1
|
Salwan R, Sharma V. Genomics of Prokaryotic Extremophiles to Unfold the Mystery of Survival in Extreme Environments. Microbiol Res 2022; 264:127156. [DOI: 10.1016/j.micres.2022.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
|
2
|
Jin S, Wang Y, Zhao X. Cold-adaptive mechanism of psychrophilic bacteria in food and its application. Microb Pathog 2022; 169:105652. [PMID: 35753601 DOI: 10.1016/j.micpath.2022.105652] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/09/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022]
Abstract
Psychrophilic bacteria are a type of microorganisms that normally grow in low-temperature environments. They are usually found in extremely cold environments. However, as people's demand for low-temperature storage of food becomes higher, psychrophilic bacteria have also begun to appear in cold storage and refrigerators, which has become a food safety hazard. In this paper, the optimal cooling strategies of psychrophilic bacteria are reviewed from the aspects of the cell membrane, psychrophilic enzymes, antifreeze proteins, cold shock proteins, gene regulation, metabolic levels and antifreeze agents, and the principle of psychrophilic mechanism is briefly described. The application of thermophilic bacteria and its products adapted to cold environments in food fields are analyzed. The purpose of this paper is to provide ideas for future research on psychrophilic bacteria based on the mechanism and application of psychrophilic bacteria.
Collapse
Affiliation(s)
- Shanshan Jin
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yizhe Wang
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
| |
Collapse
|
3
|
Full-Length Transcriptome Comparison Provides Novel Insights into the Molecular Basis of Adaptation to Different Ecological Niches of the Deep-Sea Hydrothermal Vent in Alvinocaridid Shrimps. DIVERSITY 2022. [DOI: 10.3390/d14050371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The deep-sea hydrothermal vent ecosystem is one of the extreme chemoautotrophic environments. Shinkaicaris leurokolos Kikuchi and Hashimoto, 2000, and Alvinocaris longirostris Kikuchi and Ohta, 1995, are typically co-distributed and closely related alvinocaridid shrimps in hydrothermal vent areas with different ecological niches, providing an excellent model for studying the adaptive evolution mechanism of animals in the extreme deep-sea hydrothermal vent environment. The shrimp S. leurokolos lives in close proximity to the chimney vent discharging high-temperature fluid, while A. longirostris inhabits the peripheral areas of hydrothermal vents. In this study, full-length transcriptomes of S. leurokolos and A. longirostris were generated using a combination of single-molecule real-time (SMRT) and Illumina RNA-seq technology. Expression analyses of the transcriptomes showed that among the top 30% of highly expressed genes of each species, more genes related to sulfide and heavy metal metabolism (sulfide: quinone oxidoreductase, SQR; persulfide dioxygenase, ETHE1; thiosulfate sulfurtransferase, TST, and ferritin, FRI) were specifically highly expressed in S. leurokolos, while genes involved in maintaining epibiotic bacteria or pathogen resistance (beta-1,3-glucan-binding protein, BGBP; endochitinase, CHIT; acidic mammalian chitinase, CHIA, and anti-lipopolysaccharide factors, ALPS) were highly expressed in A. longirostris. Gene family expansion analysis revealed that genes related to anti-oxidant metabolism (cytosolic manganese superoxide dismutase, SODM; glutathione S-transferase, GST, and glutathione peroxidase, GPX) and heat stress (heat shock cognate 70 kDa protein, HSP70 and heat shock 70 kDa protein cognate 4, HSP7D) underwent significant expansion in S. leurokolos, while CHIA and CHIT involved in pathogen resistance significantly expanded in A. longirostris. Finally, 66 positively selected genes (PSGs) were identified in the vent shrimp S. leurokolos. Most of the PSGs were involved in DNA repair, antioxidation, immune defense, and heat stress response, suggesting their function in the adaptive evolution of species inhabiting the extreme vent microhabitat. This study provides abundant genetic resources for deep-sea invertebrates, and is expected to lay the foundation for deep decipherment of the adaptive evolution mechanism of shrimps in a deep-sea chemosynthetic ecosystem based on further whole-genome comparison.
Collapse
|
4
|
Comparative Genomic Analyses of the Genus Nesterenkonia Unravels the Genomic Adaptation to Polar Extreme Environments. Microorganisms 2022; 10:microorganisms10020233. [PMID: 35208688 PMCID: PMC8875376 DOI: 10.3390/microorganisms10020233] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The members of the Nesterenkonia genus have been isolated from various habitats, like saline soil, salt lake, sponge-associated and the human gut, some of which are even located in polar areas. To identify their stress resistance mechanisms and draw a genomic profile across this genus, we isolated four Nesterenkonia strains from the lakes in the Tibetan Plateau, referred to as the third pole, and compared them with all other 30 high-quality Nesterenkonia genomes that are deposited in NCBI. The Heaps’ law model estimated that the pan-genome of this genus is open and the number of core, shell, cloud, and singleton genes were 993 (6.61%), 2782 (18.52%), 4117 (27.40%), and 7132 (47.47%), respectively. Phylogenomic and ANI/AAI analysis indicated that all genomes can be divided into three main clades, named NES-1, NES-2, and NES-3. The strains isolated from lakes in the Tibetan Plateau were clustered with four strains from different sources in the Antarctic and formed a subclade within NES-2, described as NES-AT. Genome features of this subclade, including GC (guanine + cytosine) content, tRNA number, carbon/nitrogen atoms per residue side chain (C/N-ARSC), and amino acid composition, in NES-AT individuals were significantly different from other strains, indicating genomic adaptation to cold, nutrient-limited, osmotic, and ultraviolet conditions in polar areas. Functional analysis revealed the enrichment of specific genes involved in bacteriorhodopsin synthesis, biofilm formation, and more diverse nutrient substance metabolism genes in the NES-AT clade, suggesting potential adaptation strategies for energy metabolism in polar environments. This study provides a comprehensive profile of the genomic features of the Nesterenkonia genus and reveals the possible mechanism for the survival of Nesterenkonia isolates in polar areas.
Collapse
|
5
|
|
6
|
Tendulkar S, Hattiholi A, Chavadar M, Dodamani S. Psychrophiles: A journey of hope. J Biosci 2021; 46:64. [PMID: 34219740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Psychrophiles are organisms living in extremely cold conditions within the temperature range of -20°C to +10°C. These organisms survive in harsh environment by modulating their genetic make-up to thrive in extremely cold conditions. These cold-adaptations are closely associated with changes in the life forms, gene expression, and proteins, enzymes, lipids, etc. This review gives a brief description of the life and genetic adaptations of psychrophiles for their survival in extreme conditions as well as the bioactive compounds that are potential antimicrobials.
Collapse
Affiliation(s)
- Shivani Tendulkar
- Dr. Prabhakar Kore Basic Science Research Center, KLE Academy of Higher Education and Research, Belagavi 590 010, India
| | | | | | | |
Collapse
|
7
|
Xiao X, Ma XL, Wang LG, Long F, Li TT, Zhou XT, Liu H, Wu LJ, Yu HQ. Anaerobic reduction of high-polarity nitroaromatic compounds by electrochemically active bacteria: Roles of Mtr respiratory pathway, molecular polarity, mediator and membrane permeability. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115943. [PMID: 33158624 DOI: 10.1016/j.envpol.2020.115943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Electrochemically active bacteria (EAB) are effective for the bioreduction of nitroaromatic compounds (NACs), but the exact reduction mechanisms are unclear yet. Therefore, 3-nitrobenzenesulfonate (NBS) was used to explore the biodegradation mechanism of NACs by EAB. Results show that NBS could be anaerobically degraded by Shewanella oneidensis MR-1. The generation of aminoaromatic compounds was accompanied with the NBS reduction, indicating that NBS was biodegraded via reductive approach by S. oneidensis MR-1. The impacts of NBS concentration and cell density on the NBS reduction were evaluated. The removal of NBS depends mainly on the transmembrane electron transfer of S. oneidensis MR-1. Impairment of Mtr respiratory pathway was found to mitigate the reduction of NBS, suggesting that the anaerobic biodegradation of NBS occurred extracellularly. Knocking out cymA severely impaired the extracellular reduction ability of S. oneidensis MR-1. However, the phenotype of ΔcymA mutant could be compensated by the exogenous electron mediators, implying the trans-outer membrane diffusion of mediators into the periplasmic space. This work provides a new insight into the anaerobic reduction of aromatic contaminants by EAB.
Collapse
Affiliation(s)
- Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiao-Lin Ma
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Lu-Guang Wang
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Fei Long
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Ting-Ting Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiang-Tong Zhou
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Hong Liu
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR, 97333, USA
| | - Li-Jun Wu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Han-Qing Yu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.
| |
Collapse
|
8
|
Physiological and Molecular Responses to Main Environmental Stressors of Microalgae and Bacteria in Polar Marine Environments. Microorganisms 2020; 8:microorganisms8121957. [PMID: 33317109 PMCID: PMC7764121 DOI: 10.3390/microorganisms8121957] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/18/2022] Open
Abstract
The Arctic and Antarctic regions constitute 14% of the total biosphere. Although they differ in their physiographic characteristics, both are strongly affected by snow and ice cover changes, extreme photoperiods and low temperatures, and are still largely unexplored compared to more accessible sites. This review focuses on microalgae and bacteria from polar marine environments and, in particular, on their physiological and molecular responses to harsh environmental conditions. The data reported in this manuscript show that exposure to cold, increase in CO2 concentration and salinity, high/low light, and/or combination of stressors induce variations in species abundance and distribution for both polar bacteria and microalgae, as well as changes in growth rate and increase in cryoprotective compounds. The use of -omics techniques also allowed to identify specific gene losses and gains which could have contributed to polar environmental adaptation, and metabolic shifts, especially related to lipid metabolism and defence systems, such as the up-regulation of ice binding proteins, chaperones and antioxidant enzymes. However, this review also provides evidence that -omics resources for polar species are still few and several sequences still have unknown functions, highlighting the need to further explore polar environments, the biology and ecology of the inhabiting bacteria and microalgae, and their interactions.
Collapse
|
9
|
Abe T, Akazawa Y, Toyoda A, Niki H, Baba T. Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes. Front Microbiol 2020; 11:1486. [PMID: 32719664 PMCID: PMC7350273 DOI: 10.3389/fmicb.2020.01486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/08/2020] [Indexed: 02/05/2023] Open
Abstract
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.
Collapse
Affiliation(s)
- Takashi Abe
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Yu Akazawa
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, National Institute of Genetics, Mishima, Japan
| | - Tomoya Baba
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan.,Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan
| |
Collapse
|
10
|
Kloska A, Cech GM, Sadowska M, Krause K, Szalewska-Pałasz A, Olszewski P. Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress. Int J Mol Sci 2020; 21:ijms21124338. [PMID: 32570789 PMCID: PMC7352654 DOI: 10.3390/ijms21124338] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 11/30/2022] Open
Abstract
Marine bacteria display significant versatility in adaptation to variations in the environment and stress conditions, including temperature shifts. Shewanella baltica plays a major role in denitrification and bioremediation in the marine environment, but is also identified to be responsible for spoilage of ice-stored seafood. We aimed to characterize transcriptional response of S. baltica to cold stress in order to achieve a better insight into mechanisms governing its adaptation. We exposed bacterial cells to 8 °C for 90 and 180 min, and assessed changes in the bacterial transcriptome with RNA sequencing validated with the RT-qPCR method. We found that S. baltica general response to cold stress is associated with massive downregulation of gene expression, which covered about 70% of differentially expressed genes. Enrichment analysis revealed upregulation of only few pathways, including aminoacyl-tRNA biosynthesis, sulfur metabolism and the flagellar assembly process. Downregulation was observed for fatty acid degradation, amino acid metabolism and a bacterial secretion system. We found that the entire type II secretion system was transcriptionally shut down at low temperatures. We also observed transcriptional reprogramming through the induction of RpoE and repression of RpoD sigma factors to mediate the cold stress response. Our study revealed how diverse and complex the cold stress response in S. baltica is.
Collapse
Affiliation(s)
- Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
- Correspondence: (A.K.); (P.O.)
| | - Grzegorz M. Cech
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Marta Sadowska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Klaudyna Krause
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Paweł Olszewski
- 3P Medicine Laboratory, International Research Agenda, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
- Correspondence: (A.K.); (P.O.)
| |
Collapse
|
11
|
Lemaire ON, Méjean V, Iobbi-Nivol C. The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic ecosystems. FEMS Microbiol Rev 2020; 44:155-170. [DOI: 10.1093/femsre/fuz031] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
ABSTRACT
The Gram-negative Shewanella bacterial genus currently includes about 70 species of mostly aquatic γ-proteobacteria, which were isolated around the globe in a multitude of environments such as surface freshwater and the deepest marine trenches. Their survival in such a wide range of ecological niches is due to their impressive physiological and respiratory versatility. Some strains are among the organisms with the highest number of respiratory systems, depending on a complex and rich metabolic network. Implicated in the recycling of organic and inorganic matter, they are important components of organism-rich oxic/anoxic interfaces, but they also belong to the microflora of a broad group of eukaryotes from metazoans to green algae. Examples of long-term biological interactions like mutualism or pathogeny have been described, although molecular determinants of such symbioses are still poorly understood. Some of these bacteria are key organisms for various biotechnological applications, especially the bioremediation of hydrocarbons and metallic pollutants. The natural ability of these prokaryotes to thrive and detoxify deleterious compounds explains their use in wastewater treatment, their use in energy generation by microbial fuel cells and their importance for resilience of aquatic ecosystems.
Collapse
Affiliation(s)
- Olivier N Lemaire
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402 Marseille, France
| | - Vincent Méjean
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402 Marseille, France
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, 13402 Marseille, France
| |
Collapse
|
12
|
Hirose A, Kasai T, Koga R, Suzuki Y, Kouzuma A, Watanabe K. Understanding and engineering electrochemically active bacteria for sustainable biotechnology. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0245-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
13
|
Berg K, Leiros I, Williamson A. Temperature adaptation of DNA ligases from psychrophilic organisms. Extremophiles 2019; 23:305-317. [DOI: 10.1007/s00792-019-01082-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/15/2019] [Indexed: 12/20/2022]
|
14
|
Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? Genome Biol Evol 2019; 11:220-231. [PMID: 30496401 PMCID: PMC6336007 DOI: 10.1093/gbe/evy262] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/25/2022] Open
Abstract
The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whereas successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding, and degrading proteins at their ambient temperatures of -1.86 °C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold. The exception was the significant overrepresentation of positions where leucine in temperate fish proteins was replaced by methionine in the notothenioid orthologues. We hypothesize that these extra methionines have been preferentially assimilated into the genome to act as redox sensors in the highly oxygenated waters of the Southern Ocean. This redox hypothesis is supported by analyses of notothenioids showing enrichment of genes associated with responses to environmental stress, particularly reactive oxygen species. So overall, although notothenioid fish show cold-associated problems with protein homeostasis, they may have modified only a selected number of biochemical pathways to work efficiently below 0 °C. Even a slight warming of the Southern Ocean might disrupt the critical functions of this handful of key pathways with considerable impacts for the functioning of this ecosystem in the future.
Collapse
Affiliation(s)
- Camille Berthelot
- Laboratoire Dynamique et Organisation des Génomes (Dyogen), Institut de Biologie de l'Ecole Normale Supérieure – UMR 8197, INSERM U1024, Paris Cedex 05, France
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, United Kingdom
| | | | - H William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Michael Peters
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | | | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| |
Collapse
|
15
|
Raymond-Bouchard I, Goordial J, Zolotarov Y, Ronholm J, Stromvik M, Bakermans C, Whyte LG. Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria. FEMS Microbiol Ecol 2018. [DOI: 10.1093/femsec/fiy023] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Isabelle Raymond-Bouchard
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jacqueline Goordial
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
- Bigelow laboratory for Ocean Sciences, 60 Bigelow Dr, East Boothbay, ME, 04544, USA
| | - Yevgen Zolotarov
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jennifer Ronholm
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Martina Stromvik
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Corien Bakermans
- Altoona College, Pennsylvania State University, 3000 Ivyside Park, Altoona, PA, 16601, USA
| | - Lyle G Whyte
- McGill University, Macdonald Campus, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| |
Collapse
|
16
|
Zhang J, Burgess JG. Enhanced eicosapentaenoic acid production by a new deep-sea marine bacterium Shewanella electrodiphila MAR441T. PLoS One 2017; 12:e0188081. [PMID: 29176835 PMCID: PMC5703452 DOI: 10.1371/journal.pone.0188081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 10/31/2017] [Indexed: 02/05/2023] Open
Abstract
Omega-3 fatty acids are products of secondary metabolism, essential for growth and important for human health. Although there are numerous reports of bacterial production of omega-3 fatty acids, less information is available on the biotechnological production of these compounds from bacteria. The production of eicosapentaenoic acid (EPA, 20:5ω3) by a new species of marine bacteria Shewanella electrodiphila MAR441T was investigated under different fermentation conditions. This strain produced a high percentage (up to 26%) of total fatty acids and high yields (mg / g of biomass) of EPA at or below the optimal growth temperature. At higher growth temperatures these values decreased greatly. The amount of EPA produced was affected by the carbon source, which also influenced fatty acid composition. This strain required Na+ for growth and EPA synthesis and cells harvested at late exponential or early stationary phase had a higher EPA content. Both the highest amounts (20 mg g-1) and highest percent EPA content (18%) occurred with growth on L-proline and (NH4)2SO4. The addition of cerulenin further enhanced EPA production to 30 mg g-1. Chemical mutagenesis using NTG allowed the isolation of mutants with improved levels of EPA content (from 9.7 to 15.8 mg g-1) when grown at 15°C. Thus, the yields of EPA could be substantially enhanced without the need for recombinant DNA technology, often a commercial requirement for food supplement manufacture.
Collapse
Affiliation(s)
- Jinwei Zhang
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratory, Exeter, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - J. Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
17
|
Hoffmann K, Hassenrück C, Salman-Carvalho V, Holtappels M, Bienhold C. Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments. Front Microbiol 2017; 8:266. [PMID: 28286496 PMCID: PMC5323390 DOI: 10.3389/fmicb.2017.00266] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/07/2017] [Indexed: 12/14/2022] Open
Abstract
Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios.
Collapse
Affiliation(s)
- Katy Hoffmann
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Biosciences, HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und MeeresforschungBremerhaven, Germany
| | - Christiane Hassenrück
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Verena Salman-Carvalho
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Biosciences, HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und MeeresforschungBremerhaven, Germany
| | - Moritz Holtappels
- Biosciences, Bentho-Pelagic Processes, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung Bremerhaven, Germany
| | - Christina Bienhold
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Biosciences, HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und MeeresforschungBremerhaven, Germany
| |
Collapse
|
18
|
Yang LL, Tang SK, Huang Y, Zhi XY. Low Temperature Adaptation Is Not the Opposite Process of High Temperature Adaptation in Terms of Changes in Amino Acid Composition. Genome Biol Evol 2015; 7:3426-33. [PMID: 26614525 PMCID: PMC4700962 DOI: 10.1093/gbe/evv232] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. However, the relationship between high and low temperature adaptations remains unclear. To investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substitutional asymmetry in pairs of homologous proteins from related species. We found that changes in amino acid composition associated with low temperature adaptation did not exhibit a coherent opposite trend when compared with changes in amino acid composition associated with high temperature adaptation. This result indicates that during their evolutionary histories the proteome-scale evolutionary patterns associated with prokaryotes exposed to low temperature environments were distinct from the proteome-scale evolutionary patterns associated with prokaryotes exposed to high temperature environments in terms of changes in amino acid composition of the proteins.
Collapse
Affiliation(s)
- Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Shu-Kun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
19
|
Huang J, Ning G, Li F, Sheng GD. Biotransformation of 2,4-dinitrotoluene by obligate marine Shewanella marisflavi EP1 under anaerobic conditions. BIORESOURCE TECHNOLOGY 2015; 180:200-206. [PMID: 25603529 DOI: 10.1016/j.biortech.2014.12.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 06/04/2023]
Abstract
Anaerobic transformation of 2,4-DNT by obligate marine Shewanella marisflavi EP1 was investigated. The cell growth of EP1 was proportional to the total amount of 2,4-DNT reduced. The eventual transformation product was 2,4-diaminotoluene, via 2-amino-4-nitrotoluene and 4-amino-2-nitrotoluene as intermediates. The presence of Cu(2+), dicumarol, metyrapone and flavins intensively influenced the reduction activity of 2,4-DNT, suggesting that dehydrogenease, menaquinone, cytochromes and flavins are essentially involved in electron transport process for 2,4-DNT reduction. These results indicate that biotransformation of 2,4-DNT by EP1 is a form of microbial anaerobic respiration. Furthermore, EP1 was capable of transforming 2,4-DNT at relatively alkaline range of pH (7-9), and at a wide range of temperature (4-40°C) and salinity (2-8% NaCl concentration). Our findings not only deepen our understanding of the environmental fate of 2,4-DNT, but also provide an extension to the application of shewanellae in the site bioremediation and/or wastewater treatment.
Collapse
Affiliation(s)
- Jiexun Huang
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Guojing Ning
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Feili Li
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - G Daniel Sheng
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| |
Collapse
|
20
|
Bae S, Lee Y, Kwon MJ, Lee W. Riboflavin-mediated RDX transformation in the presence of Shewanella putrefaciens CN32 and lepidocrocite. JOURNAL OF HAZARDOUS MATERIALS 2014; 274:24-31. [PMID: 24762697 DOI: 10.1016/j.jhazmat.2014.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/03/2014] [Accepted: 04/05/2014] [Indexed: 06/03/2023]
Abstract
The potential of riboflavin for the reductive degradation of a cyclic nitramine, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), was investigated in the presence of lepidocrocite and/or Shewanella putrefaciens CN32. RDX reduction by CN32 alone or CN32 with lepidocrocite was insignificant, while 110 μM RDX was completely reduced by CN32 with riboflavin in 78 h. The transformation products identified included nitroso metabolites, formaldehyde, and ammonium, indicating the ring cleavage of RDX. UV and visible light analysis revealed that riboflavin was microbially reduced by CN32, and that the reduced riboflavin was linked to the complete degradation of RDX. In the presence of both CN32 and lepidocrocite (γ-FeOOH), 100 μM-riboflavin increased the rate and extent of Fe(II) production as well as RDX reduction. An abiotic study also showed that Fe(II)-riboflavin complex, and Fe(II) adsorbed on lepidocrocite, reduced RDX by 48% and 21%, respectively. The findings in this study suggest that riboflavin-mediated RDX degradation pathways in subsurface environments are diverse and complex. However, riboflavin, either from bacteria or exogenous sources, can significantly increase RDX degradation. This will provide a sustainable clean-up option for explosive-contaminated subsurface environments.
Collapse
Affiliation(s)
- Sungjun Bae
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
| | - Yoonhwa Lee
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Man Jae Kwon
- Environmental Research Group, Korea Institute of Science and Technology, Saimdang-ro, Gangneung 210-340, Republic of Korea
| | - Woojin Lee
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| |
Collapse
|
21
|
Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
Collapse
|
22
|
De Maayer P, Anderson D, Cary C, Cowan DA. Some like it cold: understanding the survival strategies of psychrophiles. EMBO Rep 2014; 15:508-17. [PMID: 24671034 DOI: 10.1002/embr.201338170] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Much of the Earth's surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern "omic" technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field.
Collapse
Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | | | | | | |
Collapse
|
23
|
Bakermans C, Skidmore ML, Douglas S, McKay CP. Molecular characterization of bacteria from permafrost of the Taylor Valley, Antarctica. FEMS Microbiol Ecol 2014; 89:331-46. [DOI: 10.1111/1574-6941.12310] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 12/01/2022] Open
|
24
|
Yang Y, Chen J, Qiu D, Zhou J. Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction. BMC Microbiol 2013; 13:267. [PMID: 24274142 PMCID: PMC4222724 DOI: 10.1186/1471-2180-13-267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 11/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The completion of genome sequencing in a number of Shewanella species, which are most renowned for their metal reduction capacity, offers a basis for comparative studies. Previous work in Shewanella oneidensis MR-1 has indicated that some genes within a cluster (mtrBAC-omcA-mtrFED) were involved in iron reduction. To explore new features of iron reduction pathways, we experimentally analyzed Shewanella putrefaciens W3-18-1 since its gene cluster is considerably different from that of MR-1 in that the gene cluster encodes only four ORFs. RESULTS Among the gene cluster, two genes (mtrC and undA) were shown to encode c-type cytochromes. The ΔmtrC deletion mutant revealed significant deficiencies in reducing metals of Fe2O3, α-FeO(OH), β-FeO(OH), ferric citrate, Mn(IV) and Co(III), but not organic compounds. In contrast, no deficiency of metal reduction was observed in the ΔundA deletion mutant. Nonetheless, undA deletion resulted in progressively slower iron reduction in the absence of mtrC and fitness loss under the iron-using condition, which was indicative of a functional role of UndA in iron reduction. CONCLUSIONS These results provide physiological and biochemical evidences that UndA and MtrC of Shewanella putrefaciens W3-18-1 are involved in iron reduction.
Collapse
Affiliation(s)
- Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | | | | | | |
Collapse
|
25
|
Cheng YY, Li BB, Li DB, Chen JJ, Li WW, Tong ZH, Wu C, Yu HQ. Promotion of iron oxide reduction and extracellular electron transfer in Shewanella oneidensis by DMSO. PLoS One 2013; 8:e78466. [PMID: 24244312 PMCID: PMC3820605 DOI: 10.1371/journal.pone.0078466] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/12/2013] [Indexed: 11/18/2022] Open
Abstract
The dissimilatory metal reducing bacterium Shewanella oneidensis MR-1, known for its capacity of reducing iron and manganese oxides, has great environmental impacts. The iron oxides reducing process is affected by the coexistence of alternative electron acceptors in the environment, while investigation into it is limited so far. In this work, the impact of dimethyl sulphoxide (DMSO), a ubiquitous chemical in marine environment, on the reduction of hydrous ferric oxide (HFO) by S. oneidensis MR-1 was investigated. Results show that DMSO promoted HFO reduction by both wild type and ΔdmsE, but had no effect on the HFO reduction by ΔdmsB, indicating that such a promotion was dependent on the DMSO respiration. With the DMSO dosing, the levels of extracellular flavins and omcA expression were significantly increased in WT and further increased in ΔdmsE. Bioelectrochemical analysis show that DMSO also promoted the extracellular electron transfer of WT and ΔdmsE. These results demonstrate that DMSO could stimulate the HFO reduction through metabolic and genetic regulation in S. oneidensis MR-1, rather than compete for electrons with HFO. This may provide a potential respiratory pathway to enhance the microbial electron flows for environmental and engineering applications.
Collapse
Affiliation(s)
- Yuan-Yuan Cheng
- Department of Chemistry, University of Science & Technology of China, Hefei, China
| | - Bing-Bing Li
- School of Life Sciences, University of Science & Technology of China, Hefei, China
| | - Dao-Bo Li
- Department of Chemistry, University of Science & Technology of China, Hefei, China
| | - Jie-Jie Chen
- Department of Chemistry, University of Science & Technology of China, Hefei, China
| | - Wen-Wei Li
- Department of Chemistry, University of Science & Technology of China, Hefei, China
| | - Zhong-Hua Tong
- Department of Chemistry, University of Science & Technology of China, Hefei, China
| | - Chao Wu
- Department of Chemistry, University of Science & Technology of China, Hefei, China
- * E-mail: (CW); (HQY)
| | - Han-Qing Yu
- Department of Chemistry, University of Science & Technology of China, Hefei, China
- * E-mail: (CW); (HQY)
| |
Collapse
|
26
|
Di Nocera PP, De Gregorio E, Rocco F. GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes. BMC Genomics 2013; 14:522. [PMID: 23902135 PMCID: PMC3733652 DOI: 10.1186/1471-2164-14-522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND REPs (Repetitive Extragenic Palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. RESULTS We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species. CONCLUSIONS CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.
Collapse
Affiliation(s)
- Pier Paolo Di Nocera
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy.
| | | | | |
Collapse
|
27
|
Le PT, Ramulu HG, Guijarro L, Paganini J, Gouret P, Chabrol O, Raoult D, Pontarotti P. An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales. BMC Evol Biol 2012; 12:243. [PMID: 23234643 PMCID: PMC3575314 DOI: 10.1186/1471-2148-12-243] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 11/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species. RESULTS We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as "rhizome-like". CONCLUSIONS Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.
Collapse
Affiliation(s)
- Phuong Thi Le
- Evolutionary biology and modeling, LATP UMR-CNRS 7353, Aix-Marseille University, 13331, Marseille, France
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Arkhipova OV, Mikulinskaya GV, Galushko AS. Comparative analysis of the N-terminal sequence of Geobacter sulfurreducens AM-1 methacrylate reductase. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712050049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
29
|
Perreault NN, Crocker FH, Indest KJ, Hawari J. Involvement of cytochrome c CymA in the anaerobic metabolism of RDX by Shewanella oneidensis MR-1. Can J Microbiol 2012; 58:124-31. [DOI: 10.1139/w11-116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Nancy N. Perreault
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montréal, QC H4P 2R2, Canada
| | - Fiona H. Crocker
- US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS 39180, USA
| | - Karl J. Indest
- US Army Engineer Research and Development Center, 3909 Halls Ferry Road, Vicksburg, MS 39180, USA
| | - Jalal Hawari
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montréal, QC H4P 2R2, Canada
| |
Collapse
|
30
|
Bernstein A, Ronen Z. Biodegradation of the Explosives TNT, RDX and HMX. ENVIRONMENTAL SCIENCE AND ENGINEERING 2012. [DOI: 10.1007/978-3-642-23789-8_5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
31
|
|
32
|
Kwon MJ, O'Loughlin EJ, Antonopoulos DA, Finneran KT. Geochemical and microbiological processes contributing to the transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in contaminated aquifer material. CHEMOSPHERE 2011; 84:1223-1230. [PMID: 21664641 DOI: 10.1016/j.chemosphere.2011.05.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 05/12/2011] [Accepted: 05/13/2011] [Indexed: 05/30/2023]
Abstract
Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a potential human carcinogen, and its contamination of subsurface environments is a significant threat to public health. This study investigated abiotic and biological degradation of RDX in contaminated aquifer material. Anoxic batch systems were started with and without pre-aeration of aquifer material to distinguish initial biological RDX reduction from abiotic RDX reduction. Aerating the sediment eliminated chemical reductants in the native aquifer sediment, primarily Fe(II) sorbed to mineral surfaces. RDX (50 μM) was completely reduced and transformed to ring cleavage products when excess concentrations (2mM) of acetate or lactate were provided as the electron donor for aerated sediment. RDX was reduced concurrently with Fe(III) when acetate was provided, while RDX, Fe(III), and sulfate were reduced simultaneously with lactate amendment. Betaproteobacteria were the dominant microorganisms associated with RDX and Fe(III)/sulfate reduction. In particular, Rhodoferax spp. increased from 21% to 35% and from 28% to 60% after biostimulation by acetate and lactate, respectively. Rarefaction analyses demonstrated that microbial diversity decreased in electron-donor-amended systems with active RDX degradation. Although significant amounts of Fe(III) and/or sulfate were reduced after biostimulation, solid-phase reactive minerals such as magnetite or ferrous sulfides were not observed, suggesting that RDX reduction in the aquifer sediment is due to Fe(II) adsorbed to solid surfaces as a result of Fe(III)-reducing microbial activity. These results suggest that both biotic and abiotic processes play an important role in RDX reduction under in situ conditions.
Collapse
Affiliation(s)
- Man Jae Kwon
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States.
| | | | | | | |
Collapse
|
33
|
Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger-Desfeux C, Hommais F, Guéguen L, Daubin V, Muller D, Nesme X. Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol 2011; 3:762-81. [PMID: 21795751 PMCID: PMC3163468 DOI: 10.1093/gbe/evr070] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.
Collapse
Affiliation(s)
- Florent Lassalle
- Université de Lyon, Université Lyon 1, CNRS, INRA, Laboratoire Ecologie Microbienne Lyon, UMR 5557, USC 1193, Villeurbanne, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Aminov RI. Horizontal gene exchange in environmental microbiota. Front Microbiol 2011; 2:158. [PMID: 21845185 PMCID: PMC3145257 DOI: 10.3389/fmicb.2011.00158] [Citation(s) in RCA: 354] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 07/11/2011] [Indexed: 01/21/2023] Open
Abstract
Horizontal gene transfer (HGT) plays an important role in the evolution of life on the Earth. This view is supported by numerous occasions of HGT that are recorded in the genomes of all three domains of living organisms. HGT-mediated rapid evolution is especially noticeable among the Bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. At the heart of the HGT-driven bacterial evolution and adaptation are highly sophisticated natural genetic engineering tools in the form of a variety of mobile genetic elements (MGEs). The main aim of this review is to give a brief account of the occurrence and diversity of MGEs in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.
Collapse
Affiliation(s)
- Rustam I Aminov
- Rowett Institute of Nutrition and Health, University of Aberdeen Aberdeen, UK
| |
Collapse
|
35
|
Molecular adaptations to psychrophily: the impact of 'omic' technologies. Trends Microbiol 2010; 18:374-81. [PMID: 20646925 DOI: 10.1016/j.tim.2010.05.002] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 05/12/2010] [Accepted: 05/18/2010] [Indexed: 11/20/2022]
Abstract
The ability of cold-adapted microorganisms (generally referred to as psychrophiles) to survive is the result of molecular evolution and adaptations which, together, counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. These physiological adaptations are seen at many levels. Against a background of detailed comparative protein structural analyses, the recent surge of psychrophile proteome, genome, metagenome and transcriptome sequence data has triggered a series of sophisticated analyses of changes in global protein composition. These studies have revealed consistent and statistically robust changes in amino acid composition, interpreted as evolutionary mechanisms designed to destabilise protein structures, as well as identifying the presence of novel genes involved in cold adaptation.
Collapse
|