green part of the mat at 25 µm resolution. We observed a fine-tuned sequence of oxygenic and anoxygenic chlorophototrophs with distinctive biomarker signatures populating the microbial mat. The transition of oxic to anoxic conditions is characterized by an accumulation of biomarkers indicative of anoxygenic phototrophy. It is also identified as a clear boundary for different species and ecotypes, which adjust their biomarker inventory, particularly the interplay of quinones and chloropigments, to prevailing conditions. Colocalization of the different biomarker groups led to the identification of characteristic IPL signatures and indicates that glycosidic diether glycerolipids are diagnostic for anoxygenic phototrophs in this mat system. The zoom-in into the upper green part further reveals how oxygenic and anoxygenic phototrophs share this microenvironment and informs on subtle, microscale adjustments in lipid composition of Synechococcus spp.
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Affiliation(s)
- Lars Wörmer
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Niroshan Gajendra
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florence Schubotz
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Emily D Matys
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas W Evans
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
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15
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Kamagata Y. Recent Biofilm Studies Open a New Door in Microbial Ecology. Microbes Environ 2020; 35:ME3501rh. [PMID: 32201415 PMCID: PMC7104287 DOI: 10.1264/jsme2.me3501rh] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305–8560, Japan
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