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Gentilhomme A, Sweet C, Hennon GMM, Collins RE. Genomic signatures of cold adaptation in the family Colwelliaceae. Extremophiles 2024; 28:39. [PMID: 39177827 DOI: 10.1007/s00792-024-01356-0] [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: 05/30/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
Psychrophily is a phenotype describing microbial growth at low temperatures; elucidating the biomolecular and genomic adaptations necessary for survival in the cold is important for understanding life in extreme environments on Earth and in outer space. We used comparative genomics and temperature growth experiments of bacteria from the family Colwelliaceae to identify genomic factors correlated with optimal growth temperature (OGT). A phylogenomic analysis of 67 public and 39 newly sequenced strains revealed three main clades of Colwelliaceae. Temperature growth experiments revealed significant differences in mean OGT by clade, wherein strains of Colwelliaceae had similar growth rates at -1 °C but varied in their ability to tolerate 17 °C. Using amino acid compositional indices, a multiple linear regression model was constructed to predict the OGT of these organisms (RMSE 5.2 °C). Investigation of Colwelliaceae functional genes revealed a putative cold-adaptive gene cassette that was present in psychrophilic strains but absent in a closely related strain with a significantly higher OGT. This study also presents genomic evidence suggesting that the clade of Colwelliaceae containing Colwellia hornerae should be investigated as a new genus. These contributions offer key insights into the psychrophily phenotype and its underlying genomic foundation in the family Colwelliaceae.
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Affiliation(s)
- Anais Gentilhomme
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, Fairbanks, Alaska, 99775, USA.
| | - Charles Sweet
- Chemistry Department, U.S. Naval Academy, 572M Holloway Road, Annapolis, MD, 21402-5026, USA
| | - Gwenn M M Hennon
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, Fairbanks, Alaska, 99775, USA
| | - R Eric Collins
- Center for Earth Observation Sciences, University of Manitoba, 520 Wallace Building, Winnipeg, MB, R3T 2N2, Canada
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Malas J, Russo DC, Bollengier O, Malaska MJ, Lopes RMC, Kenig F, Meyer-Dombard DR. Biological functions at high pressure: transcriptome response of Shewanella oneidensis MR-1 to hydrostatic pressure relevant to Titan and other icy ocean worlds. Front Microbiol 2024; 15:1293928. [PMID: 38414766 PMCID: PMC10896736 DOI: 10.3389/fmicb.2024.1293928] [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: 09/13/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
High hydrostatic pressure (HHP) is a key driver of life's evolution and diversification on Earth. Icy moons such as Titan, Europa, and Enceladus harbor potentially habitable high-pressure environments within their subsurface oceans. Titan, in particular, is modeled to have subsurface ocean pressures ≥ 150 MPa, which are above the highest pressures known to support life on Earth in natural ecosystems. Piezophiles are organisms that grow optimally at pressures higher than atmospheric (0.1 MPa) pressure and have specialized adaptations to the physical constraints of high-pressure environments - up to ~110 MPa at Challenger Deep, the highest pressure deep-sea habitat explored. While non-piezophilic microorganisms have been shown to survive short exposures at Titan relevant pressures, the mechanisms of their survival under such conditions remain largely unelucidated. To better understand these mechanisms, we have conducted a study of gene expression for Shewanella oneidensis MR-1 using a high-pressure experimental culturing system. MR-1 was subjected to short-term (15 min) and long-term (2 h) HHP of 158 MPa, a value consistent with pressures expected near the top of Titan's subsurface ocean. We show that MR-1 is metabolically active in situ at HHP and is capable of viable growth following 2 h exposure to 158 MPa, with minimal pressure training beforehand. We further find that MR-1 regulates 264 genes in response to short-term HHP, the majority of which are upregulated. Adaptations include upregulation of the genes argA, argB, argC, and argF involved in arginine biosynthesis and regulation of genes involved in membrane reconfiguration. MR-1 also utilizes stress response adaptations common to other environmental extremes such as genes encoding for the cold-shock protein CspG and antioxidant defense related genes. This study suggests Titan's ocean pressures may not limit life, as microorganisms could employ adaptations akin to those demonstrated by terrestrial organisms.
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Affiliation(s)
- Judy Malas
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
| | - Daniel C. Russo
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
| | - Olivier Bollengier
- Nantes Université, Univ Angers, Le Mans Université, CNRS, Laboratoire de Planétologie et Géosciences, LPG UMR 6112, Nantes, France
| | - Michael J. Malaska
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Rosaly M. C. Lopes
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Fabien Kenig
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
| | - D'Arcy R. Meyer-Dombard
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, IL, United States
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3
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Li C, Song J, Chen Q, Ge D, Li Q, Yang Y. Whole-genome shotgun sequencing unravels the influence of environmental microbial co-infections on the treatment efficacy for severe pediatric infectious diseases. Front Microbiol 2024; 15:1308871. [PMID: 38328429 PMCID: PMC10847551 DOI: 10.3389/fmicb.2024.1308871] [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: 10/08/2023] [Accepted: 01/03/2024] [Indexed: 02/09/2024] Open
Abstract
Background The microbiome plays a pivotal role in mediating immune deviation during the development of early-life viral infections. Recurrent infections in children are considered a risk factor for disease development. This study delves into the metagenomics of the microbiome in children suffering from severe infections, seeking to identify potential sources of these infections. Aims The aim of this study was to identify the specific microorganisms and factors that significantly influence the treatment duration in patients suffering from severe infections. We sought to understand how these microbial communities and other variables may affect the treatment duration and the use of antibiotics of these patients with severe infections. Method Whole-genome shotgun sequencing was conducted on samples collected from children aged 0-14 years with severe infections, admitted to the Pediatrics Department of Xiamen First Hospital. The Kraken2 algorithm was used for taxonomic identification from sequence reads, and linear mixed models were employed to identify significant microorganisms influencing treatment duration. Colwellia, Cryptococcus, and Citrobacter were found to significantly correlate with the duration of clinical treatment. Further analysis using propensity score matching (PSM) and rank-sum test identified clinical indicators significantly associated with the presence of these microorganisms. Results Using a linear mixed model after removed the outliers, we identified that the abundance of Colwellia, Cryptococcus, and Citrobacter significantly influences the treatment duration. The presence of these microorganisms is associated with a longer treatment duration for patients. Furthermore, these microorganisms were found to impact various clinical measures. Notably, an increase in hospitalization durations and medication costs was observed in patients with these microorganisms. In patients with Colwellia, Cryptococcus, and Citrobacter, we discover significant differences in platelets levels. We also find that in patients with Cryptococcus, white blood cells, hemoglobin, and neutrophils levels are lower. Conclusion These findings suggest that Colwellia, Cryptococcus, and Citrobacter, particularly Cryptococcus, could potentially contribute to the severity of infections observed in this cohort, possibly as co-infections. These microorganisms warrant further investigation into their pathogenic roles and mechanisms of action, as their presence in combination with disease-causing organisms may have a synergistic effect on disease severity. Understanding the interplay between these microorganisms and pathogenic agents could provide valuable insights into the complex nature of severe pediatric infections and guide the development of targeted therapeutic strategies.
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Affiliation(s)
- Chengxin Li
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Jing Song
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
| | - Qihong Chen
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
| | - Dandan Ge
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
| | - Qiyuan Li
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Yungang Yang
- Department of Pediatrics, Pediatric Key Laboratory of Xiamen, The First Affiliated Hospital of Xiamen University, Institute of Pediatrics, School of Medicine, Xiamen University, Xiamen, China
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Qiu X, Hu XM, Tang XX, Huang CH, Jian HH, Lin DH. Metabolic adaptations of Microbacterium sediminis YLB-01 in deep-sea high-pressure environments. Appl Microbiol Biotechnol 2024; 108:170. [PMID: 38265689 DOI: 10.1007/s00253-023-12906-5] [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: 07/10/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 01/25/2024]
Abstract
The deep-sea environment is an extremely difficult habitat for microorganisms to survive in due to its intense hydrostatic pressure. However, the mechanisms by which these organisms adapt to such extreme conditions remain poorly understood. In this study, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01, a cold and stress-tolerant microorganism isolated from deep-sea sediments, in response to high-pressure conditions. YLB-01 cells were cultured at normal atmospheric pressure and 28 ℃ until they reached the stationary growth phase. Subsequently, the cells were exposed to either normal pressure or high pressure (30 MPa) at 4 ℃ for 7 days. Using NMR-based metabolomic and proteomic analyses of YLB-01 cells exposed to high-pressure conditions, we observed significant metabolic changes in several metabolic pathways, including amino acid, carbohydrate, and lipid metabolism. In particular, the high-pressure treatment stimulates cell division and triggers the accumulation of UDP-glucose, a critical factor in cell wall formation. This finding highlights the adaptive strategies used by YLB-01 cells to survive in the challenging high-pressure environments of the deep sea. Specifically, we discovered that YLB-01 cells regulate amino acid metabolism, promote carbohydrate metabolism, enhance cell wall synthesis, and improve cell membrane fluidity in response to high pressure. These adaptive mechanisms play essential roles in supporting the survival and growth of YLB-01 in high-pressure conditions. Our study offers valuable insights into the molecular mechanisms underlying the metabolic adaptation of deep-sea microorganisms to high-pressure environments. KEY POINTS: • NMR-based metabolomic and proteomic analyses were conducted on Microbacterium sediminis YLB-01 to investigate the significant alterations in several metabolic pathways in response to high-pressure treatment. • YLB-01 cells used adaptive strategies (such as regulated amino acid metabolism, promoted carbohydrate metabolism, enhanced cell wall synthesis, and improved cell membrane fluidity) to survive in the challenging high-pressure environment of the deep sea. • High-pressure treatment stimulated cell division and triggered the accumulation of UDP-glucose, a critical factor in cell wall formation, in Microbacterium sediminis YLB-01 cells.
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Affiliation(s)
- Xu Qiu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xiao-Min Hu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xi-Xiang Tang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
| | - Cai-Hua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen, China
| | - Hua-Hua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Hai Lin
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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5
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Marietou A, Schmidt JS, Rasmussen MR, Scoma A, Rysgaard S, Vergeynst L. The effect of hydrostatic pressure on the activity and community composition of hydrocarbon-degrading bacteria in Arctic seawater. Appl Environ Microbiol 2023; 89:e0098723. [PMID: 37943057 PMCID: PMC10686064 DOI: 10.1128/aem.00987-23] [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: 06/19/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Increased ship traffic in the Arctic region raises the risk of oil spills. With an average sea depth of 1,000 m, there is a growing concern over the potential release of oil sinking in the form of marine oil snow into deep Arctic waters. At increasing depth, the oil-degrading community is exposed to increasing hydrostatic pressure, which can reduce microbial activity. However, microbes thriving in polar regions may adapt to low temperature by modulation of membrane fluidity, which is also a well-known adaptation to high hydrostatic pressure. At mild hydrostatic pressures up to 8-12 MPa, we did not observe an altered microbial activity or community composition, whereas comparable studies using deep-sea or sub-Arctic microbial communities with in situ temperatures of 4-5°C showed pressure-induced effects at 10-15 MPa. Our results suggest that the psychrophilic nature of the underwater microbial communities in the Arctic may be featured by specific traits that enhance their fitness at increasing hydrostatic pressure.
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Affiliation(s)
- Angeliki Marietou
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | | | - Martin R. Rasmussen
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Alberto Scoma
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Søren Rysgaard
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Leendert Vergeynst
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
- Centre for Water Technology (WATEC), Aarhus University, Aarhus, Denmark
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6
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Coker JA. 'All About' Extremophiles. Fac Rev 2023; 12:27. [PMID: 38027090 PMCID: PMC10630985 DOI: 10.12703/r/12-27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Despite common perception, most of Earth is what is often referred to as an 'extreme environment.' Yet to the organisms that call these places home, it is simply that (home). They have adapted to thrive in these environments and, in the process, have evolved many unique adaptations at the molecular- and 'omic-level. Scientists' interest in these organisms has typically been in how they and their products can be harnessed for biotechnological applications and the environments where they are found, while the general public's veers more toward a fascination with their deviation from the 'norm'. However, these organisms have so much more to tell us about Life and the myriad ways there are to perform 'simple' biological processes.
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Affiliation(s)
- James A Coker
- Center for Biotechnology Education, Advanced Academic Programs, Krieger School of Arts and Sciences, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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7
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Li F, Burger A, Eppley JM, Poff KE, Karl DM, DeLong EF. Planktonic microbial signatures of sinking particle export in the open ocean's interior. Nat Commun 2023; 14:7177. [PMID: 37935690 PMCID: PMC10630432 DOI: 10.1038/s41467-023-42909-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
A considerable amount of particulate carbon produced by oceanic photosynthesis is exported to the deep-sea by the "gravitational pump" (~6.8 to 7.7 Pg C/year), sequestering it from the atmosphere for centuries. How particulate organic carbon (POC) is transformed during export to the deep sea however is not well understood. Here, we report that dominant suspended prokaryotes also found in sinking particles serve as informative tracers of particle export processes. In a three-year time series from oceanographic campaigns in the Pacific Ocean, upper water column relative abundances of suspended prokaryotes entrained in sinking particles decreased exponentially from depths of 75 to 250 m, conforming to known depth-attenuation patterns of carbon, energy, and mass fluxes in the epipelagic zone. Below ~250 m however, the relative abundance of suspended prokaryotes entrained in sinking particles increased with depth. These results indicate that microbial entrainment, colonization, and sinking particle formation are elevated at mesopelagic and bathypelagic depths. Comparison of suspended and sinking particle-associated microbes provides information about the depth-variability of POC export and biotic processes, that is not evident from biogeochemical data alone.
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Affiliation(s)
- Fuyan Li
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Andrew Burger
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - John M Eppley
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Kirsten E Poff
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
- McDonogh School, Owings Mills, MD, USA
| | - David M Karl
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Edward F DeLong
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, USA.
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, USA.
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Weber L, Gilat A, Maillot N, Byrne D, Arnoux P, Giudici-Orticoni MT, Méjean V, Ilbert M, Genest O, Rosenzweig R, Dementin S. Bacterial adaptation to cold: Conservation of a short J-domain co-chaperone and its protein partners in environmental proteobacteria. Environ Microbiol 2023; 25:2447-2464. [PMID: 37549929 DOI: 10.1111/1462-2920.16478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Bacterial genomes are a huge reservoir of genes encoding J-domain protein co-chaperones that recruit the molecular chaperone DnaK to assist protein substrates involved in survival, adaptation, or fitness. The atc operon of the aquatic mesophilic bacterium Shewanella oneidensis encodes the proteins AtcJ, AtcA, AtcB, and AtcC, and all of them, except AtcA, are required for growth at low temperatures. AtcJ is a short J-domain protein that interacts with DnaK, but also with AtcC through its 21 amino acid C-terminal domain. This interaction network is critical for cold growth. Here, we show that AtcJ represents a subfamily of short J-domain proteins that (i) are found in several environmental, mostly aquatic, β- or ɣ-proteobacteria and (ii) contain a conserved PX7 W motif in their C-terminal extension. Using a combination of NMR, biochemical and genetic approaches, we show that the hydrophobic nature of the tryptophan of the S. oneidensis AtcJ PX7 W motif determines the strong AtcJ-AtcC interaction essential for cold growth. The AtcJ homologues are encoded by operons containing at least the S. oneidensis atcA, atcB, and atcC homologues. These findings suggest a conserved network of DnaK and Atc proteins necessary for low-temperature growth and, given the variation in the atc operons, possibly for other biological functions.
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Affiliation(s)
- Lana Weber
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Atar Gilat
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathanael Maillot
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Deborah Byrne
- Protein Expression Facility, Aix-Marseille University, French National Center for Scientific Research (CNRS), IMM FR3479, Marseille, France
| | - Pascal Arnoux
- Institute of Biosciences and Biotechnologies of Aix-Marseille (BIAM UMR7265), Aix-Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), French National Center for Scientific Research (CNRS), Saint Paul-Lez-Durance, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Vincent Méjean
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Marianne Ilbert
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Olivier Genest
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sébastien Dementin
- Laboratory of Bioenergetics and Protein Engineering (BIP UMR 7281), Aix-Marseille University, French National Center for Scientific Research (CNRS), Marseille, France
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Ganesh Kumar A, Manisha D, Nivedha Rajan N, Sujitha K, Magesh Peter D, Kirubagaran R, Dharani G. Biodegradation of phenanthrene by piezotolerant Bacillus subtilis EB1 and genomic insights for bioremediation. MARINE POLLUTION BULLETIN 2023; 194:115151. [PMID: 37453166 DOI: 10.1016/j.marpolbul.2023.115151] [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: 11/15/2022] [Revised: 04/28/2023] [Accepted: 06/04/2023] [Indexed: 07/18/2023]
Abstract
A marine strain B. subtilis EB1, isolated from Equator water, showed excellent degradation towards a wide range of hydrocarbons. Degradation studies revealed dense growth with 93 % and 83 % removal of phenanthrene within 72 h at 0.1 and 20 MPa, respectively. The identification of phenanthrene degradation metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 3,983,989 bp with 4331 annotated genes. The genome provided the genetic compartments, which includes monooxygenase, dioxygenase, dehydrogenase, biosurfactant synthesis catabolic genes for the biodegradation of aromatic compounds. Detailed COG and KEGG pathway analysis confirmed the genes involved in the oxygenation reaction of hydrocarbons, piezotolerance, siderophores, chemotaxis and transporter systems which were specific to adaptation for survival in extreme marine habitat. The results of this study will be a key to design an optimal bioremediation strategy for oil contaminated extreme marine environment.
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Affiliation(s)
- A Ganesh Kumar
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India.
| | - D Manisha
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - N Nivedha Rajan
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - K Sujitha
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - D Magesh Peter
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - R Kirubagaran
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
| | - G Dharani
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, Tamil Nadu, India
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Scheffer G, Gieg LM. The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface. Microorganisms 2023; 11:1629. [PMID: 37512802 PMCID: PMC10384521 DOI: 10.3390/microorganisms11071629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed.
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Affiliation(s)
- Gabrielle Scheffer
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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11
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Hu G, Wang Y, Xue R, Liu T, Zhou Z, Yang Z. Effects of the Exopolysaccharide from Lactiplantibacillus plantarum HMX2 on the Growth Performance, Immune Response, and Intestinal Microbiota of Juvenile Turbot, Scophthalmus maximus. Foods 2023; 12:2051. [PMID: 37238869 PMCID: PMC10217481 DOI: 10.3390/foods12102051] [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: 04/19/2023] [Revised: 05/08/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
In this study, the exopolysaccharide (EPS) from Lactiplantibacillus plantarum (HMX2) was isolated from Chinese Northeast Sauerkraut. Its effects on juvenile turbot were investigated by adding different concentrations of HMX2-EPS (C: 0 mg/kg, H1: 100 mg/kg, H2: 500 mg/kg) to the feed. Compared with the control group, HMX2-EPS significantly improved the growth performance of juvenile turbot. The activities of antioxidant enzymes, digestive enzymes, and immune-related enzymes were significantly increased. HMX2-EPS could also increase the secretion of inflammatory factors and enhance the immune response of turbot by regulating the IFN signal transduction pathway and exhibit stronger survival rates after the A. hydrophila challenge. Moreover, HMX2-EPS could improve the diversity of intestinal microbiota in juvenile fish, increase the abundance of potential probiotics, and reduce the abundance of pathogenic bacteria. The function of gut microbes in metabolism and the immune system could also be improved. All results showed better effects with high concentrations of HMX2-EPS. These results indicated that HMX2-EPS supplementation in the diet could promote growth, improve antioxidant activity, digestive capacity, and immunity capacity, and actively regulate the intestinal microbiota of juvenile turbot. In conclusion, this study might provide basic technical and scientific support for the application of L. plantarum in aquatic feed.
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Affiliation(s)
| | | | | | | | | | - Zhennai Yang
- Key Laboratory of Geriatric Nutrition and Health of Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, No. 11 Fu-Cheng Road, Hai-Dian District, Beijing 100048, China; (G.H.); (Y.W.); (R.X.); (T.L.); (Z.Z.)
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12
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Chen X, Huang W, Liu C, Song H, Waiho K, Lin D, Fang JKH, Hu M, Kwan KY, Wang Y. Intestinal response of mussels to nano-TiO 2 and pentachlorophenol in the presence of predator. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161456. [PMID: 36640886 DOI: 10.1016/j.scitotenv.2023.161456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
With the development of industry, agriculture and intensification of human activities, a large amount of nano-TiO2 dioxide and pentachlorophenol have entered aquatic environment, causing potential impacts on the health of aquatic animals and ecosystems. We investigated the effects of predators, pentachlorophenol (PCP) and nano titanium dioxide (nano-TiO2) on the gut health (microbiota and digestive enzymes) of the thick-shelled mussel Mytilus coruscus. Nano-TiO2, as the photocatalyst for PCP, enhanced to toxic effects of PCP on the intestinal health of mussels, and they made the mussels more vulnerable to the stress from predators. Nano-TiO2 particles with smaller size exerted a larger negative effect on digestive enzymes, whereas the size effect on gut bacteria was insignificant. The presence of every two of the three factors significantly affected the population richness and diversity of gut microbiota. Our findings revealed that the presence of predators, PCP, and nano-TiO2 promoted the proliferation of pathogenic bacteria and inhibited digestive enzyme activity. This research investigated the combined stress on marine mussels caused by nanoparticles and pesticides in the presence of predators and established a theoretical framework for explaining the adaptive mechanisms in gut microbes and the link between digestive enzymes and gut microbiota.
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Affiliation(s)
- Xiang Chen
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Science, Beibu Gulf University, Qinzhou City, China; International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wei Huang
- Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Chunhua Liu
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Hanting Song
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - James K H Fang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Menghong Hu
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Kit Yue Kwan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Science, Beibu Gulf University, Qinzhou City, China
| | - Youji Wang
- International Research Center for Marine Biosciences, Shanghai Ocean University, Ministry of Science and Technology, China; Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China.
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13
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Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.
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Affiliation(s)
- Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Barbara Bayer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
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14
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Amano C, Zhao Z, Sintes E, Reinthaler T, Stefanschitz J, Kisadur M, Utsumi M, Herndl GJ. Limited carbon cycling due to high-pressure effects on the deep-sea microbiome. NATURE GEOSCIENCE 2022; 15:1041-1047. [PMID: 36504693 PMCID: PMC9726642 DOI: 10.1038/s41561-022-01081-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone-between 1,000 and 4,000 m depth-~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.
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Affiliation(s)
- Chie Amano
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Eva Sintes
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Instituto Español de Oceanografía-CSIC, Centro Oceanográfico de Baleares, Palma de Mallorca, Spain
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Julia Stefanschitz
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- Present Address: Marine Evolutionary Ecology, Deep-Sea Biology Group, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Murat Kisadur
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Motoo Utsumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Texel, The Netherlands
- Vienna Metabolomics & Proteomics Center, University of Vienna, Vienna, Austria
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15
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Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean. Appl Environ Microbiol 2022; 88:e0057522. [PMID: 35916502 PMCID: PMC9397096 DOI: 10.1128/aem.00575-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.
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16
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Sieg J, Sandmeier CC, Lieske J, Meents A, Lemmen C, Streit WR, Rarey M. Analyzing structural features of proteins from deep-sea organisms. Proteins 2022; 90:1521-1537. [PMID: 35313380 DOI: 10.1002/prot.26337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022]
Abstract
Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deep-sea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.
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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
| | | | - Julia Lieske
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | | | - Wolfgang R Streit
- Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
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17
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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18
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Microbiomes of Hadal Fishes across Trench Habitats Contain Similar Taxa and Known Piezophiles. mSphere 2022; 7:e0003222. [PMID: 35306867 PMCID: PMC9044967 DOI: 10.1128/msphere.00032-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hadal snailfishes are the deepest-living fishes in the ocean, inhabiting trenches from depths of ∼6,000 to 8,000 m. While the microbial communities in trench environments have begun to be characterized, the microbes associated with hadal megafauna remain relatively unknown. Here, we describe the gut microbiomes of two hadal snailfishes, Pseudoliparis swirei (Mariana Trench) and Notoliparis kermadecensis (Kermadec Trench), using 16S rRNA gene amplicon sequencing. We contextualize these microbiomes with comparisons to the abyssal macrourid Coryphaenoides yaquinae and the continental shelf-dwelling snailfish Careproctus melanurus. The microbial communities of the hadal snailfishes were distinct from their shallower counterparts and were dominated by the same sequences related to the Mycoplasmataceae and Desulfovibrionaceae. These shared taxa indicate that symbiont lineages have remained similar to the ancestral symbiont since their geographic separation or that they are dispersed between geographically distant trenches and subsequently colonize specific hosts. The abyssal and hadal fishes contained sequences related to known, cultured piezophiles, microbes that grow optimally under high hydrostatic pressure, including Psychromonas, Moritella, and Shewanella. These taxa are adept at colonizing nutrient-rich environments present in the deep ocean, such as on particles and in the guts of hosts, and we hypothesize they could make a dietary contribution to deep-sea fishes by degrading chitin and producing fatty acids. We characterize the gut microbiota within some of the deepest fishes to provide new insight into the diversity and distribution of host-associated microbial taxa and the potential of these animals, and the microbes they harbor, for understanding adaptation to deep-sea habitats. IMPORTANCE Hadal trenches, characterized by high hydrostatic pressures and low temperatures, are one of the most extreme environments on our planet. By examining the microbiome of abyssal and hadal fishes, we provide insight into the diversity and distribution of host-associated life at great depth. Our findings show that there are similar microbial populations in fishes geographically separated by thousands of miles, reflecting strong selection for specific microbial lineages. Only a few psychropiezophilic taxa, which do not reflect the diversity of microbial life at great depth, have been successfully isolated in the laboratory. Our examination of deep-sea fish microbiomes shows that typical high-pressure culturing methodologies, which have largely remained unchanged since the pioneering work of Claude ZoBell in the 1950s, may simulate the chemical environment found in animal guts and helps explain why the same deep-sea genera are consistently isolated.
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19
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Fan S, Wang M, Ding W, Li YX, Zhang YZ, Zhang W. Scientific and technological progress in the microbial exploration of the hadal zone. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:127-137. [PMID: 37073349 PMCID: PMC10077178 DOI: 10.1007/s42995-021-00110-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/11/2021] [Indexed: 05/03/2023]
Abstract
The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.
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Affiliation(s)
- Shen Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Meng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
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20
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Wani AK, Akhtar N, Sher F, Navarrete AA, Américo-Pinheiro JHP. Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems. Arch Microbiol 2022; 204:144. [PMID: 35044532 DOI: 10.1007/s00203-022-02757-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 01/01/2023]
Abstract
Microorganisms are ubiquitous on Earth and can inhabit almost every environment. In a complex heterogeneous environment or in face of ecological disturbance, the microbes adjust to fluctuating environmental conditions through a cascade of cellular and molecular systems. Their habitats differ from cold microcosms of Antarctica to the geothermal volcanic areas, terrestrial to marine, highly alkaline zones to the extremely acidic areas and freshwater to brackish water sources. The diverse ecological microbial niches are attributed to the versatile, adaptable nature under fluctuating temperature, nutrient availability and pH of the microorganisms. These organisms have developed a series of mechanisms to face the environmental changes and thereby keep their role in mediate important ecosystem functions. The underlying mechanisms of adaptable microbial nature are thoroughly investigated at the cellular, genetic and molecular levels. The adaptation is mediated by a spectrum of processes like natural selection, genetic recombination, horizontal gene transfer, DNA damage repair and pleiotropy-like events. This review paper provides the fundamentals insight into the microbial adaptability besides highlighting the molecular network of microbial adaptation under different environmental conditions.
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Affiliation(s)
- Atif Khurshid Wani
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Nahid Akhtar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Farooq Sher
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
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21
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Zhong H, Sun H, Liu R, Zhan Y, Huang X, Ju F, Zhang XH. Comparative Genomic Analysis of Labrenzia aggregata ( Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions. Front Microbiol 2022; 12:770370. [PMID: 34970235 PMCID: PMC8712697 DOI: 10.3389/fmicb.2021.770370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.
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Affiliation(s)
- Haohui Zhong
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory of Marine Science and Technology, Qingdao, China
| | - Hao Sun
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ronghua Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yuanchao Zhan
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xinyu Huang
- School of Engineering, Westlake University, Hangzhou, China.,Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Feng Ju
- School of Engineering, Westlake University, Hangzhou, China.,Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory of Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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Anammox bacteria drive fixed nitrogen loss in hadal trench sediments. Proc Natl Acad Sci U S A 2021; 118:2104529118. [PMID: 34764222 DOI: 10.1073/pnas.2104529118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 01/04/2023] Open
Abstract
Benthic N2 production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N2 production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N2 production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N2 production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis.
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Zhang WJ, Zhang C, Zhou S, Li XG, Mangenot S, Fouteau S, Guerin T, Qi XQ, Yang J, Bartlett DH, Wu LF. Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench. Microb Genom 2021; 7:000591. [PMID: 34319226 PMCID: PMC8477399 DOI: 10.1099/mgen.0.000591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/20/2021] [Indexed: 01/19/2023] Open
Abstract
Hadal trenches are the deepest but underexplored ecosystems on the Earth. Inhabiting the trench bottom is a group of micro-organisms termed obligate piezophiles that grow exclusively under high hydrostatic pressures (HHP). To reveal the genetic and physiological characteristics of their peculiar lifestyles and microbial adaptation to extreme high pressures, we sequenced the complete genome of the obligately piezophilic bacterium Moritella yayanosii DB21MT-5 isolated from the deepest oceanic sediment at the Challenger Deep, Mariana Trench. Through comparative analysis against pressure sensitive and deep-sea piezophilic Moritella strains, we identified over a hundred genes that present exclusively in hadal strain DB21MT-5. The hadal strain encodes fewer signal transduction proteins and secreted polysaccharases, but has more abundant metal ion transporters and the potential to utilize plant-derived saccharides. Instead of producing osmolyte betaine from choline as other Moritella strains, strain DB21MT-5 ferments on choline within a dedicated bacterial microcompartment organelle. Furthermore, the defence systems possessed by DB21MT-5 are distinct from other Moritella strains but resemble those in obligate piezophiles obtained from the same geographical setting. Collectively, the intensive comparative genomic analysis of an obligately piezophilic strain Moritella yayanosii DB21MT-5 demonstrates a depth-dependent distribution of energy metabolic pathways, compartmentalization of important metabolism and use of distinct defence systems, which likely contribute to microbial adaptation to the bottom of hadal trench.
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Affiliation(s)
- Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Chan Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- Present address: College of Horticulture, Hainan University, No. 58, Renmin Avenue, Haikou, PR China
| | - Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Sophie Mangenot
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Thomas Guerin
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA
| | - Long-Fei Wu
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Aix-Marseille Université, CNRS, LCB UMR 7257, IMM, IM2B, Marseille, France
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Ganesh Kumar A, Manisha D, Sujitha K, Magesh Peter D, Kirubagaran R, Dharani G. Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil. Sci Rep 2021; 11:9347. [PMID: 33931710 PMCID: PMC8087790 DOI: 10.1038/s41598-021-88525-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
A deep-sea fungus Aspergillus sydowii BOBA1 isolated from marine sediment at a depth of 3000 m was capable of degrading spent engine (SE) oil. The response of immobilized fungi towards degradation at elevated pressure was studied in customized high pressure reactors without any deviation in simulating in situ deep-sea conditions. The growth rate of A. sydowii BOBA1 in 0.1 MPa was significantly different from the growth at 10 MPa pressure. The degradation percentage reached 71.2 and 82.5% at atmospheric and high pressure conditions, respectively, within a retention period of 21 days. The complete genome sequence of BOBA1 consists of 38,795,664 bp in size, comprises 2582 scaffolds with predicted total coding genes of 18,932. A total of 16,247 genes were assigned with known functions and many families found to have a potential role in PAHs and xenobiotic compound metabolism. Functional genes controlling the pathways of hydrocarbon and xenobiotics compound degrading enzymes such as dioxygenase, decarboxylase, hydrolase, reductase and peroxidase were identified. The spectroscopic and genomic analysis revealed the presence of combined catechol, gentisate and phthalic acid degradation pathway. These results of degradation and genomic studies evidenced that this deep-sea fungus could be employed to develop an eco-friendly mycoremediation technology to combat the oil polluted marine environment. This study expands our knowledge on piezophilic fungi and offer insight into possibilities about the fate of SE oil in deep-sea.
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Affiliation(s)
- A. Ganesh Kumar
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - D. Manisha
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - K. Sujitha
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - D. Magesh Peter
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - R. Kirubagaran
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
| | - G. Dharani
- grid.454780.a0000 0001 0683 2228Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Chennai, 600100 Tamil Nadu India
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