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Wassel MA, Makabe-Kobayashi Y, Iqbal MM, Takatani T, Sakakura Y, Hamasaki K. The impact of tetrodotoxin (TTX) on the gut microbiome in juvenile tiger pufferfish, Takifugu rubripes. Sci Rep 2024; 14:16684. [PMID: 39085277 PMCID: PMC11291987 DOI: 10.1038/s41598-024-66112-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Tetrodotoxin (TTX) is a potent neurotoxin that accumulates in Takifugu rubripes, commonly known as pufferfish, through the ingestion of TTX-bearing organisms as part of their food chain. Although researchers believe that pufferfish use TTX to relieve stress, data are not currently available on how TTX affects the gut microbiota of pufferfish. To address this gap, our study aimed to investigate whether administering TTX to fish could alter their gut microbiota and overall health under various salinity conditions, including 30.0 ppt, 8.5 ppt, and 1.7 ppt salinity, which represent full-strength, isosmotic, and low-salinity stress, respectively. We analyzed the effect of TTX ingestion on the community structure, core microbiome, and metabolic capabilities of the gut microbiome using high-throughput sequencing technologies. The predominant bacterial taxa within the gut microbiome were Firmicutes (21-85%), Campilobacterota (2.8-67%), Spirochaetota (0.5-14%), and Proteobacteria (0.7-9.8%), with Mycoplasma, uncultured Arcobacteraceae, Brevinema, Vibrio, Rubritalea, and uncultured Pirellulaceae as core genera. Our findings indicated that the impact of TTX on high-abundance genera at 30.0 ppt and 8.5 ppt salinity levels was negligible, indicating their stability and resilience to TTX ingestion. However, at 1.7 ppt, TTX-fed fish showed a significant increase in uncultured Arcobacteraceae. Furthermore, our analysis of TTX-fed fish revealed taxonomic alterations in low-abundance taxa, which altered the predicted functions of the gut microbiota at all salinity levels. These results suggest that TTX administration could cause subtle effects on the metabolic functions of gut microbial communities. Overall, our study provides insights into the complex relationship between a TTX-accumulating animal, T. rubripes, and its gut microbiota.
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Affiliation(s)
- Mai A Wassel
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
- Genetics and Genetic Engineering Research Group, National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt.
| | - Yoko Makabe-Kobayashi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Tomohiro Takatani
- Graduate School of Integrated Science and Technology, Nagasaki University, 1‑14 Bunkyo, Nagasaki, 852‑8521, Japan
| | - Yoshitaka Sakakura
- Graduate School of Integrated Science and Technology, Nagasaki University, 1‑14 Bunkyo, Nagasaki, 852‑8521, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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Zhang M, He T, Wu Q, Chen M, Liang X. Hydroxylamine supplementation accelerated the rates of cell growth, aerobic denitrification and nitrous oxide emission of Pseudomonas taiwanensis EN-F2. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120826. [PMID: 38608579 DOI: 10.1016/j.jenvman.2024.120826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Hydroxylamine can disrupt the protein translation process of most reported nitrogen-converting bacteria, and thus hinder the reproduction of bacteria and nitrogen conversion capacity. However, the effect of hydroxylamine on the denitrification ability of strain EN-F2 is unclear. In this study, the cell growth, aerobic denitrification ability, and nitrous oxide (N2O) emission by Pseudomonas taiwanensis were carefully investigated by addition of hydroxylamine at different concentrations. The results demonstrated that the rates of nitrate and nitrite reduction were enhanced by 2.51 and 2.78 mg/L/h after the addition of 8.0 and 12.0 mg/L hydroxylamine, respectively. The N2O production from nitrate and nitrite reaction systems were strongly promoted by 4.39 and 8.62 mg/L, respectively, through the simultaneous acceleration of cell growth and both of nitrite and nitrate reduction. Additionally, the enzymatic activities of nitrate reductase and nitrite reductase climbed from 0.13 and 0.01 to 0.22 and 0.04 U/mg protein when hydroxylamine concentration increased from 0 to 6.0 and 12.0 mg/L. This may be the main mechanism for controlling the observed higher denitrification rate and N2O release. Overall, hydroxylamine supplementation supported the EN-F2 strain cell growth, denitrification and N2O emission rates.
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Affiliation(s)
- Manman Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Tengxia He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Qifeng Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Mengping Chen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Xiwen Liang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
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Deng W, Zhao Z, Li Y, Cao R, Chen M, Tang K, Wang D, Fan W, Hu A, Chen G, Chen CTA, Zhang Y. Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem. MICROBIOME 2023; 11:270. [PMID: 38049915 PMCID: PMC10696704 DOI: 10.1186/s40168-023-01712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/27/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms. RESULTS We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions. CONCLUSIONS Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.
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Affiliation(s)
- Wenchao Deng
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China.
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yufang Li
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Rongguang Cao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Deli Wang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Wei Fan
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Guangcheng Chen
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Chen-Tung Arthur Chen
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung Taiwan, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China.
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4
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Cheng R, Li X, Jiang L, Gong L, Geslin C, Shao Z. Virus diversity and interactions with hosts in deep-sea hydrothermal vents. MICROBIOME 2022; 10:235. [PMID: 36566239 PMCID: PMC9789665 DOI: 10.1186/s40168-022-01441-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The deep sea harbors many viruses, yet their diversity and interactions with hosts in hydrothermal ecosystems are largely unknown. Here, we analyzed the viral composition, distribution, host preference, and metabolic potential in different habitats of global hydrothermal vents, including vent plumes, background seawater, diffuse fluids, and sediments. RESULTS From 34 samples collected at eight vent sites, a total of 4662 viral populations (vOTUs) were recovered from the metagenome assemblies, encompassing diverse phylogenetic groups and defining many novel lineages. Apart from the abundant unclassified viruses, tailed phages are most predominant across the global hydrothermal vents, while single-stranded DNA viruses, including Microviridae and small eukaryotic viruses, also constitute a significant part of the viromes. As revealed by protein-sharing network analysis, hydrothermal vent viruses formed many novel genus-level viral clusters and are highly endemic to specific vent sites and habitat types. Only 11% of the vOTUs can be linked to hosts, which are the key microbial taxa of hydrothermal habitats, such as Gammaproteobacteria and Campylobacterota. Intriguingly, vent viromes share some common metabolic features in that they encode auxiliary genes that are extensively involved in the metabolism of carbohydrates, amino acids, cofactors, and vitamins. Specifically, in plume viruses, various auxiliary genes related to methane, nitrogen, and sulfur metabolism were observed, indicating their contribution to host energy conservation. Moreover, the prevalence of sulfur-relay pathway genes indicated the significant role of vent viruses in stabilizing the tRNA structure, which promotes host adaptation to steep environmental gradients. CONCLUSIONS The deep-sea hydrothermal systems hold untapped viral diversity with novelty. They may affect both vent prokaryotic and eukaryotic communities and modulate host metabolism related to vent adaptability. More explorations are needed to depict global vent virus diversity and its roles in this unique ecosystem. Video Abstract.
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Affiliation(s)
- Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resource, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Xiaofeng Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Claire Geslin
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
- Sino-French Laboratory of Deep-Sea Microbiology (MICROBSEA-LIA), Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Sino-French Laboratory of Deep-Sea Microbiology (MICROBSEA-LIA), Plouzané, France.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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5
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Smedile F, Foustoukos DI, Patwardhan S, Mullane K, Schlegel I, Adams MW, Schut GJ, Giovannelli D, Vetriani C. Adaptations to high pressure of Nautilia sp. strain PV-1, a piezophilic Campylobacterium (aka Epsilonproteobacterium) isolated from a deep-sea hydrothermal vent. Environ Microbiol 2022; 24:6164-6183. [PMID: 36271901 PMCID: PMC10092268 DOI: 10.1111/1462-2920.16256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
Physiological and gene expression studies of deep-sea bacteria under pressure conditions similar to those experienced in their natural habitat are critical for understanding growth kinetics and metabolic adaptations to in situ conditions. The Campylobacterium (aka Epsilonproteobacterium) Nautilia sp. strain PV-1 was isolated from hydrothermal fluids released from an active deep-sea hydrothermal vent at 9° N on the East Pacific Rise. Strain PV-1 is a piezophilic, moderately thermophilic, chemolithoautotrophic anaerobe that conserves energy by coupling the oxidation of hydrogen to the reduction of nitrate or elemental sulfur. Using a high-pressure-high temperature continuous culture system, we established that strain PV-1 has the shortest generation time of all known piezophilic bacteria and we investigated its protein expression pattern in response to different hydrostatic pressure regimes. Proteogenomic analyses of strain PV-1 grown at 20 and 5 MPa showed that pressure adaptation is not restricted to stress response or homeoviscous adaptation but extends to enzymes involved in central metabolic pathways. Protein synthesis, motility, transport, and energy metabolism are all affected by pressure, although to different extents. In strain PV-1, low-pressure conditions induce the synthesis of phage-related proteins and an overexpression of enzymes involved in carbon fixation.
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Affiliation(s)
- Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Institute of Polar Science (ISP-CNR), Messina, Italy
| | - Dionysis I Foustoukos
- Earth and Planets Laboratory, Carnegie Institution of Washington, Washington, District of Columbia, USA
| | - Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Kelli Mullane
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Ian Schlegel
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Michael W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
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6
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Zhang X, Huang Y, Liu Y, Xu W, Pan J, Zheng X, Du H, Zhang C, Lu Z, Zou D, Liu Z, Cai M, Xiong J, Zhu Y, Dong Z, Jiang H, Dong H, Jiang J, Luo Z, Huang L, Li M. An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales. Mol Biol Evol 2022; 39:6742362. [PMID: 36181435 PMCID: PMC9585477 DOI: 10.1093/molbev/msac213] [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: 12/15/2022] Open
Abstract
Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.
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Affiliation(s)
- Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huan Du
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Juquan Jiang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Li
- Corresponding author: E-mail:
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Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins. THE ISME JOURNAL 2022; 16:1119-1129. [PMID: 34862473 PMCID: PMC8940962 DOI: 10.1038/s41396-021-01161-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/01/2022]
Abstract
Microbial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.
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8
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Okubo T, Toyoda A, Fukuhara K, Uchiyama I, Harigaya Y, Kuroiwa M, Suzuki T, Murakami Y, Suwa Y, Takami H. The physiological potential of anammox bacteria as revealed by their core genome structure. DNA Res 2021; 28:6046978. [PMID: 33367889 PMCID: PMC7814187 DOI: 10.1093/dnares/dsaa028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/04/2020] [Indexed: 01/25/2023] Open
Abstract
We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2− reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH2OH by self-production for anammox metabolism.
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Affiliation(s)
- Takashi Okubo
- Marine Microbiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Kohei Fukuhara
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Ikuo Uchiyama
- Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji, Okazaki 444-8585, Japan
| | - Yuhki Harigaya
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Megumi Kuroiwa
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Takuma Suzuki
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Yuka Murakami
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Yuichi Suwa
- Department of Biological Sciences, Chuo University, Bunkyo, Tokyo 112-8851, Japan
| | - Hideto Takami
- Marine Microbiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa 277-8564, Japan
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9
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Wang S, Jiang L, Hu Q, Cui L, Zhu B, Fu X, Lai Q, Shao Z, Yang S. Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas. Front Microbiol 2021; 12:626705. [PMID: 33717015 PMCID: PMC7952632 DOI: 10.3389/fmicb.2021.626705] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.
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Affiliation(s)
- Shasha Wang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
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10
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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11
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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12
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Catchpole RJ, Forterre P. The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor. Mol Biol Evol 2020; 36:2737-2747. [PMID: 31504731 PMCID: PMC6878951 DOI: 10.1093/molbev/msz180] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Reverse gyrase (RG) is the only protein found ubiquitously in hyperthermophilic organisms, but absent from mesophiles. As such, its simple presence or absence allows us to deduce information about the optimal growth temperature of long-extinct organisms, even as far as the last universal common ancestor of extant life (LUCA). The growth environment and gene content of the LUCA has long been a source of debate in which RG often features. In an attempt to settle this debate, we carried out an exhaustive search for RG proteins, generating the largest RG data set to date. Comprising 376 sequences, our data set allows for phylogenetic reconstructions of RG with unprecedented size and detail. These RG phylogenies are strikingly different from those of universal proteins inferred to be present in the LUCA, even when using the same set of species. Unlike such proteins, RG does not form monophyletic archaeal and bacterial clades, suggesting RG emergence after the formation of these domains, and/or significant horizontal gene transfer. Additionally, the branch lengths separating archaeal and bacterial groups are very short, inconsistent with the tempo of evolution from the time of the LUCA. Despite this, phylogenies limited to archaeal RG resolve most archaeal phyla, suggesting predominantly vertical evolution since the time of the last archaeal ancestor. In contrast, bacterial RG indicates emergence after the last bacterial ancestor followed by significant horizontal transfer. Taken together, these results suggest a nonhyperthermophilic LUCA and bacterial ancestor, with hyperthermophily emerging early in the evolution of the archaeal and bacterial domains.
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Affiliation(s)
- Ryan J Catchpole
- Département de Microbiologie, Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Paris, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Patrick Forterre
- Département de Microbiologie, Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Paris, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, University of Paris-Saclay, Gif-sur-Yvette, France
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13
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Couturier M, Gadelle D, Forterre P, Nadal M, Garnier F. The reverse gyrase TopR1 is responsible for the homeostatic control of DNA supercoiling in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 2019; 113:356-368. [PMID: 31713907 DOI: 10.1111/mmi.14424] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/06/2019] [Accepted: 11/10/2019] [Indexed: 11/28/2022]
Abstract
Maintaining an appropriate DNA topology with DNA-based processes (DNA replication, transcription and recombination) is crucial for all three domains of life. In bacteria, the homeostatic regulation for controlling DNA supercoiling relies on antagonistic activities of two DNA topoisomerases, TopoI and gyrase. In hyperthermophilic crenarchaea, the presence of such a regulatory system is suggested as two DNA topoisomerases, TopoVI and reverse gyrase, catalyze antagonistic activities. To test this hypothesis, we estimated and compared the number of the TopoVI with that of the two reverse gyrases, TopR1 and TopR2, in Sulfolobus solfataricus cells maintained either at 80 or at 88°C, or reciprocally shifted from one temperature to the other. From the three DNA topoisomerases, TopR1 is the only one exhibiting significant quantitative variations in response to the up- and down-shifts. In addition, the corresponding intrinsic activities of these three DNA topoisomerases were tested in vitro at both temperatures. Although temperature modulates the three DNA topoisomerases activities, TopR1 is the sole topoisomerase able to function at high temperature. Altogether, results presented in this study demonstrate, for the first time, that the DNA topological state of a crenarchaeon is regulated via a homeostatic control, which is mainly mediated by the fine-tuning of TopR1.
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Affiliation(s)
- Mohea Couturier
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France
| | - Danièle Gadelle
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France
| | - Marc Nadal
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France.,Institut Jacques Monod, UMR 8621 CNRS-Université Paris Diderot, Paris Cedex 13, France
| | - Florence Garnier
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, Orsay Cedex, France.,Institut Jacques Monod, UMR 8621 CNRS-Université Paris Diderot, Paris Cedex 13, France.,Biology Department, Université Versailles St-Quentin, Versailles, France
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14
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Lebrato M, Wang YV, Tseng LC, Achterberg EP, Chen XG, Molinero JC, Bremer K, Westernströer U, Söding E, Dahms HU, Küter M, Heinath V, Jöhnck J, Konstantinou KI, Yang YJ, Hwang JS, Garbe-Schönberg D. Earthquake and typhoon trigger unprecedented transient shifts in shallow hydrothermal vents biogeochemistry. Sci Rep 2019; 9:16926. [PMID: 31729442 PMCID: PMC6858458 DOI: 10.1038/s41598-019-53314-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 10/30/2019] [Indexed: 12/03/2022] Open
Abstract
Shallow hydrothermal vents are of pivotal relevance for ocean biogeochemical cycles, including seawater dissolved heavy metals and trace elements as well as the carbonate system balance. The Kueishan Tao (KST) stratovolcano off Taiwan is associated with numerous hydrothermal vents emitting warm sulfur-rich fluids at so-called White Vents (WV) and Yellow Vent (YV) that impact the surrounding seawater masses and habitats. The morphological and biogeochemical consequences caused by a M5.8 earthquake and a C5 typhoon (“Nepartak”) hitting KST (12th May, and 2nd–10th July, 2016) were studied within a 10-year time series (2009–2018) combining aerial drone imagery, technical diving, and hydrographic surveys. The catastrophic disturbances triggered landslides that reshaped the shoreline, burying the seabed and, as a consequence, native sulfur accretions that were abundant on the seafloor disappeared. A significant reduction in venting activity and fluid flow was observed at the high-temperature YV. Dissolved Inorganic Carbon (DIC) maxima in surrounding seawater reached 3000–5000 µmol kg−1, and Total Alkalinity (TA) drawdowns were below 1500–1000 µmol kg−1 lasting for one year. A strong decrease and, in some cases, depletion of dissolved elements (Cd, Ba, Tl, Pb, Fe, Cu, As) including Mg and Cl in seawater from shallow depths to the open ocean followed the disturbance, with a recovery of Mg and Cl to pre-disturbance concentrations in 2018. The WV and YV benthic megafauna exhibited mixed responses in their skeleton Mg:Ca and Sr:Ca ratios, not always following directions of seawater chemical changes. Over 70% of the organisms increased skeleton Mg:Ca ratio during rising DIC (higher CO2) despite decreasing seawater Mg:Ca ratios showing a high level of resilience. KST benthic organisms have historically co-existed with such events providing them ecological advantages under extreme conditions. The sudden and catastrophic changes observed at the KST site profoundly reshaped biogeochemical processes in shallow and offshore waters for one year, but they remained transient in nature, with a possible recovery of the system within two years.
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Affiliation(s)
- Mario Lebrato
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany. .,Bazaruto Center for Scientific Studies (BCSS), Benguerra Island, Mozambique.
| | - Yiming V Wang
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Li-Chun Tseng
- National Taiwan Ocean University, Keelung City, Taiwan
| | | | - Xue-Gang Chen
- Ocean College, Zhejiang University, Zhoushan City, China
| | - Juan-Carlos Molinero
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany.,Marine Biodiversity, Exploitation and Conservation (MARBEC), IRD/CNRS/IFREMER/University of Montpellier, Montpellier, France
| | - Karen Bremer
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany
| | | | - Emanuel Söding
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany
| | | | - Marie Küter
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany
| | - Verena Heinath
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany
| | - Janika Jöhnck
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany
| | | | | | | | - Dieter Garbe-Schönberg
- Institute of Geosciences, Kiel University (CAU), Kiel, Germany.,Jacobs University Bremen gGmbH, Bremen, Germany
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15
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Kruse S, Goris T, Westermann M, Adrian L, Diekert G. Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria. Nat Commun 2018; 9:4872. [PMID: 30451902 PMCID: PMC6242987 DOI: 10.1038/s41467-018-07342-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 10/24/2018] [Indexed: 02/04/2023] Open
Abstract
Hydrogen-producing bacteria are of environmental importance, since hydrogen is a major electron donor for prokaryotes in anoxic ecosystems. Epsilonproteobacteria are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report hydrogen production upon pyruvate fermentation for free-living Epsilonproteobacteria, Sulfurospirillum spp. The amount of hydrogen produced is different in two subgroups of Sulfurospirillum spp., represented by S. cavolei and S. multivorans. The former produces more hydrogen and excretes acetate as sole organic acid, while the latter additionally produces lactate and succinate. Hydrogen production can be assigned by differential proteomics to a hydrogenase (similar to hydrogenase 4 from E. coli) that is more abundant during fermentation. A syntrophic interaction is established between Sulfurospirillum multivorans and Methanococcus voltae when cocultured with lactate as sole substrate, as the former cannot grow fermentatively on lactate alone and the latter relies on hydrogen for growth. This might hint to a yet unrecognized role of Epsilonproteobacteria as hydrogen producers in anoxic microbial communities. Epsilonproteobacteria, such as Sulfurospirillum, can use molecular hydrogen as an electron donor for respiration. Here, the authors show that Sulfurospirillum can, in addition, release hydrogen during fermentation, allowing metabolic interactions with other hydrogen-consuming microorganisms.
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Affiliation(s)
- Stefan Kruse
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743, Jena, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743, Jena, Germany.
| | - Martin Westermann
- Center for Electron Microscopy of the University Hospital Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.,Fachgebiet Geobiotechnologie, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743, Jena, Germany
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16
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Jelen B, Giovannelli D, Falkowski PG, Vetriani C. Elemental sulfur reduction in the deep‐sea vent thermophile,
Thermovibrio ammonificans. Environ Microbiol 2018; 20:2301-2316. [DOI: 10.1111/1462-2920.14280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/10/2018] [Accepted: 05/12/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Benjamin Jelen
- Environmental Biophysics and Molecular Ecology Program Rutgers University, New Brunswick New Brunswick NJ 08901 USA
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences Rutgers University New Brunswick NJ 08901 USA
- Institute of Marine Science National Research Council Ancona 60125 Italy
- Earth‐Life Science Institute Tokyo Institute of Technology Tokyo 152‐8550 Japan
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program Rutgers University, New Brunswick New Brunswick NJ 08901 USA
- Department of Marine and Coastal Sciences Rutgers University New Brunswick NJ 08901 USA
- Department of Earth and Planetary Sciences Rutgers University New Brunswick NJ 08854 USA
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences Rutgers University New Brunswick NJ 08901 USA
- Department of Biochemistry and Microbiology Rutgers University New Brunswick NJ 08901 USA
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17
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Tang K, Zhang Y, Lin D, Han Y, Chen CTA, Wang D, Lin YS, Sun J, Zheng Q, Jiao N. Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity. Front Microbiol 2018. [PMID: 29527196 PMCID: PMC5829616 DOI: 10.3389/fmicb.2018.00279] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile genetic potential to adapt to the unique environmental conditions.
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Affiliation(s)
- Kai Tang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Dan Lin
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yu Han
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Deli Wang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yu-Shih Lin
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
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18
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [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: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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19
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Nagata R, Takaki Y, Tame A, Nunoura T, Muto H, Mino S, Sawayama S, Takai K, Nakagawa S. Lebetimonas natsushimae sp. nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough. Syst Appl Microbiol 2017; 40:352-356. [PMID: 28690052 DOI: 10.1016/j.syapm.2017.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 10/19/2022]
Abstract
A moderately thermophilic, strictly anaerobic, chemoautotrophic bacterium, designated strain HS1857T, was isolated from a deep-sea hydrothermal vent at the Noho site in the Mid-Okinawa Trough. Strain HS1857T grew between 35 and 63°C (optimum 55°C), in the presence of 10-55gl-1 NaCl (optimum 25gl-1), and pH 5.5-7.1 (optimum 6.4). Growth occurred with molecular hydrogen as the electron donor and elemental sulfur, nitrate, or selenate as the electron acceptors. Formate could serve as an alternative electron donor with nitrate as an electron acceptor. During growth with nitrate as the electron acceptor, strain HS1857T produced ammonium and formed a biofilm. CO2 was utilized as the sole carbon source. The G+C content of the genomic DNA was 33.2mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HS1857T is a member of the order Nautiliales, showing a sequence similarity of 95.0% with Lebetimonas acidiphila Pd55T. The fatty acid composition was similar to that of L. acidiphila, which was dominated by C18:0 (47.0%) and C18:1 (23.7%). Based on the genomic, chemotaxonomic, phenotypic characteristics, the name Lebetimonas natsushimae sp. nov., is proposed. The type strain is HS1857T (=NBRC 112478T=DSM 104102T).
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Affiliation(s)
- Ryousuke Nagata
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Akihiro Tame
- Department of Technical Services, Marine Works Japan, Ltd., Yokosuka, Japan
| | - Takuro Nunoura
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan; Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
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20
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Haase D, Hermann B, Einsle O, Simon J. Epsilonproteobacterial hydroxylamine oxidoreductase (
ε
Hao): characterization of a ‘missing link’ in the multihaem cytochrome
c
family. Mol Microbiol 2017; 105:127-138. [DOI: 10.1111/mmi.13690] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Doreen Haase
- Microbial Energy Conversion and Biotechnology, Department of BiologyTechnische Universität DarmstadtSchnittspahnstraße 1064287Darmstadt Germany
| | - Bianca Hermann
- Lehrstuhl Biochemie, Institut für BiochemieAlbert‐Ludwigs‐Universität FreiburgAlbertstrasse 2179104Freiburg Germany
| | - Oliver Einsle
- Lehrstuhl Biochemie, Institut für BiochemieAlbert‐Ludwigs‐Universität FreiburgAlbertstrasse 2179104Freiburg Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of BiologyTechnische Universität DarmstadtSchnittspahnstraße 1064287Darmstadt Germany
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21
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Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P. Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 2017; 8:682. [PMID: 28484436 PMCID: PMC5401914 DOI: 10.3389/fmicb.2017.00682] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022] Open
Abstract
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
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Affiliation(s)
- David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Donovan H. Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, KingstonRI, USA
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan
| | - Stefan M. Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
| | - Barbara J. Campbell
- Department of Biological Sciences, Life Science Facility, Clemson University, ClemsonSC, USA
| | - Thomas E. Hanson
- School of Marine Science and Policy, College of Earth, Ocean, and Environment, Delaware Biotechnology Institute, University of Delaware, NewarkDE, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut CreekCA, USA
| | - Martin G. Klotz
- Department of Biology and School of Earth and Environmental Sciences, Queens College of the City University of New York, New YorkNY, USA
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
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22
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Slobodkina GB, Mardanov AV, Ravin NV, Frolova AA, Chernyh NA, Bonch-Osmolovskaya EA, Slobodkin AI. Respiratory Ammonification of Nitrate Coupled to Anaerobic Oxidation of Elemental Sulfur in Deep-Sea Autotrophic Thermophilic Bacteria. Front Microbiol 2017; 8:87. [PMID: 28194142 PMCID: PMC5276818 DOI: 10.3389/fmicb.2017.00087] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/12/2017] [Indexed: 02/05/2023] Open
Abstract
Respiratory ammonification of nitrate is the microbial process that determines the retention of nitrogen in an ecosystem. To date, sulfur-dependent dissimilatory nitrate reduction to ammonium has been demonstrated only with sulfide as an electron donor. We detected a novel pathway that couples the sulfur and nitrogen cycles. Thermophilic anaerobic bacteria Thermosulfurimonas dismutans and Dissulfuribacter thermophilus, isolated from deep-sea hydrothermal vents, grew autotrophically with elemental sulfur as an electron donor and nitrate as an electron acceptor producing sulfate and ammonium. The genomes of both bacteria contain a gene cluster that encodes a putative nitrate ammonification enzyme system. Nitrate reduction occurs via a Nap-type complex. The reduction of produced nitrite to ammonium does not proceed via the canonical Nrf system because nitrite reductase NrfA is absent in the genomes of both microorganisms. The genome of D. thermophilus encodes a complete sulfate reduction pathway, while the Sox sulfur oxidation system is missing, as shown previously for T. dismutans. Thus, in high-temperature environments, nitrate ammonification with elemental sulfur may represent an unrecognized route of primary biomass production. Moreover, the anaerobic oxidation of sulfur compounds coupled to growth has not previously been demonstrated for the members of Thermodesulfobacteria or Deltaproteobacteria, which were considered exclusively as participants of the reductive branch of the sulfur cycle.
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Affiliation(s)
- Galina B Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Anastasia A Frolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Nikolay A Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Elizaveta A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Alexander I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
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23
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Sorokin DY, Messina E, Smedile F, Roman P, Damsté JSS, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Kublanov IV, Samarov NI, Toshchakov SV, La Cono V, Yakimov MM. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. ISME JOURNAL 2017; 11:1245-1260. [PMID: 28106880 PMCID: PMC5437934 DOI: 10.1038/ismej.2016.203] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 12/20/2022]
Abstract
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Messina, Italy
| | | | - Pawel Roman
- Sub-department of Environmental Technology, Wageningen University, Wageningen, The Netherlands.,Wetsus, Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Sergio Ciordia
- Proteomics Unit, National Center for Biotechnology, CSIC, Madrid, Spain
| | - Maria Carmen Mena
- Proteomics Unit, National Center for Biotechnology, CSIC, Madrid, Spain
| | | | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, UK.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nazar I Samarov
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | | | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Messina, Italy.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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24
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Oshiki M, Ali M, Shinyako-Hata K, Satoh H, Okabe S. Hydroxylamine-dependent anaerobic ammonium oxidation (anammox) by “Candidatus
Brocadia sinica”. Environ Microbiol 2016; 18:3133-43. [DOI: 10.1111/1462-2920.13355] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering; National Institute of Technology, Nagaoka College; Nagaoka Niigata 940-8532 Japan
| | - Muhammad Ali
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal; 23955-6900 Saudi Arabia
| | - Kaori Shinyako-Hata
- Tokyo Engineering Consultants Co., Ltd., Kasumigaseki, Chioyadaku, Tokyo 100-0013, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
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25
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Degli Esposti M, Martinez Romero E. A survey of the energy metabolism of nodulating symbionts reveals a new form of respiratory complex I. FEMS Microbiol Ecol 2016; 92:fiw084. [DOI: 10.1093/femsec/fiw084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 01/18/2023] Open
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26
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Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent. ISME JOURNAL 2016; 10:1925-38. [PMID: 26872039 PMCID: PMC5029171 DOI: 10.1038/ismej.2015.258] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 01/13/2023]
Abstract
The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched 13C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.
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27
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Degli Esposti M. Genome Analysis of Structure-Function Relationships in Respiratory Complex I, an Ancient Bioenergetic Enzyme. Genome Biol Evol 2015; 8:126-47. [PMID: 26615219 PMCID: PMC4758237 DOI: 10.1093/gbe/evv239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) is a ubiquitous bioenergetic enzyme formed by over 40 subunits in eukaryotes and a minimum of 11 subunits in bacteria. Recently, crystal structures have greatly advanced our knowledge of complex I but have not clarified the details of its reaction with ubiquinone (Q). This reaction is essential for bioenergy production and takes place in a large cavity embedded within a conserved module that is homologous to the catalytic core of Ni-Fe hydrogenases. However, how a hydrogenase core has evolved into the protonmotive Q reductase module of complex I has remained unclear. This work has exploited the abundant genomic information that is currently available to deduce structure-function relationships in complex I that indicate the evolutionary steps of Q reactivity and its adaptation to natural Q substrates. The results provide answers to fundamental questions regarding various aspects of complex I reaction with Q and help re-defining the old concept that this reaction may involve two Q or inhibitor sites. The re-definition leads to a simplified classification of the plethora of complex I inhibitors while throwing a new light on the evolution of the enzyme function.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genova, Italy Center for Genomic Sciences, UNAM, Cuernavaca, Mexico
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28
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Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H, Steen IH. Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria. Front Microbiol 2015; 6:987. [PMID: 26441916 PMCID: PMC4584990 DOI: 10.3389/fmicb.2015.00987] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/04/2015] [Indexed: 01/18/2023] Open
Abstract
In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.
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Affiliation(s)
- Irene Roalkvam
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Karine Drønen
- UniResearch, Centre for Integrated Petroleum Research Bergen, Norway
| | - Runar Stokke
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Frida L Daae
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
| | - Ida H Steen
- Centre for Geobiology, University of Bergen Bergen, Norway ; Department of Biology, University of Bergen Bergen, Norway
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29
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Han Y, Perner M. The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines. Front Microbiol 2015; 6:989. [PMID: 26441918 PMCID: PMC4584964 DOI: 10.3389/fmicb.2015.00989] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 09/04/2015] [Indexed: 01/11/2023] Open
Abstract
Sulfurimonas species are commonly isolated from sulfidic habitats and numerous 16S rRNA sequences related to Sulfurimonas species have been identified in chemically distinct environments, such as hydrothermal deep-sea vents, marine sediments, the ocean's water column, and terrestrial habitats. In some of these habitats, Sulfurimonas have been demonstrated to play an important role in chemoautotrophic processes. Sulfurimonas species can grow with a variety of electron donors and acceptors, which may contribute to their widespread distribution. Multiple copies of one type of enzyme (e.g., sulfide:quinone reductases and hydrogenases) may play a pivotal role in Sulfurimonas' flexibility to colonize disparate environments. Many of these genes appear to have been acquired through horizontal gene transfer which has promoted adaptations to the distinct habitats. Here we summarize Sulfurimonas' versatile energy metabolisms and link their physiological properties to their global distribution.
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Affiliation(s)
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Biocenter Klein Flottbek, University of HamburgHamburg, Germany
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30
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Stokke R, Dahle H, Roalkvam I, Wissuwa J, Daae FL, Tooming-Klunderud A, Thorseth IH, Pedersen RB, Steen IH. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environ Microbiol 2015; 17:4063-77. [PMID: 26147346 DOI: 10.1111/1462-2920.12970] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/25/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022]
Abstract
Little is known about how lithoautotrophic primary production is connected to microbial organotrophic consumption in hydrothermal systems. Using a multifaceted approach, we analysed the structure and metabolic capabilities within a biofilm growing on the surface of a black smoker chimney in the Loki's Castle vent field. Imaging revealed the presence of rod-shaped Bacteroidetes growing as ectobionts on long, sheathed microbial filaments (> 100 μm) affiliated with the Sulfurovum genus within Epsilonproteobacteria. The filaments were composed of a thick (> 200 nm) stable polysaccharide, representing a substantial fraction of organic carbon produced by primary production. An integrated -omics approach enabled us to assess the metabolic potential and in situ metabolism of individual taxonomic and morphological groups identified by imaging. Specifically, we provide evidence that organotrophic Bacteroidetes attach to and glide along the surface of Sulfurovum filaments utilizing organic polymers produced by the lithoautotrophic Sulfurovum. Furthermore, in situ expression of acetyl-CoA synthetase by Sulfurovum suggested the ability to assimilate acetate, indicating recycling of organic matter in the biofilm. This study expands our understanding of the lifestyles of Epsilonproteobacteria in hydrothermal vents, their metabolic properties and co-operative interactions in deep-sea hydrothermal vent food webs.
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Affiliation(s)
- Runar Stokke
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Irene Roalkvam
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Juliane Wissuwa
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Frida Lise Daae
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Ingunn H Thorseth
- Centre for Geobiology.,Department of Earth Science, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Rolf B Pedersen
- Centre for Geobiology.,Department of Earth Science, University of Bergen, Allegaten 41, 5020, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology.,Department of Biology, University of Bergen, Allegaten 41, 5020, Bergen, Norway
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31
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Zhang W, Wang Y, Bougouffa S, Tian R, Cao H, Li Y, Cai L, Wong YH, Zhang G, Zhou G, Zhang X, Bajic VB, Al-Suwailem A, Qian PY. Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool. Environ Microbiol 2015; 17:4089-104. [DOI: 10.1111/1462-2920.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Weipeng Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yong Wang
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
| | - Salim Bougouffa
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Renmao Tian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Huiluo Cao
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yongxin Li
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Lin Cai
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yue Him Wong
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Gen Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Guowei Zhou
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Xixiang Zhang
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Abdulaziz Al-Suwailem
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
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32
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Sorokin DY, Kublanov IV, Gavrilov SN, Rojo D, Roman P, Golyshin PN, Slepak VZ, Smedile F, Ferrer M, Messina E, La Cono V, Yakimov MM. Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon. ISME JOURNAL 2015; 10:240-52. [PMID: 25978546 DOI: 10.1038/ismej.2015.79] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 04/06/2015] [Accepted: 04/10/2015] [Indexed: 01/30/2023]
Abstract
Archaea domain is comprised of many versatile taxa that often colonize extreme habitats. Here, we report the discovery of strictly anaerobic extremely halophilic euryarchaeon, capable of obtaining energy by dissimilatory reduction of elemental sulfur using acetate as the only electron donor and forming sulfide and CO2 as the only products. This type of respiration has never been observed in hypersaline anoxic habitats and is the first example of such metabolic capability in the entire Archaea domain. We isolated and cultivated these unusual organisms, selecting one representative strain, HSR2, for detailed characterization. Our studies including physiological tests, genome sequencing, gene expression, metabolomics and [(14)C]-bicarbonate assimilation assays revealed that HSR2 oxidized acetate completely via the tricarboxylic acid cycle. Anabolic assimilation of acetate occurred via activated glyoxylate bypass and anaplerotic carboxylation. HSR2 possessed sulfurtransferase and an array of membrane-bound polysulfide reductase genes, all of which were expressed during the growth. Our findings suggest the biogeochemical contribution of haloarchaea in hypersaline anoxic environments must be reconsidered.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei N Gavrilov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - David Rojo
- Center for Metabolomics and Bioanalysis, Faculty of Pharmacy, CEU San Pablo University, Boadilla del Monte, Spain
| | - Pawel Roman
- Sub-department of Environmental Technology, Wageningen University, Wageningen, The Netherlands.,Wetsus, Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands
| | | | - Vladlen Z Slepak
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Messina, Italy
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Proteomic Insights into Sulfur Metabolism in the Hydrogen-Producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1. Int J Mol Sci 2015; 16:9167-95. [PMID: 25915030 PMCID: PMC4463584 DOI: 10.3390/ijms16059167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/14/2015] [Indexed: 11/17/2022] Open
Abstract
The hyperthermophilic archaeon Thermococcus onnurineus NA1 has been shown to produce H₂ when using CO, formate, or starch as a growth substrate. This strain can also utilize elemental sulfur as a terminal electron acceptor for heterotrophic growth. To gain insight into sulfur metabolism, the proteome of T. onnurineus NA1 cells grown under sulfur culture conditions was quantified and compared with those grown under H₂-evolving substrate culture conditions. Using label-free nano-UPLC-MSE-based comparative proteomic analysis, approximately 38.4% of the total identified proteome (589 proteins) was found to be significantly up-regulated (≥1.5-fold) under sulfur culture conditions. Many of these proteins were functionally associated with carbon fixation, Fe-S cluster biogenesis, ATP synthesis, sulfur reduction, protein glycosylation, protein translocation, and formate oxidation. Based on the abundances of the identified proteins in this and other genomic studies, the pathways associated with reductive sulfur metabolism, H₂-metabolism, and oxidative stress defense were proposed. The results also revealed markedly lower expression levels of enzymes involved in the sulfur assimilation pathway, as well as cysteine desulfurase, under sulfur culture condition. The present results provide the first global atlas of proteome changes triggered by sulfur, and may facilitate an understanding of how hyperthermophilic archaea adapt to sulfur-rich, extreme environments.
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Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism. Appl Environ Microbiol 2015; 81:3142-56. [PMID: 25724961 DOI: 10.1128/aem.00039-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Large sulfur-oxidizing bacteria in the family Beggiatoaceae are important players in the global sulfur cycle. This group contains members of the well-known genera Beggiatoa, Thioploca, and Thiomargarita but also recently identified and relatively unknown candidate taxa, including "Candidatus Thiopilula" spp. and "Ca. Thiophysa" spp. We discovered a population of "Ca. Thiopilula" spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to Thiomargarita spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 μm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados "Ca. Thiopilula" organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for "Ca. Thiopilula" and other sulfur-oxidizing microorganisms in the community. The novel observations of "Ca. Thiopilula" and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful Beggiatoaceae group and thus offer insight into the composition and ecology of deep cold seep microbial communities.
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35
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Anderson RE, Sogin ML, Baross JA. Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics. PLoS One 2014; 9:e109696. [PMID: 25279954 PMCID: PMC4184897 DOI: 10.1371/journal.pone.0109696] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts’ functional capabilities.
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Affiliation(s)
- Rika E. Anderson
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Mitchell L. Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - John A. Baross
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, Washington, United States of America
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36
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Couturier M, Bizard AH, Garnier F, Nadal M. Insight into the cellular involvement of the two reverse gyrases from the hyperthermophilic archaeon Sulfolobus solfataricus. BMC Mol Biol 2014; 15:18. [PMID: 25200003 PMCID: PMC4183072 DOI: 10.1186/1471-2199-15-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/27/2014] [Indexed: 12/12/2022] Open
Abstract
Background Reverse gyrases are DNA topoisomerases characterized by their unique DNA positive-supercoiling activity. Sulfolobus solfataricus, like most Crenarchaeota, contains two genes each encoding a reverse gyrase. We showed previously that the two genes are differently regulated according to temperature and that the corresponding purified recombinant reverse gyrases have different enzymatic characteristics. These observations suggest a specialization of functions of the two reverse gyrases. As no mutants of the TopR genes could be obtained in Sulfolobales, we used immunodetection techniques to study the function(s) of these proteins in S. solfataricus in vivo. In particular, we investigated whether one or both reverse gyrases are required for the hyperthermophilic lifestyle. Results For the first time the two reverse gyrases of S. solfataricus have been discriminated at the protein level and their respective amounts have been determined in vivo. Actively dividing S. solfataricus cells contain only small amounts of both reverse gyrases, approximately 50 TopR1 and 125 TopR2 molecules per cell at 80°C. S. solfataricus cells are resistant at 45°C for several weeks, but there is neither cell division nor replication initiation; these processes are fully restored upon a return to 80°C. TopR1 is not found after three weeks at 45°C whereas the amount of TopR2 remains constant. Enzymatic assays in vitro indicate that TopR1 is not active at 45°C but that TopR2 exhibits highly positive DNA supercoiling activity at 45°C. Conclusions The two reverse gyrases of S. solfataricus are differently regulated, in terms of protein abundance, in vivo at 80°C and 45°C. TopR2 is present both at high and low temperatures and is therefore presumably required whether cells are dividing or not. By contrast, TopR1 is present only at high temperature where the cell division occurs, suggesting that TopR1 is required for controlling DNA topology associated with cell division activity and/or life at high temperature. Our findings in vitro that TopR1 is able to positively supercoil DNA only at high temperature, and TopR2 is active at both temperatures are consistent with them having different functions within the cells.
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Affiliation(s)
| | | | - Florence Garnier
- Université Versailles St-Quentin, 45 avenue des Etats-Unis, Versailles 78035, France.
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37
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Genome stability: recent insights in the topoisomerase reverse gyrase and thermophilic DNA alkyltransferase. Extremophiles 2014; 18:895-904. [DOI: 10.1007/s00792-014-0662-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/18/2014] [Indexed: 10/24/2022]
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38
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Gao B, Lara-Tejero M, Lefebre M, Goodman AL, Galán JE. Novel components of the flagellar system in epsilonproteobacteria. mBio 2014; 5:e01349-14. [PMID: 24961693 PMCID: PMC4073491 DOI: 10.1128/mbio.01349-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/02/2014] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Motility is essential for the pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a cell wall-anchored motor using chemical energy. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant differences in the flagellar structures of different bacterial species. The molecular bases for these differences, however, are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens Campylobacter jejuni and Helicobacter pylori, are among the most divergent. Using next-generation sequencing combined with transposon mutagenesis, we have conducted a comprehensive high-throughput genetic screen in Campylobacter jejuni, which identified several novel components of its flagellar system. Biochemical analyses detected interactions between the identified proteins and known components of the flagellar machinery, and in vivo imaging located them to the bacterial poles, where flagella assemble. Most of the identified new components are conserved within but restricted to epsilonproteobacteria. These studies provide insight into the divergent flagella of this group of bacteria and highlight the complexity of this remarkable structure, which has adapted to carry out its conserved functions in the context of widely diverse bacterial species. IMPORTANCE Motility is essential for the normal physiology and pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a motor that uses chemical energy as fuel. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown significant divergence in the flagellar structures across bacterial species. However, the molecular bases for these differences are not understood. The flagella from epsilonproteobacteria, which include the bacterial pathogens Campylobacter jejuni and Helicobacter pylori, are among the most divergent. We conducted a comprehensive genetic screen in Campylobacter jejuni and identified several novel components of the flagellar system. These studies provide important information to understand how flagella have adapted to function in the context of widely diverse sets of bacterial species and bring unique insight into the evolution and function of this remarkable bacterial organelle.
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Affiliation(s)
- Beile Gao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Maria Lara-Tejero
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Matthew Lefebre
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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Vetriani C, Voordeckers JW, Crespo-Medina M, O'Brien CE, Giovannelli D, Lutz RA. Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap). ISME JOURNAL 2014; 8:1510-21. [PMID: 24430487 DOI: 10.1038/ismej.2013.246] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/01/2013] [Accepted: 12/03/2013] [Indexed: 11/10/2022]
Abstract
Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.
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Affiliation(s)
- Costantino Vetriani
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - James W Voordeckers
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Melitza Crespo-Medina
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Charles E O'Brien
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Donato Giovannelli
- 1] Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA [2] Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA [3] Institute of Marine Science - ISMAR, National Research Council of Italy, CNR, Ancona, Italy
| | - Richard A Lutz
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
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40
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Whitehead A. Evolutionary Genomics of Environmental Pollution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:321-37. [DOI: 10.1007/978-94-007-7347-9_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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41
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Yakimov MM, La Cono V, Slepak VZ, La Spada G, Arcadi E, Messina E, Borghini M, Monticelli LS, Rojo D, Barbas C, Golyshina OV, Ferrer M, Golyshin PN, Giuliano L. Microbial life in the Lake Medee, the largest deep-sea salt-saturated formation. Sci Rep 2013; 3:3554. [PMID: 24352146 PMCID: PMC3867751 DOI: 10.1038/srep03554] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 12/03/2013] [Indexed: 11/25/2022] Open
Abstract
Deep-sea hypersaline anoxic lakes (DHALs) of the Eastern Mediterranean represent some of the most hostile environments on our planet. We investigated microbial life in the recently discovered Lake Medee, the largest DHAL found to-date. Medee has two unique features: a complex geobiochemical stratification and an absence of chemolithoautotrophic Epsilonproteobacteria, which usually play the primary role in dark bicarbonate assimilation in DHALs interfaces. Presumably because of these features, Medee is less productive and exhibits reduced diversity of autochthonous prokaryotes in its interior. Indeed, the brine community almost exclusively consists of the members of euryarchaeal MSBL1 and bacterial KB1 candidate divisions. Our experiments utilizing cultivation and [14C]-assimilation, showed that these organisms at least partially rely on reductive cleavage of osmoprotectant glycine betaine and are engaged in trophic cooperation. These findings provide novel insights into how prokaryotic communities can adapt to salt-saturated conditions and sustain active metabolism at the thermodynamic edge of life.
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Affiliation(s)
- Michail M Yakimov
- 1] Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy [2]
| | - Violetta La Cono
- 1] Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy [2]
| | - Vladlen Z Slepak
- 1] Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136 [2]
| | - Gina La Spada
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Erika Arcadi
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Mireno Borghini
- Institute for Marine Sciences, ISMAR-CNR, Forte S.Teresa, 19136 Pozzuolo di Lerici, La Spezia, Italy
| | - Luis S Monticelli
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - David Rojo
- Center for Metabolomics and Bioanalysis, University CEU San Pablo, Boadilla del Monte, 28668 Madrid, Spain
| | - Coral Barbas
- Center for Metabolomics and Bioanalysis, University CEU San Pablo, Boadilla del Monte, 28668 Madrid, Spain
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, ECW Bldg Deiniol Rd, Bangor, Gwynedd LL57 2UW, UK
| | - Manuel Ferrer
- 1] Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain [2]
| | - Peter N Golyshin
- 1] School of Biological Sciences, Bangor University, ECW Bldg Deiniol Rd, Bangor, Gwynedd LL57 2UW, UK [2]
| | - Laura Giuliano
- 1] Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy [2] Mediterranean Science Commission (CIESM), 16 bd de Suisse, MC 98000, Monaco
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Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microb Cell Fact 2013; 12:118. [PMID: 24274140 PMCID: PMC4222884 DOI: 10.1186/1475-2859-12-118] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/21/2013] [Indexed: 11/17/2022] Open
Abstract
Background The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals. Results Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism. Conclusions iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.
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Affiliation(s)
- Harish Nagarajan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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Meyer JL, Huber JA. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME JOURNAL 2013; 8:867-80. [PMID: 24257443 DOI: 10.1038/ismej.2013.206] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/02/2013] [Accepted: 10/13/2013] [Indexed: 11/09/2022]
Abstract
Chemolithoautotrophic Epsilonproteobacteria are ubiquitous in sulfidic, oxygen-poor habitats, including hydrothermal vents, marine oxygen minimum zones, marine sediments and sulfidic caves and have a significant role in cycling carbon, hydrogen, nitrogen and sulfur in these environments. The isolation of diverse strains of Epsilonproteobacteria and the sequencing of their genomes have revealed that this group has the metabolic potential to occupy a wide range of niches, particularly at dynamic deep-sea hydrothermal vents. We expand on this body of work by examining the population genomics of six strains of Lebetimonas, a vent-endemic, thermophilic, hydrogen-oxidizing Epsilonproteobacterium, from a single seamount in the Mariana Arc. Using Lebetimonas as a model for anaerobic, moderately thermophilic organisms in the warm, anoxic subseafloor environment, we show that genomic content is highly conserved and that recombination is limited between closely related strains. The Lebetimonas genomes are shaped by mobile genetic elements and gene loss as well as the acquisition of novel functional genes by horizontal gene transfer, which provide the potential for adaptation and microbial speciation in the deep sea. In addition, these Lebetimonas genomes contain two operons of nitrogenase genes with different evolutionary origins. Lebetimonas expressed nifH during growth with nitrogen gas as the sole nitrogen source, thus providing the first evidence of nitrogen fixation in any Epsilonproteobacteria from deep-sea hydrothermal vents. In this study, we provide a comparative overview of the genomic potential within the Nautiliaceae as well as among more distantly related hydrothermal vent Epsilonproteobacteria to broaden our understanding of microbial adaptation and diversity in the deep sea.
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Affiliation(s)
- Julie L Meyer
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA
| | - Julie A Huber
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA
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Rusch A, Gaidos E. Nitrogen-cycling bacteria and archaea in the carbonate sediment of a coral reef. GEOBIOLOGY 2013; 11:472-484. [PMID: 23849004 DOI: 10.1111/gbi.12048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 06/10/2013] [Indexed: 06/02/2023]
Abstract
In the coarse-grained carbonate sediments of coral reefs, advective porewater flow and the respiration of organic matter establish redox zones that are the scene of microbially mediated transformations of N compounds. To investigate the geobiology of N cycling in reef sediments, the benthic microbiota of Checker Reef in Kaneohe Bay, Hawaii, were surveyed for candidate nitrate reducers, ammonifying nitrite reducers, aerobic and anaerobic ammonia oxidizers (anammox) by identifying phylotypes of their key metabolic genes (napA, narG, nrfA, amoA) and ribotypes (unique RNA sequences) of anammox-like 16S rRNA. Putative proteobacteria with the catalytic potential for nitrate reduction were identified in oxic, interfacial and anoxic habitats. The estimated richness of napA (≥202 in anoxic sediment) and narG (≥373 and ≥441 in oxic and interfacial sediment, respectively) indicates a diverse guild of nitrate reducers. The guild of nrfA hosts in interfacial reef sediment was dominated by Vibrio species. The identified members of the aerobic ammonium oxidizing guild (amoA hosts) were Crenarchaeota or close relatives of Nitrosomonadales. Putative anammox bacteria were detected in the RNA pool of Checker Reef sediment. More than half of these ribotypes show ≥90% identity with homologous sequences of Scalindua spp., while no evidence was found for members of the genera Brocadia or Kuenenia. In addition to exploring the diversity of these four nitrogen-cycling microbial guilds in coral reef sediments, the abundances of aerobic ammonium oxidizers (amoA), nitrite oxidizers (nxrAB), ammonifying nitrite reducers (nrfA) and denitrifiers (nosZ) were estimated using real-time PCR. Representatives of all targeted guilds were detected, suggesting that most processes of the biogeochemical N cycle can be catalyzed by the benthic microbiota of tropical coral reefs.
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Affiliation(s)
- A Rusch
- Department of Geology and Geophysics, University of Hawaii at Mānoa, Honolulu, HI, USA.
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Functional metagenomic investigations of microbial communities in a shallow-sea hydrothermal system. PLoS One 2013; 8:e72958. [PMID: 23940820 PMCID: PMC3735525 DOI: 10.1371/journal.pone.0072958] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 07/22/2013] [Indexed: 12/20/2022] Open
Abstract
Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria (Thiomicrospira-like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin-Bassham-Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems.
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Pérez-Rodríguez I, Bohnert KA, Cuebas M, Keddis R, Vetriani C. Detection and phylogenetic analysis of the membrane-bound nitrate reductase (Nar) in pure cultures and microbial communities from deep-sea hydrothermal vents. FEMS Microbiol Ecol 2013; 86:256-67. [PMID: 23889124 DOI: 10.1111/1574-6941.12158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 05/17/2013] [Accepted: 06/04/2013] [Indexed: 11/28/2022] Open
Abstract
Over the past few years the relevance of nitrate respiration in microorganisms from deep-sea hydrothermal vents has become evident. In this study, we surveyed the membrane-bound nitrate reductase (Nar) encoding gene in three different deep-sea vent microbial communities from the East Pacific Rise and the Mid-Atlantic Ridge. Additionally, we tested pure cultures of vent strains for their ability to reduce nitrate and for the presence of the NarG-encoding gene in their genomes. By using the narG gene as a diagnostic marker for nitrate-reducing bacteria, we showed that nitrate reductases related to Gammaproteobacteria of the genus Marinobacter were numerically prevalent in the clone libraries derived from a black smoker and a diffuse flow vent. In contrast, NarG sequences retrieved from a community of filamentous bacteria located about 50 cm above a diffuse flow vent revealed the presence of a yet to be identified group of enzymes. 16S rRNA gene-inferred community compositions, in accordance with previous studies, showed a shift from Alpha- and Gammaproteobacteria to Epsilonproteobacteria as the vent fluids become warmer and more reducing. Based on these findings, we argue that Nar-catalyzed nitrate reduction is likely relevant in temperate and less reducing environments where Alpha- and Gammaproteobacteria are more abundant and where nitrate concentrations reflect that of background deep seawater.
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Affiliation(s)
- Ileana Pérez-Rodríguez
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
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47
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Campbell BJ, Polson SW, Zeigler Allen L, Williamson SJ, Lee CK, Wommack KE, Cary SC. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities. Front Microbiol 2013; 4:182. [PMID: 23898323 PMCID: PMC3721025 DOI: 10.3389/fmicb.2013.00182] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/17/2013] [Indexed: 02/01/2023] Open
Abstract
Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.
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Affiliation(s)
- Barbara J Campbell
- Department of Biological Sciences, Life Science Facility, Clemson University Clemson, SC, USA
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48
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Hanson TE, Campbell BJ, Kalis KM, Campbell MA, Klotz MG. Nitrate ammonification by Nautilia profundicola AmH: experimental evidence consistent with a free hydroxylamine intermediate. Front Microbiol 2013; 4:180. [PMID: 23847604 PMCID: PMC3701875 DOI: 10.3389/fmicb.2013.00180] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/15/2013] [Indexed: 11/13/2022] Open
Abstract
The process of nitrate reduction via nitrite controls the fate and bioavailability of mineral nitrogen within ecosystems; i.e., whether it is retained as ammonium (ammonification) or lost as nitrous oxide or dinitrogen (denitrification). Here, we present experimental evidence for a novel pathway of microbial nitrate reduction, the reverse hydroxylamine:ubiquinone reductase module (reverse-HURM) pathway. Instead of a classical ammonia-forming nitrite reductase that performs a 6 electron-transfer process, the pathway is thought to employ two catalytic redox modules operating in sequence: the reverse-HURM reducing nitrite to hydroxylamine followed by a hydroxylamine reductase that converts hydroxylamine to ammonium. Experiments were performed on Nautilia profundicola strain AmH, whose genome sequence led to the reverse-HURM pathway proposal. N. profundicola produced ammonium from nitrate, which was assimilated into biomass. Furthermore, genes encoding the catalysts of the reverse-HURM pathway were preferentially expressed during growth of N. profundicola on nitrate as an electron acceptor relative to cultures grown on polysulfide as an electron acceptor. Finally, nitrate-grown cells of N. profundicola were able to rapidly and stoichiometrically convert high concentrations of hydroxylamine to ammonium in resting cell assays. These experiments are consistent with the reverse-HURM pathway and a free hydroxylamine intermediate, but could not definitively exclude direct nitrite reduction to ammonium by the reverse-HURM with hydroxylamine as an off-pathway product. N. profundicola and related organisms are models for a new pathway of nitrate ammonification that may have global impact due to the wide distribution of these organisms in hypoxic environments and symbiotic or pathogenic associations with animal hosts.
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Affiliation(s)
- Thomas E Hanson
- School of Marine Science and Policy, University of Delaware Newark, DE, USA ; Delaware Biotechnology Institute, University of Delaware Newark, DE, USA
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van Wolferen M, Ajon M, Driessen AJM, Albers SV. How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions. Extremophiles 2013; 17:545-63. [PMID: 23712907 DOI: 10.1007/s00792-013-0552-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/12/2013] [Indexed: 01/24/2023]
Abstract
Transfer of DNA has been shown to be involved in genome evolution. In particular with respect to the adaptation of bacterial species to high temperatures, DNA transfer between the domains of bacteria and archaea seems to have played a major role. In addition, DNA exchange between similar species likely plays a role in repair of DNA via homologous recombination, a process that is crucial under DNA damaging conditions such as high temperatures. Several mechanisms for the transfer of DNA have been described in prokaryotes, emphasizing its general importance. However, until recently, not much was known about this process in prokaryotes growing in highly thermophilic environments. This review describes the different mechanisms of DNA transfer in hyperthermophiles, and how this may contribute to the survival and adaptation of hyperthermophilic archaea and bacteria to extreme environments.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
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50
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van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJCT, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SCM, Op den Camp HJM, Stunnenberg HG, Amann R, Kuypers MMM, Jetten MSM. The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol 2013; 15:1275-89. [PMID: 22568606 PMCID: PMC3655542 DOI: 10.1111/j.1462-2920.2012.02774.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 11/28/2022]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
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Affiliation(s)
- Jack van de Vossenberg
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Dagmar Woebken
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Wouter J Maalcke
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Nijmegen Centre for Mitochondrial Disorders, Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Bas E Dutilh
- CMBI, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Eva M Janssen-Megens
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Guus Roeselers
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jia Yan
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Daan Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jolein Gloerich
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Wim Geerts
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Erwin van der Biezen
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Wendy Pluk
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Kees-Jan Francoijs
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Lina Russ
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Phyllis Lam
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | | | | | - Suzanne C M Haaijer
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Henk G Stunnenberg
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Rudi Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of TechnologyDelft, the Netherlands
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