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Shi M, Li Q, Wang Y, He LS. The somatic genome of Eptatretus okinoseanus reveals the adaptation to deep-sea oligotrophic environment. BMC Genomics 2024; 25:807. [PMID: 39192189 DOI: 10.1186/s12864-024-10727-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 08/20/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Hagfishes are fascinating creatures that typically inhabit the deep sea. The deep sea is characterized by its lack of sunlight, primary productivity, and diminishing biomass with increasing ocean depth. Therefore, hagfishes living in this environment must develop effective survival strategies to adapt to the limited food supply. Deep-sea hagfishes have been observed to survive without food intake for up to one year. In this study, we have assembled a high-quality somatic genome of the deep-sea hagfish (Eptatretus okinoseanus) captured below 1,000 m. We compared the genome of E. okinoseanus with the genomes of inshore hagfish, lampreys, and other related species to investigate the genetic factors underlying the deep-sea hagfish adaptations to the environment. RESULTS The E. okinoseanus somatic genome was estimated to be 1.89 Gb and assembled into 17 pseudochromosomes. Phylogenetic analysis showed that shallow-sea and deep-sea hagfishes diverged approximately 58.8 million years ago. We found Perilipin gene family was significantly expanded in deep sea E. okinoseanus, which promotes triacylglycerol storage. Furthermore, a series of genes involved in fatty acid synthesis and metabolism, blood glucose regulation, and metabolic rate regulation were also expanded, rapid evolution or positive selection, and these changes contribute to their efficiency in energy utilization. Among these genes, the positively selected gene JNK may play an important role in energy metabolism. In addition, the olfactory receptors of the deep-sea hagfish were significantly expanded to 86, and three conserved motifs present only in hagfishes olfactory receptors were identified, which may facilitate the rapid localization of carrion. CONCLUSIONS This study provides valuable genomic resources for insights into the survival strategies of deep-sea hagfishes in oligotrophic environments.
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Affiliation(s)
- Mengke Shi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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2
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Yu Y, Liu NH, Teng ZJ, Chen Y, Wang P, Zhang YZ, Fu HH, Chen XL, Zhang YQ. Evidence for archaeal metabolism of D-amino acids in the deep marine sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174723. [PMID: 39002603 DOI: 10.1016/j.scitotenv.2024.174723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
The deep marine sediments represent a major repository of organic matter whilst hosting a great number of uncultivated microbes. Microbial metabolism plays a key role in the recycling of organic matter in the deep marine sediments. D-amino acids (DAAs) and DAA-containing muropeptides, an important group of organic matter in the deep marine sediments, are primarily derived from bacterial peptidoglycan decomposition. Archaea are abundant in the deep ocean microbiome, yet their role in DAA metabolism remains poorly studied. Here, we report bioinformatic investigation and enzymatic characterization of deep marine sedimentary archaea involved in DAA metabolism. Our analyses suggest that a variety of archaea, particularly the Candidatus Bathyarchaeota and the Candidatus Lokiarchaeaota, can metabolize DAAs. DAAs are converted into L-amino acids via amino acid racemases (Ala racemase, Asp racemase and broad substrate specificity amino acid racemase), and converted into α-keto acid via d-serine ammonia-lyase, whereas DAA-containing di-/tri-muropeptides can be hydrolyzed by peptidases (dipeptidase and D-aminopeptidase). Overall, this study reveals the identity and activity of deep marine sedimentary archaea involved in DAA metabolism, shedding light on the mineralization and biogeochemical cycling of DAAs in the deep marine sediments.
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Affiliation(s)
- Yang Yu
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Ning-Hua Liu
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Zhao-Jie Teng
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Yin Chen
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; School of Life Sciences, University of Warwick, Coventry, UK; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Hui-Hui Fu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Yu-Qiang Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China.
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3
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He S, Xie Y, Bai H, Peng Y, Jin Y. Numerical computation and experimental assessment of a pressure-retaining gas-tight sediment sampler. Sci Rep 2024; 14:14548. [PMID: 38914696 PMCID: PMC11196725 DOI: 10.1038/s41598-024-65588-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024] Open
Abstract
The pressure of the recovered sample is intricately connected to seawater temperature, the recovery velocity, and the pressure of the pre-charged gas. To better understand the sample pressure dynamics during the sampling recovery process, we focus on a gas-tight sediment sampler, delving into its pressure-compensation and pressure-retaining mechanisms. A comprehensive thermal and thermodynamic analysis is conducted throughout the entire pressure-retaining sampling process, examining the temporal variations in the temperatures of seawater and nitrogen within the sampler at various descending velocities. The heat transfer and thermodynamics are examined throughout the entire pressure-retaining sampling process to determine how changes in the temperatures of seawater and nitrogen, as well as the descent velocity, affect the pressure-retaining performance. The influence of pre-charging pressure and recovery velocities on the pressure-retaining performance of the sampler is examined. Then the proposed numerical model was well verified by the ultra-high-pressure vessel experiments of the sampler under 115 MPa. Finally, the sea trial results further verified the accuracy of the numerical model.
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Affiliation(s)
- Shudong He
- School of Intelligent Manufacturing and Mechanical Engineering, Hunan Institute of Technology, Hengyang, 421002, China.
| | - Yangbin Xie
- School of Intelligent Manufacturing and Mechanical Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Haocen Bai
- School of Intelligent Manufacturing and Mechanical Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Youduo Peng
- National-Local Joint Engineering Laboratory of Marine Resources Exploration Equipment and Safety Technology, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Yongping Jin
- National-Local Joint Engineering Laboratory of Marine Resources Exploration Equipment and Safety Technology, Hunan University of Science and Technology, Xiangtan, 411201, China
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4
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Meyer NR, Morono Y, Dekas AE. Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs. Appl Environ Microbiol 2024; 90:e0044624. [PMID: 38709099 PMCID: PMC11334695 DOI: 10.1128/aem.00446-24] [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: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The marine subsurface is a long-term sink of atmospheric carbon dioxide with significant implications for climate on geologic timescales. Subsurface microbial cells can either enhance or reduce carbon sequestration in the subsurface, depending on their metabolic lifestyle. However, the activity of subsurface microbes is rarely measured. Here, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to quantify anabolic activity in 3,203 individual cells from the thermally altered deep subsurface in the Guaymas Basin, Mexico (3-75 m below the seafloor, 0-14°C). We observed that a large majority of cells were active (83%-100%), although the rates of biomass generation were low, suggesting cellular maintenance rather than doubling. Mean single-cell activity decreased with increasing sediment depth and temperature and was most strongly correlated with porewater sulfate concentrations. Intracommunity heterogeneity in microbial activity decreased with increasing sediment depth and age. Using a dual-isotope labeling approach, we determined that all active cells analyzed were heterotrophic, deriving the majority of their cellular carbon from organic sources. However, we also detected inorganic carbon assimilation in these heterotrophic cells, likely via processes such as anaplerosis, and determined that inorganic carbon contributes at least 5% of the total biomass carbon in heterotrophs in this community. Our results demonstrate that the deep marine biosphere at Guaymas Basin is largely active and contributes to subsurface carbon cycling primarily by not only assimilating organic carbon but also fixing inorganic carbon. Heterotrophic assimilation of inorganic carbon may be a small yet significant and widespread underappreciated source of labile carbon in the global subsurface. IMPORTANCE The global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of microbial activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay, we found that the majority of cells are active, that activity is likely driven by the availability of energy, and that although heterotrophy is the dominant metabolism, both organic and inorganic carbon are used to generate biomass. Using a new approach, we quantified inorganic carbon assimilation by heterotrophs and highlighted the importance of this often-overlooked mode of carbon assimilation in the subsurface and beyond.
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Affiliation(s)
- Nicolette R. Meyer
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avantgarde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Anne E. Dekas
- Department of Earth System Science, Stanford University, Stanford, California, USA
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5
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Herlemann DPR, Tammert H, Kivistik C, Käiro K, Kisand V. Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water. Microbiologyopen 2024; 13:e13. [PMID: 38825966 PMCID: PMC11144953 DOI: 10.1002/mbo3.1413] [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: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 06/04/2024] Open
Abstract
The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.
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Affiliation(s)
- Daniel P. R. Herlemann
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Department of Biological OceanographyLeibniz Institute for Baltic Sea Research Warnemünde (IOW)RostockGermany
| | - Helen Tammert
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
| | - Carmen Kivistik
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Kairi Käiro
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Veljo Kisand
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
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6
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Zhu M, Dai X. Shaping of microbial phenotypes by trade-offs. Nat Commun 2024; 15:4238. [PMID: 38762599 PMCID: PMC11102524 DOI: 10.1038/s41467-024-48591-9] [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: 02/06/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024] Open
Abstract
Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.
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Affiliation(s)
- Manlu Zhu
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Xiongfeng Dai
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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7
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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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8
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Yadav P, Das J, Sundharam SS, Krishnamurthi S. Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach. Microorganisms 2024; 12:397. [PMID: 38399801 PMCID: PMC10892101 DOI: 10.3390/microorganisms12020397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.
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Affiliation(s)
- Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Shiva S. Sundharam
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
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9
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Zhu M, Mu H, Dai X. Integrated control of bacterial growth and stress response by (p)ppGpp in Escherichia coli: A seesaw fashion. iScience 2024; 27:108818. [PMID: 38299113 PMCID: PMC10828813 DOI: 10.1016/j.isci.2024.108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/02/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
To thrive in nature, bacteria have to reproduce efficiently under favorable conditions and persist during stress. The global strategy that integrates the growth control and stress response remains to be explored. Here, we find that a moderate induction of (p)ppGpp reduces growth rate but significantly enhances the stress tolerance of E. coli, resulting from a global resource re-allocation from ribosome synthesis to the synthesis of stress-responsive proteins. Strikingly, the activation of stress response by (p)ppGpp is still largely retained in the absence of RpoS. In addition, (p)ppGpp induction could activate the catabolism of alanine and arginine, facilitating the adaption of bacteria to nutrient downshift. Our work demonstrates that the activation of stress response by (p)ppGpp could occur in an RpoS-independent manner and (p)ppGpp enables bacteria to integrate the control of growth and stress response in a seesaw fashion, thus acting as an important global regulator of the bacterial fitness landscape.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Haoyan Mu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
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10
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Thorpe CL, Crawford R, Hand RJ, Radford JT, Corkhill CL, Pearce CI, Neeway JJ, Plymale AE, Kruger AA, Morris K, Boothman C, Lloyd JR. Microbial interactions with phosphorus containing glasses representative of vitrified radioactive waste. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132667. [PMID: 37839373 DOI: 10.1016/j.jhazmat.2023.132667] [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: 06/24/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023]
Abstract
The presence of phosphorus in borosilicate glass (at 0.1 - 1.3 mol% P2O5) and in iron-phosphate glass (at 53 mol% P2O5) stimulated the growth and metabolic activity of anaerobic bacteria in model systems. Dissolution of these phosphorus containing glasses was either inhibited or accelerated by microbial metabolic activity, depending on the solution chemistry and the glass composition. The breakdown of organic carbon to volatile fatty acids increased glass dissolution. The interaction of microbially reduced Fe(II) with phosphorus-containing glass under anoxic conditions decreased dissolution rates, whereas the interaction of Fe(III) with phosphorus-containing glass under oxic conditions increased glass dissolution. Phosphorus addition to borosilicate glasses did not significantly affect the microbial species present, however, the diversity of the microbial community was enhanced on the surface of the iron phosphate glass. Results demonstrate the potential for microbes to influence the geochemistry of radioactive waste disposal environments with implication for wasteform durability.
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Affiliation(s)
- C L Thorpe
- Immobilization Science Laboratory, Sir Robert Hadfield Building, University of Sheffield, S1 3JD, UK.
| | - R Crawford
- Immobilization Science Laboratory, Sir Robert Hadfield Building, University of Sheffield, S1 3JD, UK
| | - R J Hand
- Immobilization Science Laboratory, Sir Robert Hadfield Building, University of Sheffield, S1 3JD, UK
| | - J T Radford
- Immobilization Science Laboratory, Sir Robert Hadfield Building, University of Sheffield, S1 3JD, UK
| | - C L Corkhill
- Immobilization Science Laboratory, Sir Robert Hadfield Building, University of Sheffield, S1 3JD, UK; School of Earth Sciences, The University of Bristol, Bristol, UK
| | - C I Pearce
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - J J Neeway
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - A E Plymale
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - A A Kruger
- Office of River Protection, US Department of Energy, Richland, WA, USA
| | - K Morris
- Williamson Research Centre and Research Centre for Radwaste Disposal, Williamson Building, University of Manchester, 176 Oxford Road, M13 9PL, UK
| | - C Boothman
- Williamson Research Centre and Research Centre for Radwaste Disposal, Williamson Building, University of Manchester, 176 Oxford Road, M13 9PL, UK
| | - J R Lloyd
- Williamson Research Centre and Research Centre for Radwaste Disposal, Williamson Building, University of Manchester, 176 Oxford Road, M13 9PL, UK
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11
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Verrone V, Gupta A, Laloo AE, Dubey RK, Hamid NAA, Swarup S. Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167757. [PMID: 37852479 DOI: 10.1016/j.scitotenv.2023.167757] [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: 07/18/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.
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Affiliation(s)
- Valeria Verrone
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Abhishek Gupta
- Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore.
| | - Andrew Elohim Laloo
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore
| | - Rama Kant Dubey
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Nur Ashikin Abdul Hamid
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Sanjay Swarup
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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12
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Metze F, Vollmers J, Lenk F, Kaster AK. First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones. Front Microbiol 2023; 14:1241810. [PMID: 38053553 PMCID: PMC10694467 DOI: 10.3389/fmicb.2023.1241810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 10/03/2023] [Indexed: 12/07/2023] Open
Abstract
The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In this study, we present the first shotgun metagenomics study of unamplified DNA from sediment samples from different depths in this stratified environment. Bioinformatic analyses showed a shift from a heterotrophic, Chloroflexota-dominated community above the upper SMTZ to a chemolithoautotrophic Proteobacteria-dominated community below the secondary SMTZ. The reintroduction of sulfate likely enables respiration and boosts active cells that oxidize acetate, iron, and complex carbohydrates to degrade dead biomass in this low-abundance, low-diversity environment. In addition, analyses showed many proteins of unknown function as well as novel metagenome-assembled genomes (MAGs). The study provides new insights into microbial communities in this habitat, enabled by an improved DNA extraction protocol that allows a less biased view of taxonomic composition and metabolic activities, as well as uncovering novel taxa. Our approach presents the first successful attempt at unamplified shotgun sequencing samples from beyond 50 meters below the seafloor and opens new ways for capturing the true diversity and functional potential of deep-sea sediments.
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Affiliation(s)
| | | | | | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz, Karlsruhe, Germany
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Hao M, Wang M, Tang T, Zhao D, Yin S, Shi Y, Liu X, Wudong G, Yang Y, Zhang M, Qi L, Zhou D, Liu W, Jin Y, Wang A. Regulation of the Gene for Alanine Racemase Modulates Amino Acid Metabolism with Consequent Alterations in Cell Wall Properties and Adhesive Capability in Brucella spp. Int J Mol Sci 2023; 24:16145. [PMID: 38003334 PMCID: PMC10671322 DOI: 10.3390/ijms242216145] [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: 09/09/2023] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Brucella, a zoonotic facultative intracellular pathogenic bacterium, poses a significant threat both to human health and to the development of the livestock industry. Alanine racemase (Alr), the enzyme responsible for alanine racemization, plays a pivotal role in regulating virulence in this bacterium. Moreover, Brucella mutants with alr gene deletions (Δalr) exhibit potential as vaccine candidates. However, the mechanisms that underlie the detrimental effects of alr knockouts on Brucella pathogenicity remain elusive. Here, initially, we conducted a bioinformatics analysis of Alr, which demonstrated a high degree of conservation of the protein within Brucella spp. Subsequent metabolomics studies unveiled alterations in amino acid pathways following deletion of the alr gene. Furthermore, alr deletion in Brucella suis S2 induced decreased resistance to stress, antibiotics, and other factors. Transmission electron microscopy of simulated macrophage intracellular infection revealed damage to the cell wall in the Δalr strain, whereas propidium iodide staining and alkaline phosphatase and lactate dehydrogenase assays demonstrated alterations in cell membrane permeability. Changes in cell wall properties were revealed by measurements of cell surface hydrophobicity and zeta potential. Finally, the diminished adhesion capacity of the Δalr strain was shown by immunofluorescence and bacterial enumeration assays. In summary, our findings indicate that the alr gene that regulates amino acid metabolism in Brucella influences the properties of the cell wall, which modulates bacterial adherence capability. This study is the first demonstration that Alr impacts virulence by modulating bacterial metabolism, thereby providing novel insights into the pathogenic mechanisms of Brucella spp.
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Affiliation(s)
- Mingyue Hao
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Minghui Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Ting Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Danyu Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Shurong Yin
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yong Shi
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Xiaofang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Gaowa Wudong
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yuanhao Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Mengyu Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Lin Qi
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Dong Zhou
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Wei Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling District, Xianyang 712100, China; (M.H.); (M.W.); (T.T.); (D.Z.); (S.Y.); (Y.S.); (X.L.); (G.W.); (Y.Y.); (M.Z.); (L.Q.); (D.Z.); (W.L.); (Y.J.)
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Northwest A&F University, Yangling District, Xianyang 712100, China
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14
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Gusmão ACB, Peres FV, Paula FS, Pellizari VH, Kolm HE, Signori CN. Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean. Int Microbiol 2023; 26:1041-1051. [PMID: 37093322 DOI: 10.1007/s10123-023-00358-w] [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: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.
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Affiliation(s)
- Ana Carolina Bercini Gusmão
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil.
| | - Francielli Vilela Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Hedda Elisabeth Kolm
- Department of Oceanography, Center for Marine Studies, Federal University of Paraná, Pontal do Paraná, Brazil
| | - Camila Negrão Signori
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
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15
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Lu M, Luo X, Jiao JJ, Li H, Kuang X, Wang X, Feng Y, Zheng C. Uncovering the processes of microbial community assembly in the near-surface sediments of a climate-sensitive glacier-fed lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118714. [PMID: 37542806 DOI: 10.1016/j.jenvman.2023.118714] [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: 03/15/2023] [Revised: 07/09/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
Glacier-fed lakes are characterized by cold temperatures, high altitudes, and nutrient-poor conditions. Despite these challenging conditions, near-surface sediments of glacier-fed lakes harbor rich microbial communities that are critical for ecosystem functioning and serve as a bridge between aquatic ecology and the deep subsurface biosphere. However, there is limited knowledge regarding the microbial communities and their assembly processes in these sediments, which are highly vulnerable to climate change. To fill this knowledge gap, this study systematically analyzed environmental variables, microbial communities, diversity, co-occurrence relationships, and community assembly processes in the near-surface sediments of a glacier-fed lake in the Tibetan Plateau. The results revealed distinct vertical gradients in microbial diversity and subcommunities, highlighting the significant influence of selection processes and adaptive abilities on microbial communities. Specifically, specialists played a crucial role within the overall microbial communities. Microbial assembly was primarily driven by homogeneous selection, but its influence declined with increasing depth. In contrast, homogenizing dispersal showed an opposite pattern, and the bottom layer exhibited heterogeneous selection and undominated processes. These patterns of microbial assembly were primarily driven by environmental gradients, with significant contributions from processes associated to ammonium and organic matter deposition, as well as chemical precipitation in response to a warming climate. This study enhances our understanding of the microbial communities and assembly processes in the near-surface sediments of glacier-fed lakes and sheds light on geo-microbiological processes in climate-sensitive lacustrine sediments.
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Affiliation(s)
- Meiqing Lu
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin Luo
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China
| | - Jiu Jimmy Jiao
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, China.
| | - Hailong Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xingxing Kuang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuejing Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuqing Feng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chunmiao Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, 518055, China
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16
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Butterworth SJ, Barton F, Lloyd JR. Extremophilic microbial metabolism and radioactive waste disposal. Extremophiles 2023; 27:27. [PMID: 37839067 PMCID: PMC10577106 DOI: 10.1007/s00792-023-01312-4] [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: 03/02/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.
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Affiliation(s)
- Sarah Jane Butterworth
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK
| | - Franky Barton
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
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17
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Seto M, Kondoh M. Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity. Ecol Lett 2023; 26:1714-1725. [PMID: 37458207 DOI: 10.1111/ele.14287] [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: 01/30/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 10/19/2023]
Abstract
Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co-evolution of life and Earth.
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Affiliation(s)
- Mayumi Seto
- Department of Chemistry, Biology, and Environmental Sciences, Nara Women's University, Nara, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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18
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Zhu M, Wang Q, Mu H, Han F, Wang Y, Dai X. A fitness trade-off between growth and survival governed by Spo0A-mediated proteome allocation constraints in Bacillus subtilis. SCIENCE ADVANCES 2023; 9:eadg9733. [PMID: 37756393 PMCID: PMC10530083 DOI: 10.1126/sciadv.adg9733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Growth and survival are key determinants of bacterial fitness. However, how resource allocation of bacteria could reconcile these two traits to maximize fitness remains poorly understood. Here, we find that the resource allocation strategy of Bacillus subtilis does not lead to growth maximization on various carbon sources. Survival-related pathways impose strong proteome constraints on B. subtilis. Knockout of a master regulator gene, spo0A, triggers a global resource reallocation from survival-related pathways to biosynthesis pathways, further strongly stimulating the growth of B. subtilis. However, the fitness of spo0A-null strain is severely compromised because of various disadvantageous phenotypes (e.g., abolished sporulation and enhanced cell lysis). In particular, it also exhibits a strong defect in peptide utilization, being unable to efficiently recycle nutrients from the lysed cell debris to maintain long-term viability. Our work uncovers a fitness trade-off between growth and survival that governed by Spo0A-mediated proteome allocation constraints in B. subtilis, further shedding light on the fundamental design principle of bacteria.
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Affiliation(s)
| | | | | | - Fei Han
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei province, China
| | - Yanling Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei province, China
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19
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George AB, Wang T, Maslov S. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints. THE ISME JOURNAL 2023; 17:1482-1494. [PMID: 37380829 PMCID: PMC10432562 DOI: 10.1038/s41396-023-01455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.
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Affiliation(s)
- Ashish B George
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tong Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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20
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Kanaan G, Hoehler TM, Iwahana G, Deming JW. Modeled energetics of bacterial communities in ancient subzero brines. Front Microbiol 2023; 14:1206641. [PMID: 37564288 PMCID: PMC10411740 DOI: 10.3389/fmicb.2023.1206641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
Cryopeg brines are isolated volumes of hypersaline water in subzero permafrost. The cryopeg system at Utqiaġvik, Alaska, is estimated to date back to 40 ka BP or earlier, a remnant of a late Pleistocene Ocean. Surprisingly, the cryopeg brines contain high concentrations of organic carbon, including extracellular polysaccharides, and high densities of bacteria. How can these physiologically extreme, old, and geologically isolated systems support such an ecosystem? This study addresses this question by examining the energetics of the Utqiaġvik cryopeg brine ecosystem. Using literature-derived assumptions and new measurements on archived borehole materials, we first estimated the quantity of organic carbon when the system formed. We then considered two bacterial growth trajectories to calculate the lower and upper bounds of the cell-specific metabolic rate of these communities. These bounds represent the first community estimates of metabolic rate in a subzero hypersaline environment. To assess the plausibility of the different growth trajectories, we developed a model of the organic carbon cycle and applied it to three borehole scenarios. We also used dissolved inorganic carbon and nitrogen measurements to independently estimate the metabolic rate. The model reconstructs the growth trajectory of the microbial community and predicts the present-day cell density and organic carbon content. Model input included measured rates of the in-situ enzymatic conversion of particulate to dissolved organic carbon under subzero brine conditions. A sensitivity analysis of model parameters was performed, revealing an interplay between growth rate, cell-specific metabolic rate, and extracellular enzyme activity. This approach allowed us to identify plausible growth trajectories consistent with the observed bacterial densities in the cryopeg brines. We found that the cell-specific metabolic rate in this system is relatively high compared to marine sediments. We attribute this finding to the need to invest energy in the production of extracellular enzymes, for generating bioavailable carbon from particulate organic carbon, and the production of extracellular polysaccharides for cryoprotection and osmoprotection. These results may be relevant to other isolated systems in the polar regions of Earth and to possible ice-bound brines on worlds such as Europa, Enceladus, and Mars.
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Affiliation(s)
- Georges Kanaan
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, WA, United States
| | | | - Go Iwahana
- International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Jody W. Deming
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, WA, United States
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21
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Li H, Zhou H, Yang S, Dai X. Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities. Appl Environ Microbiol 2023; 89:e0070123. [PMID: 37404136 PMCID: PMC10370332 DOI: 10.1128/aem.00701-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023] Open
Abstract
Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.
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Affiliation(s)
- Haizhou Li
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Shanghai, China
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Shanshan Yang
- College of Marine Science and Technology, China University of Geosciences, Wuhan, Hubei, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institutes of Microbiology, Chinese Academy of Sciences, Beijing, China
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22
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Schubert F, Kallmeyer J. Liquid scintillation counting at the limit of detection in biogeosciences. Front Microbiol 2023; 14:1194848. [PMID: 37485520 PMCID: PMC10361571 DOI: 10.3389/fmicb.2023.1194848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
Liquid scintillation is widely used to quantify the activity of radioisotopes. We present an overview of the technique and its application to biogeosciences, particularly for turnover rate measurements. Microbial communities and their metabolism are notoriously difficult to analyze in low energy environments as biomass is exceedingly sparse and turnover rates low. Highly sensitive methods, such as liquid scintillation counting, are required to investigate low metabolic rates and conclusively differentiate them from the background noise of the respective analyzer. We conducted a series of experiments to explore the effects of luminescence, measurement time and temperature on scintillation measurements. Luminescence, the spontaneous emission of photons, disproportionally affects samples within the first few hours after sample preparation and can be minimized by following simple guidelines. Short measurement times will negatively affect liquid scintillation analysis or if background noise makes up a significant proportion of the detected events. Measurement temperature affected liquid scintillation analysis only when the temperature during the measurement reached approximately 30°C or higher, i.e. the liquid scintillation analyzer was placed in an environment without temperature control, but not in cases where chemicals were stored at elevated temperatures prior to measurement. Basic understanding on the functionality of a liquid scintillation analyzer and simple precautions prior to the measurement can significantly lower the minimum detection limit and therefore allow for determination of low turnover rates previously lost in the background noise.
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23
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Chen Y, Dai T, Li N, Li Q, Lyu Y, Di P, Lyu L, Zhang S, Li J. Environmental heterogeneity shapes the C and S cycling-associated microbial community in Haima's cold seeps. Front Microbiol 2023; 14:1199853. [PMID: 37502402 PMCID: PMC10370420 DOI: 10.3389/fmicb.2023.1199853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/07/2023] [Indexed: 07/29/2023] Open
Abstract
Environmental heterogeneity in cold seeps is usually reflected by different faunal aggregates. The sediment microbiome, especially the geochemical cycling-associated communities, sustains the ecosystem through chemosynthesis. To date, few studies have paid attention to the structuring and functioning of geochemical cycling-associated communities relating to environmental heterogeneity in different faunal aggregates of cold seeps. In this study, we profiled the microbial community of four faunal aggregates in the Haima cold seep, South China Sea. Through a combination of geochemical and meta-omics approaches, we have found that geochemical variables, such as sulfate and calcium, exhibited a significant variation between different aggregates, indicating changes in the methane flux. Anaerobic methanotrophic archaea (ANME), sulfate-reducing, and sulfide-oxidizing bacteria (SRB and SOB) dominated the microbial community but varied in composition among the four aggregates. The diversity of archaea and bacteria exhibited a strong correlation between sulfate, calcium, and silicate. Interspecies co-exclusion inferred by molecular ecological network analysis increased from non-seep to clam aggregates and peaked at the mussel aggregate. The networked geochemical cycling-associated species showed an obvious aggregate-specific distribution pattern. Notably, hydrocarbon oxidation and sulfate reduction by ANME and SRB produced carbonate and sulfide, driving the alkalization of the sediment environment, which may impact the microbial communities. Collectively, these results highlighted that geofluid and microbial metabolism together resulted in environmental heterogeneity, which shaped the C and S cycling-associated microbial community.
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Affiliation(s)
- Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Tianjiao Dai
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Niu Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Pengfei Di
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Jie Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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24
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Yue XL, Xu L, Cui L, Fu GY, Xu XW. Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean. Mar Genomics 2023; 70:101045. [PMID: 37245381 DOI: 10.1016/j.margen.2023.101045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.
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Affiliation(s)
- Xiao-Lan Yue
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China; Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Ge-Yi Fu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China; Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.
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25
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Yin Z, Zheng R, Li L, Xi S, Luan Z, Sun C, Zhang X. In situ Raman quantitative monitoring of methanogenesis: Culture experiments of a deep-sea cold seep methanogenic archaeon. Front Microbiol 2023; 14:1128064. [PMID: 37089553 PMCID: PMC10115991 DOI: 10.3389/fmicb.2023.1128064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Gas production from several metabolic pathways is a necessary process that accompanies the growth and central metabolism of some microorganisms. However, accurate and rapid nondestructive detection of gas production is still challenging. To this end, gas chromatography (GC) is primarily used, which requires sampling and sample preparation. Furthermore, GC is expensive and difficult to operate. Several researchers working on microbial gases are looking forward to a new method to accurately capture the gas trends within a closed system in real-time. In this study, we developed a precise quantitative analysis for headspace gas in Hungate tubes using Raman spectroscopy. This method requires only a controlled focus on the gas portion inside Hungate tubes, enabling nondestructive, real-time, continuous monitoring without the need for sampling. The peak area ratio was selected to establish a calibration curve with nine different CH4–N2 gaseous mixtures and a linear relationship was observed between the peak area ratio of methane to nitrogen and their molar ratios (A(CH4)/A(N2) = 6.0739 × n(CH4)/n(N2)). The results of in situ quantitative analysis using Raman spectroscopy showed good agreement with those of GC in the continuous monitoring of culture experiments of a deep-sea cold seep methanogenic archaeon. This method significantly improves the detection efficiency and shows great potential for in situ quantitative gas detection in microbiology. It can be a powerful complementary tool to GC.
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Affiliation(s)
- Ziyu Yin
- CAS Key Laboratory of Marine Geology and Environment and CAS Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology and Laboratory for Marine Biology and Biotechnology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rikuan Zheng
- CAS Key Laboratory of Marine Geology and Environment and CAS Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology and Laboratory for Marine Biology and Biotechnology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
| | - Lianfu Li
- CAS Key Laboratory of Marine Geology and Environment and CAS Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology and Laboratory for Marine Biology and Biotechnology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
| | - Shichuan Xi
- CAS Key Laboratory of Marine Geology and Environment and CAS Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology and Laboratory for Marine Biology and Biotechnology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhendong Luan
- CAS Key Laboratory of Marine Geology and Environment and CAS Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology and Laboratory for Marine Biology and Biotechnology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chaomin Sun
- CAS Key Laboratory of Marine Geology and Environment and CAS Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology and Laboratory for Marine Biology and Biotechnology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhang
- CAS Key Laboratory of Marine Geology and Environment and CAS Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Geology and Laboratory for Marine Biology and Biotechnology, Pilot Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Xin Zhang,
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26
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Cai L, Weinbauer MG, Xie L, Zhang R. The smallest in the deepest: the enigmatic role of viruses in the deep biosphere. Natl Sci Rev 2023; 10:nwad009. [PMID: 36960220 PMCID: PMC10029852 DOI: 10.1093/nsr/nwad009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
It is commonly recognized that viruses control the composition, metabolism, and evolutionary trajectories of prokaryotic communities, with resulting vital feedback on ecosystem functioning and nutrient cycling in a wide range of ecosystems. Although the deep biosphere has been estimated to be the largest reservoir for viruses and their prokaryotic hosts, the biology and ecology of viruses therein remain poorly understood. The deep virosphere is an enigmatic field of study in which many critical questions are still to be answered. Is the deep virosphere simply a repository for deeply preserved, non-functioning virus particles? Or are deep viruses infectious agents that can readily infect suitable hosts and subsequently shape microbial populations and nutrient cycling? Can the cellular content released by viral lysis, and even the organic structures of virions themselves, serve as the source of bioavailable nutrients for microbial activity in the deep biosphere as in other ecosystems? In this review, we synthesize our current knowledge of viruses in the deep biosphere and seek to identify topics with the potential for substantial discoveries in the future.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Markus G Weinbauer
- Sorbonne Universités, UPMC, Université Paris 06, CNRS, Laboratoire d’Océanographie de Villefranche (LOV), Villefranche BP28, France
| | - Le Xie
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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27
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Zhang C, Liu X, Shi LD, Li J, Xiao X, Shao Z, Dong X. Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments. NPJ Biofilms Microbiomes 2023; 9:13. [PMID: 36991068 PMCID: PMC10060404 DOI: 10.1038/s41522-023-00382-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.
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Affiliation(s)
- Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xi Xiao
- Key Laboratory of Marine Mineral Resources, Ministry of Natural Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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28
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Lyu L, Fang K, Zhu Z, Li J, Chen Y, Wang L, Mai Z, Li Q, Zhang S. Bioaccumulation of emerging persistent organic pollutants in the deep-sea cold seep ecosystems: Evidence from chlorinated paraffin. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130472. [PMID: 36455324 DOI: 10.1016/j.jhazmat.2022.130472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Persistent organic pollutants (POPs) are highly toxic and can accumulate in marine organisms, causing nonnegligible harm to the global marine ecosystem. The Cold seep is an essential marine ecosystem with the critical ecological function of maintaining the deep-sea carbon cycle and buffering global climate change. However, the environmental impact of emerging POPs in the deep-sea cold seep ecosystem is unknown. Here, we investigated the potential pollution of chlorinated paraffins (CPs) and their bioaccumulation in the cold seep ecosystem. High concentrations of CPs were detected in the cold seep ecosystems, where CPs bioaccumulated by the keystone species of deep-sea mussels can be released into the surface sediment and vertically migrate into the deeper sediment. Furthermore, more toxic CPs were accumulated from transforming other CPs in the cold seep ecosystem. Our study provides the first evidence that high concentrations of POPs are bioaccumulated by deep-sea mussels in the cold seep ecosystem, causing adverse ecological effects. The discovery of CPs bioaccumulation in the deep-sea cold seep ecosystem is a crucial mechanism affecting deep-sea carbon transport and cycling. This study has important guiding significance for revealing the deep-sea carbon cycle process, addressing global climate change, and making deep-sea ecological and environmental protection policies.
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Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, Guangdong, China
| | - Kejing Fang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, Guangdong, China
| | - Zhenchang Zhu
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, Guangdong, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, Guangdong, China
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, Guangdong, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, Guangdong, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, Guangdong, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, Guangdong, China.
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29
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Zhang C, Fang YX, Yin X, Lai H, Kuang Z, Zhang T, Xu XP, Wegener G, Wang JH, Dong X. The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules. MICROBIOME 2023; 11:37. [PMID: 36864529 PMCID: PMC9979476 DOI: 10.1186/s40168-023-01482-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/30/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization. RESULTS Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons. CONCLUSIONS These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yun-Xin Fang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hongfei Lai
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Zenggui Kuang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Tianxueyu Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Xiang-Po Xu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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30
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Zhu M, Dai X. Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift. Nat Commun 2023; 14:467. [PMID: 36709335 PMCID: PMC9884231 DOI: 10.1038/s41467-023-36254-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/20/2023] [Indexed: 01/30/2023] Open
Abstract
Timely adaptation to nutrient downshift is crucial for bacteria to maintain fitness during feast and famine cycle in the natural niche. However, the molecular mechanism that ensures the timely adaption of bacterial growth to nutrient downshift remains poorly understood. Here, we quantitatively investigated the adaptation of Escherichia coli to various kinds of nutrient downshift. We found that relA deficient strain, which is devoid of stringent response, exhibits a significantly longer growth lag than wild type strain during adapting to both amino acid downshift and carbon downshift. Quantitative proteomics show that increased (p)ppGpp level promotes the growth adaption of bacteria to amino acid downshift via triggering the proteome resource re-allocation from ribosome synthesis to amino acid biosynthesis. Such type of proteome re-allocation is significantly delayed in the relA-deficient strain, which underlies its longer lag than wild type strain during amino acid downshift. During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. Our studies shed light on the fundamental strategy of bacteria to maintain fitness under nutrient-fluctuating environments.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China.
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Bioactivity and Metabolome Mining of Deep-Sea Sediment-Derived Microorganisms Reveal New Hybrid PKS-NRPS Macrolactone from Aspergillus versicolor PS108-62. Mar Drugs 2023; 21:md21020095. [PMID: 36827136 PMCID: PMC9961484 DOI: 10.3390/md21020095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Despite low temperatures, poor nutrient levels and high pressure, microorganisms thrive in deep-sea environments of polar regions. The adaptability to such extreme environments renders deep-sea microorganisms an encouraging source of novel, bioactive secondary metabolites. In this study, we isolated 77 microorganisms collected by a remotely operated vehicle from the seafloor in the Fram Strait, Arctic Ocean (depth of 2454 m). Thirty-two bacteria and six fungal strains that represented the phylogenetic diversity of the isolates were cultured using an One-Strain-Many-Compounds (OSMAC) approach. The crude EtOAc extracts were tested for antimicrobial and anticancer activities. While antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium was common for many isolates, only two bacteria displayed anticancer activity, and two fungi inhibited the pathogenic yeast Candida albicans. Due to bioactivity against C. albicans and rich chemical diversity based on molecular network-based untargeted metabolomics, Aspergillus versicolor PS108-62 was selected for an in-depth chemical investigation. A chemical work-up of the SPE-fractions of its dichloromethane subextract led to the isolation of a new PKS-NRPS hybrid macrolactone, versicolide A (1), a new quinazoline (-)-isoversicomide A (3), as well as three known compounds, burnettramic acid A (2), cyclopenol (4) and cyclopenin (5). Their structures were elucidated by a combination of HRMS, NMR, [α]D, FT-IR spectroscopy and computational approaches. Due to the low amounts obtained, only compounds 2 and 4 could be tested for bioactivity, with 2 inhibiting the growth of C. albicans (IC50 7.2 µg/mL). These findings highlight, on the one hand, the vast potential of the genus Aspergillus to produce novel chemistry, particularly from underexplored ecological niches such as the Arctic deep sea, and on the other, the importance of untargeted metabolomics for selection of marine extracts for downstream chemical investigations.
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Chen J, Zeng H, Lv W, Sun N, Wang C, Xu W, Hu M, Gan X, He L, He S, Fang C. Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2251-8. [PMID: 36648612 DOI: 10.1007/s11427-022-2251-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 01/18/2023]
Abstract
High hydrostatic pressure, low temperature, and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments. Here, we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel (MAE, Ilyophis brunneus, captured below a depth of 3,500 m) by using Illumina, PacBio, and Hi-C sequencing. We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes. The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes. Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species, European eel, ∼111.9 Mya and experienced a rapid evolution. The genome evolutionary analyses primarily revealed the following: (i) under high hydrostatic pressure, the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability; ACOX1 may enhance the fluidity of cell membrane and maintain transport activity; the expansion of ABCC12 gene family may enhance the integrity of DNA; (ii) positively selected HARS likely maintain the transcription ability at low temperatures; and (iii) energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and mTOR signaling pathways.
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Affiliation(s)
- Jie Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Xu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingliang Hu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lisheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Chengchi Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Sangodkar N, Gonsalves MJ, Nazareth DR. Macrofaunal Distribution, Diversity, and Its Ecological Interaction at the Cold Seep Site of Krishna-Godavari Basin, East Coast of India. MICROBIAL ECOLOGY 2023; 85:61-75. [PMID: 34982193 DOI: 10.1007/s00248-021-01942-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Cold seeps are characterized by typical endemic communities with associated microorganisms that depend on sulfide, methane, reduced nitrogenous compounds, and metals as electron donors for their survival through chemosynthesis. The discovery of an active cold seep site in January 2018 in the Krishna-Godavari (K-G) basin of Bay of Bengal was followed by a transit cruise in March 2018 to investigate the distribution and diversity of macrofauna. Further, the ambient sediment and pore water biochemistry were estimated to understand its relationship with macrofauna and the microbial associates of the sediment. Samples were collected at a water depth of around 1750 m at 3 stations: SP1, SP2, and SP3, using the box corer. The benthic fauna at the sites consisted mainly of Bivalvia, shrimps of Caridea family, Gastropoda species, Malacostraca species, Polychaeta, and few species of Echinoidea, Ophiuroidea, and Echiura. A total of 2313 macrofaunal individuals belonging to 8 classes, 18 families, and 20 species were identified from all the three stations. The communities were diverse at these sites with an average Shannon diversity index of 1.64 and are closely related to the lineages previously studied in ecologically similar environments. Most of the macrofauna were found to be filter feeders preferring a low organic carbon environment. Relict vesicomyid clams at the present study site suggest the succession from vesicomyids to the present composition of bivalve mussels and siboglinid worms. The microbial associates in the sediment significantly correlated with methane and hydrogen sulfide concentrations. The study suggests that the K-G basin cold seep serves as a conducive environment for the flourishing of benthic communities and therefore can support a rich biodiversity.
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Affiliation(s)
- Nitisha Sangodkar
- Aqua-Geomicrobiology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau, Goa, 403 001, India
| | - Maria Judith Gonsalves
- Aqua-Geomicrobiology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India.
| | - Delcy R Nazareth
- Aqua-Geomicrobiology Laboratory, Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
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Jiang Q, Jing H, Liu H, Du M. Biogeographic distributions of microbial communities associated with anaerobic methane oxidation in the surface sediments of deep-sea cold seeps in the South China Sea. Front Microbiol 2022; 13:1060206. [PMID: 36620029 PMCID: PMC9822730 DOI: 10.3389/fmicb.2022.1060206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Cold seeps are oasis for the microbes in the deep-sea ecosystems, and various cold seeps are located along the northern slope of the South China Sea (SCS). However, by far most microbial ecological studies were limited to specific cold seep in the SCS, and lack of comparison between different regions. Here, the surface sediments (0-4 cm) from the Site F/Haima cold seeps and the Xisha trough in the SCS were used to elucidate the biogeography of microbial communities, with particular interest in the typical functional groups involved in the anaerobic oxidation of methane (AOM) process. Distinct microbial clusters corresponding to the three sampling regions were formed, and significantly higher gene abundance of functional groups were present in the cold seeps than the trough. This biogeographical distribution could be explained by the geochemical characteristics of sediments, such as total nitrogen (TN), total phosphorus (TP), nitrate (NO3 -), total sulfur (TS) and carbon to nitrogen ratios (C/N). Phylogenetic analysis demonstrated that mcrA and pmoA genotypes were closely affiliated with those from wetland and mangroves, where denitrifying anaerobic methane oxidation (DAMO) process frequently occurred; and highly diversified dsrB genotypes were revealed as well. In addition, significantly higher relative abundance of NC10 group was found in the Xisha trough, suggesting that nitrite-dependent DAMO (N-DAMO) process was more important in the hydrate-bearing trough, although its potential ecological contribution to AOM deserves further investigation. Our study also further demonstrated the necessity of combining functional genes and 16S rRNA gene to obtain a comprehensive picture of the population shifts of natural microbial communities among different oceanic regions.
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Affiliation(s)
- Qiuyun Jiang
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,*Correspondence: Hongmei Jing,
| | - Hao Liu
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mengran Du
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas. mSystems 2022; 7:e0086422. [PMID: 36342154 PMCID: PMC9765461 DOI: 10.1128/msystems.00864-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on a global scale. Microorganisms play an important role in mineralizing them therein, but these are yet to be identified in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found that members of the family Marinifilaceae (MF) occurred as some of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea in both marginal and oceanic areas. This taxon is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups in the phylogenomic tree. Based on metagenomic and metatranscriptomic analyses, we described the metabolic features and in situ metabolizing activities of different subgroups. The MF-2 subgroup, which dominates plant detritus-enriched cultures, specializes in polysaccharide degradation and lignin oxidation and has high transcriptional activities of related genes in situ. Intriguingly, members of this subgroup encode a nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, other subgroups dominating the animal tissue-supported microbiomes are distinguished from MF-2 with regard to carbon and nitrogen metabolism and exhibit high transcriptional activity for proteolysis in situ. Despite these metabolic divergences of MF lineages, they show high in situ transcriptional activities for organic fermentation and anaerobic respiration (reductions of metal and/or dimethyl sulfoxide). These results highlight the role of previously unrecognized Marinifilaceae bacteria in organic matter mineralization in marine environments by coupling carbon and nitrogen cycling with metal and sulfur. IMPORTANCE Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated. It was the dominant taxon thriving on plant and animal biomasses in our in situ incubator, as well as in whale falls and wood falls. At least 9 subgroups were revealed, and they were widely distributed in oceans globally but predominant in organic-matter-rich environments, with an average relative abundance of 8.3%. Different subgroups display a preference for the degradation of different macromolecules (polysaccharides, lignin, and protein) and adapt to their environments via special metabolic mechanisms.
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Mu H, Han F, Wang Q, Wang Y, Dai X, Zhu M. Recent functional insights into the magic role of (p)ppGpp in growth control. Comput Struct Biotechnol J 2022; 21:168-175. [PMID: 36544478 PMCID: PMC9747358 DOI: 10.1016/j.csbj.2022.11.063] [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] [Received: 10/14/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Rapid growth and survival are two key traits that enable bacterial cells to thrive in their natural habitat. The guanosine tetraphosphate and pentaphosphate [(p)ppGpp], also known as "magic spot", is a key second messenger inside bacterial cells as well as chloroplasts of plants and green algae. (p)ppGpp not only controls various stages of central dogma processes (replication, transcription, ribosome maturation and translation) and central metabolism but also regulates various physiological processes such as pathogenesis, persistence, motility and competence. Under extreme conditions such as nutrient starvation, (p)ppGpp-mediated stringent response is crucial for the survival of bacterial cells. This mini-review highlights some of the very recent progress on the key role of (p)ppGpp in bacterial growth control in light of cellular resource allocation and cell size regulation. We also briefly discuss some recent functional insights into the role of (p)ppGpp in plants and green algae from the angle of growth and development and further discuss several important open directions for future studies.
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Affiliation(s)
| | | | - Qian Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Yanling Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
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37
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Imachi H, Nobu MK, Miyazaki M, Tasumi E, Saito Y, Sakai S, Ogawara M, Ohashi A, Takai K. Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study. Nat Protoc 2022; 17:2784-2814. [PMID: 36104596 DOI: 10.1038/s41596-022-00735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022]
Abstract
In microbiology, cultivation is a central approach for uncovering novel physiology, ecology, and evolution of microorganisms, but conventional methods have left many microorganisms found in nature uncultured. To overcome the limitations of traditional methods and culture indigenous microorganisms, we applied a two-stage approach: enrichment/activation of indigenous organisms by using a continuous-flow down-flow hanging sponge bioreactor and subsequent selective batch cultivation. Here, we provide a protocol for this bioreactor-mediated technique using activation of deep marine sediment microorganisms and downstream isolation of a syntrophic co-culture containing an archaeon closely related to the eukaryote ancestor (Candidatus Promethearchaeum syntrophicum strain MK-D1) as an example. Both stages can easily be tailored to target other environments and organisms by modifying the inoculum, feed solution/gases, attachment material and/or cultivation media. We anaerobically incubate polyurethane sponges inoculated with deep-sea methane seep sediment in a reactor at 10 °C and feed anaerobic artificial seawater medium and methane. Once phylogenetically diverse and metabolically active microorganisms are adapted to synthetic conditions in the reactor, we transition to growing community samples in glass tubes with the above medium, simple substrates and selective compounds (e.g., antibiotics). To accommodate for the slow growth anticipated for target organisms, primary cultures can be incubated for ≥6-12 months and analyzed for community composition even when no cell turbidity is observed. One casamino acid- and antibiotic-amended culture prepared in this way led to the enrichment of uncultured archaea. Through successive transfer in vitro combined with molecular growth monitoring, we successfully obtained the target archaeon with its partner methanogen as a pure syntrophic co-culture.
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Affiliation(s)
- Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
| | - Eiji Tasumi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yumi Saito
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sanae Sakai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Miyuki Ogawara
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, Okazaki, Japan
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Kokoulin MS, Dmitrenok PS, Romanenko LA. Structure of the Lipooligosaccharide from the Deep-Sea Marine Bacterium Idiomarina zobellii KMM 231 T, Isolated at a Depth of 4000 Meters. Mar Drugs 2022; 20:700. [PMID: 36355023 PMCID: PMC9695755 DOI: 10.3390/md20110700] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/06/2022] [Accepted: 11/06/2022] [Indexed: 05/31/2024] Open
Abstract
The structural characterization of lipopolysaccharides has critical implications for some biomedical applications, and marine bacteria are an inimitable source of new glyco-structures potentially usable in medicinal chemistry. On the other hand, lipopolysaccharides of marine Gram-negative bacteria present certain structural features that can help the understanding of the adaptation processes. The deep-sea marine Gram-negative bacterium Idiomarina zobellii KMM 231T, isolated from a seawater sample taken at a depth of 4000 m, represents an engaging microorganism to investigate in terms of its cell wall components. Here, we report the structural study of the R-type lipopolysaccharide isolated from I. zobellii KMM 231T that was achieved through a multidisciplinary approach comprising chemical analyses, NMR spectroscopy, and MALDI mass spectrometry. The lipooligosaccharide turned out to be characterized by a novel and unique pentasaccharide skeleton containing a very short mono-phosphorylated core region and comprising terminal neuraminic acid. The lipid A was revealed to be composed of a classical disaccharide backbone decorated by two phosphate groups and acylated by i13:0(3-OH) in amide linkage, i11:0 (3-OH) as primary ester-linked fatty acids, and i11:0 as a secondary acyl chain.
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Affiliation(s)
- Maxim S. Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159/2, Prospect 100 let Vladivostoku, Vladivostok 690022, Russia
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Yoshida-Takashima Y, Takaki Y, Yoshida M, Zhang Y, Nunoura T, Takai K. Genomic insights into phage-host interaction in the deep-sea chemolithoautotrophic Campylobacterota, Nitratiruptor. ISME COMMUNICATIONS 2022; 2:108. [PMID: 37938718 PMCID: PMC9723563 DOI: 10.1038/s43705-022-00194-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023]
Abstract
The genus Nitratiruptor represents one of the most numerically abundant chemolithoautotrophic Campylobacterota populations in the mixing zones of habitats between hydrothermal fluids and ambient seawater in deep-sea hydrothermal environments. We isolated and characterized four novel temperate phages (NrS-2, NrS-3, NrS-4, and NrS-5) having a siphoviral morphology, infecting Nitratiruptor strains from the Hatoma Knoll hydrothermal field in the southern-Okinawa Trough, Japan, and conducted comparative genomic analyses among Nitratiruptor strains and their phages. The Nitratiruptor temperate phages shared many potential core genes (e.g., integrase, Cro, two structural proteins, lysozyme, and MazG) with each other despite their diverse morphological and genetic features. Some homologs of coding sequences (CDSs) of the temperate phages were dispersed throughout the non-prophage regions of the Nitratiruptor genomes. In addition, several regions of the phage genome sequences matched to spacer sequences within clustered regularly interspaced short palindromic repeats (CRISPR) in Nitratiruptor genomes. Moreover, a restriction-modification system found in a temperate phage affected an epigenetic feature of its host. These results strongly suggested a coevolution of temperate phages and their host genomes via the acquisition of temperate phages, the CRISPR systems, the nucleotide substitution, and the epigenetic regulation during multiple phage infections in the deep-sea environments.
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Affiliation(s)
- Yukari Yoshida-Takashima
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mitsuhiro Yoshida
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yi Zhang
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takuro Nunoura
- Deep-Sea Bioresource Research Group, Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Wietz M, Metfies K, Bienhold C, Wolf C, Janssen F, Salter I, Boetius A. Impact of preservation method and storage period on ribosomal metabarcoding of marine microbes: Implications for remote automated samplings. Front Microbiol 2022; 13:999925. [PMID: 36160263 PMCID: PMC9490091 DOI: 10.3389/fmicb.2022.999925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Automated sampling technologies can enhance the temporal and spatial resolution of marine microbial observations, particularly in remote and inaccessible areas. A critical aspect of automated microbiome sampling is the preservation of nucleic acids over long-term autosampler deployments. Understanding the impact of preservation method on microbial metabarcoding is essential for implementing genomic observatories into existing infrastructure, and for establishing best practices for the regional and global synthesis of data. The present study evaluates the effect of two preservatives commonly used in autosampler deployments (mercuric chloride and formalin) and two extraction kits (PowerWater and NucleoSpin) on amplicon sequencing of 16S and 18S rRNA gene over 50 weeks of sample storage. Our results suggest the combination of mercuric chloride preservation and PowerWater extraction as most adequate for 16S and 18S rRNA gene amplicon-sequencing from the same seawater sample. This approach provides consistent information on species richness, diversity and community composition in comparison to control samples (nonfixed, filtered and frozen) when stored up to 50 weeks at in situ temperature. Preservation affects the recovery of certain taxa, with specific OTUs becoming overrepresented (SAR11 and diatoms) or underrepresented (Colwellia and pico-eukaryotes) after preservation. In case eukaryotic sequence information is the sole target, formalin preservation and NucleoSpin extraction performed best. Our study contributes to the design of long-term autonomous microbial observations in remote ocean areas, allowing cross-comparison of microbiome dynamics across sampling devices (e.g., water and particle samplers) and marine realms.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christian Wolf
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Felix Janssen
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Torshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations. mSystems 2022; 7:e0058822. [PMID: 35950761 PMCID: PMC9426432 DOI: 10.1128/msystems.00588-22] [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: 12/24/2022] Open
Abstract
Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (ΔrG'), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism's ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.
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Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps. mSystems 2022; 7:e0032022. [PMID: 35938718 PMCID: PMC9426478 DOI: 10.1128/msystems.00320-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.
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Pither MD, Sun ML, Speciale I, Silipo A, Zhang YZ, Molinaro A, Di Lorenzo F. Structural determination of the lipid A from the deep-sea bacterium Zunongwangia profunda SM-A87: a small-scale approach. Glycoconj J 2022; 39:565-578. [PMID: 35930130 PMCID: PMC9470727 DOI: 10.1007/s10719-022-10076-6] [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] [Received: 05/30/2022] [Revised: 07/04/2022] [Accepted: 07/09/2022] [Indexed: 11/10/2022]
Abstract
Zunongwangia profunda SM-A87 is a deep-sea sedimentary bacterium from the phylum Bacteroidetes, representing a new genus of Flavobacteriaceae. It was previously investigated for its capability of yielding high quantities of capsular polysaccharides (CPS) with interesting rheological properties, including high viscosity and tolerance to high salinities and temperatures. However, as a Gram-negative, Z. profunda SM-A87 also expresses lipopolysaccharides (LPS) as the main components of the external leaflet of its outer membrane. Here, we describe the isolation and characterization of the glycolipid part of this LPS, i.e. the lipid A, which was achieved by-passing the extraction procedure of the full LPS and by working on the ethanol precipitation product, which contained both the CPS fraction and bacterial cells. To this aim a dual approach was adopted and all analyses confirmed the isolation of Z. profunda SM-A87 lipid A that turned out to be a blend of species with high levels of heterogeneity both in the acylation and phosphorylation pattern, as well as in the hydrophilic backbone composition. Mono-phosphorylated tetra- and penta-acylated lipid A species were identified and characterized by a high content of branched, odd-numbered, and unsaturated fatty acid chains as well as, for some species, by the presence of a hybrid disaccharide backbone.
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Affiliation(s)
- Molly Dorothy Pither
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 80126, Naples, Italy
| | - Mei-Ling Sun
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Immacolata Speciale
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 80055, Portici, Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 80126, Naples, Italy
| | - Yu-Zhong Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, People's Republic of China
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia, 80126, Naples, Italy
| | - Flaviana Di Lorenzo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università, 80055, Portici, Naples, Italy.
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Chan J, Geng D, Pan B, Zhang Q, Xu Q. Gut Microbial Divergence Between Three Hadal Amphipod Species from the Isolated Hadal Trenches. MICROBIAL ECOLOGY 2022; 84:627-637. [PMID: 34545412 DOI: 10.1007/s00248-021-01851-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Amphipods are the dominant scavenging metazoan species in the hadal trenches at water depths below 6,000 m. The gut microbiota have been considered to be contribution to the adaptation of deep-sea organisms; however, few comparative analyses of animal gut microbiota between different isolated hadal environments have been done so far. Here, we employed high-throughput 16S rRNA sequencing to compare the gut microbial taxonomic composition and functional potential diversity of three hadal amphipod species, Hirondellea gigas, Bathycallisoma schellenbergi, and Alicella gigantea, collected from the Mariana Trench, Marceau Trench, and New Britain Trench in the Pacific Ocean, respectively. Results showed that different community compositions were detected across all the amphipod specimens based on the analyses of alpha-diversity, hierarchical cluster tree, and PCoA (principal coordinate analysis). Moreover, almost no correlation was observed between genera overrepresented in different amphipods by microbe-microbe correlations analysis, which suggested that the colonization of symbionts were host-specific. At genus level, Psychromonas was dominant in H. gigas, and Candidatus Hepatoplasma was overall dominant in A. gigantea and B. schellenbergi. Comparison of the functional potential showed that, though three hadal amphipod species shared the same predominant functional pathways, the abundances of those most shared pathways showed distinct differences across all the specimens. These findings pointed to the enrichment of particular functional pathways in the gut microbiota of the different isolated trench amphipods. Moreover, in terms of species relative abundance, alpha-diversity and beta-diversity, there was high similarity of gut microbiota between the two A. gigantea populations, which dwelled in two different localities of the same hadal trench. Altogether, this study provides an initial investigation into the gut-microbial interactions and evolution at the hadal depths within amphipod. Each of these three amphipod species would be a model taxa for future studies investigating the influence habitat difference and geography on gut-microbial communities.
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Affiliation(s)
- Jiulin Chan
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Daoqiang Geng
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China
| | - Qiming Zhang
- Shanghai Rainbowfish Ocean Technology Co., Ltd., Lingang New City, Shanghai, 201306, People's Republic of China
| | - Qianghua Xu
- Shanghai Engineering Research Center of Hadal Science & Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China.
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Lingang New City, Shanghai, 201306, People's Republic of China.
- National Distant-water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, 201306, People's Republic of China.
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McClain CR, Bryant SR, Hanks G, Bowles MW. Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans. ASTROBIOLOGY 2022; 22:1009-1028. [PMID: 35549348 DOI: 10.1089/ast.2021.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.
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Affiliation(s)
- Craig R McClain
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - S River Bryant
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Granger Hanks
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
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Jing H, Xiao X, Zhang Y, Li Z, Jian H, Luo Y, Han Z. Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench. Microbiol Spectr 2022; 10:e0198821. [PMID: 35768947 PMCID: PMC9241748 DOI: 10.1128/spectrum.01988-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/28/2022] [Indexed: 11/20/2022] Open
Abstract
The unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis. IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.
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Affiliation(s)
- Hongmei Jing
- Chinese Academy of Sciences (CAS) Key Laboratory for Experimental Study under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory, ZhuHai, China
- Hong Kong University of Science and Technology (HKUST)-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Xiang Xiao
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory for Experimental Study under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yingfeng Luo
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhuang Han
- Chinese Academy of Sciences (CAS) Key Laboratory for Experimental Study under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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47
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Cario A, Larzillière M, Nguyen O, Alain K, Marre S. High-Pressure Microfluidics for Ultra-Fast Microbial Phenotyping. Front Microbiol 2022; 13:866681. [PMID: 35677901 PMCID: PMC9168469 DOI: 10.3389/fmicb.2022.866681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023] Open
Abstract
Here, we present a novel methodology based on high-pressure microfluidics to rapidly perform temperature-based phenotyping of microbial strains from deep-sea environments. The main advantage concerns the multiple on-chip temperature conditions that can be achieved in a single experiment at pressures representative of the deep-sea, overcoming the conventional limitations of large-scale batch metal reactors to conduct fast screening investigations. We monitored the growth of the model strain Thermococcus barophilus over 40 temperature and pressure conditions, without any decompression, in only 1 week, whereas it takes weeks or months with conventional approaches. The results are later compared with data from the literature. An additional example is also shown for a hydrogenotrophic methanogen strain (Methanothermococcus thermolithotrophicus), demonstrating the robustness of the methodology. These microfluidic tools can be used in laboratories to accelerate characterizations of new isolated species, changing the widely accepted paradigm that high-pressure microbiology experiments are time-consuming.
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Affiliation(s)
- Anaïs Cario
- Univ. Bordeaux, CNRS, Bordeaux INP, ICMCB, UMR 5026, Pessac, France
- *Correspondence: Anaïs Cario,
| | - Marina Larzillière
- Univ. Bordeaux, CNRS, Bordeaux INP, ICMCB, UMR 5026, Pessac, France
- CNRS, Univ. Brest, Ifremer, IRP 1211 MicrobSea, Unité de Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Plouzané, France
| | - Olivier Nguyen
- Univ. Bordeaux, CNRS, Bordeaux INP, ICMCB, UMR 5026, Pessac, France
| | - Karine Alain
- CNRS, Univ. Brest, Ifremer, IRP 1211 MicrobSea, Unité de Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Plouzané, France
| | - Samuel Marre
- Univ. Bordeaux, CNRS, Bordeaux INP, ICMCB, UMR 5026, Pessac, France
- Samuel Marre,
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48
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Li Q, Liu Y, Li G, Wang Z, Zheng Z, Sun Y, Lei N, Li Q, Zhang W. Review of the Impact of Whale Fall on Biodiversity in Deep-Sea Ecosystems. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.885572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
“Whale Fall” is a collective term for the whale carcass, the process of dead whale fall, and the formed deep-sea ecosystem. The whale fall process produces a lot of unstable organic matter that has a significant impact on deep-sea ecosystems. Scientists speculate that organic matter input is the source of energy and material for organisms in deep-sea ecosystems. In the seafloor of the North Pacific, whale fall supports the survival of at least 12,490 organisms of 43 species, contributing to the prosperity of deep-sea life. Due to the specificity of the time and space of the formation of whale fall, there are few studies on whale fall and its impact on the deep-sea ecosystem. This article summarizes and analyses the current research status on the distribution of whale fall and its impact on the deep-sea ecosystem at home and abroad. The results show that the current distribution of whale fall is mainly concentrated in the Pacific and Atlantic regions, and the research on the impact of whale fall on deep-sea ecosystems focuses on the formation process, degradation rate and impact on deep-sea biological systems. This article has some significance to the understanding of biodiversity and ecosystem succession in the deep-sea “desert area.”
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Liu R, Wei X, Song W, Wang L, Cao J, Wu J, Thomas T, Jin T, Wang Z, Wei W, Wei Y, Zhai H, Yao C, Shen Z, Du J, Fang J. Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats. MICROBIOME 2022; 10:75. [PMID: 35538590 PMCID: PMC9088039 DOI: 10.1186/s40168-022-01263-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 03/24/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND The deep sea harbors the majority of the microbial biomass in the ocean and is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches-the deepest part of the ocean. RESULTS In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. In total, 62 metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family, and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g., benzoate), polyaromatic hydrocarbons (e.g., fluorene), polychlorobiphenyl (e.g., 4-chlorobiphenyl), and organochlorine compounds (e.g., chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g., trehalose) and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits suggest that Chloroflexi may follow a "feast-or-famine" metabolic strategy, i.e., preferentially consume labile OM and store the energy intracellularly under OM-rich conditions, and utilize the stored energy or degrade recalcitrant OM for survival under OM-limited condition. CONCLUSION This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi and highlights their significance in deep-sea carbon, sulfur, and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for survival under variable and heterogenic OM inputs in the deep ocean. Video Abstract.
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Affiliation(s)
- Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China.
| | - Xing Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Weizhi Song
- Centre for Marine Science & Innovation and School of Biological Earth and Environmental Science, University of New South Wales, Kensington, Australia
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiaxin Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Torsten Thomas
- Centre for Marine Science & Innovation and School of Biological Earth and Environmental Science, University of New South Wales, Kensington, Australia
| | - Tao Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zixuan Wang
- Tidal Flat Research Center of Jiangsu Province, Nanjing, Jiangsu, China
| | - Wenxia Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Haofeng Zhai
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Cheng Yao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Ziyi Shen
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiangtao Du
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI, USA.
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50
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Nandy P. The role of sigma factor competition in bacterial adaptation under prolonged starvation. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35594140 DOI: 10.1099/mic.0.001195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study of adaptive microbial evolution in the laboratory can illuminate the genetic mechanisms of gaining fitness under a pre-defined set of selection factors. Laboratory evolution of bacteria under long-term starvation has gained importance in recent years because of its ability to uncover adaptive strategies that overcome prolonged nutrient limitation, a condition often encountered by natural microbes. In this evolutionary paradigm, bacteria are maintained in an energy-restricted environment in a growth phase called long-term stationary phase (LTSP). This phase is characterized by a stable, viable population size and highly dynamic genetic changes. Multiple independent iterations of LTSP evolution experiments have given rise to mutants that are slow-growing compared to the ancestor. Although the antagonistic regulation between rapid growth and the stress response is well-known in bacteria (especially Escherichia coli), the growth deficit of many LTSP-adapted mutants has not been explored in detail. In this review, I pinpoint the trade-off between growth and stress response as a dominant driver of evolutionary strategies under prolonged starvation. Focusing on mainly E. coli-based research, I discuss the various affectors and regulators of the competition between sigma factors to occupy their targets on the genome, and assess its effect on growth advantage in stationary phase (GASP). Finally, I comment on some crucial issues that hinder the progress of the field, including identification of novel metabolites in nutrient-depleted media, and the importance of using multidisciplinary research to resolve them.
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Affiliation(s)
- Pabitra Nandy
- National Centre for Biological Sciences (NCBS-TIFR), Bangalore, India.,Max Planck Institute for Evolutionary Biology, Plӧn, Germany
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