Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes

[1]  A. Barausse,et al.  Editorial: Fluctuating Habitats: Ecological Relevance of Environmental Variability and Predictability on Species, Communities, and Ecosystems , 2022, Frontiers in Ecology and Evolution.

[2]  M. Huber,et al.  The latitudinal temperature gradient and its climate dependence as inferred from foraminiferal δ18O over the past 95 million years , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Farooq Sher,et al.  Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems , 2022, Archives of Microbiology.

[4]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[5]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[6]  M. Ferrer,et al.  Use of Flavin-Containing Monooxygenases for Conversion of Trimethylamine in Salmon Protein Hydrolysates , 2020, Applied and Environmental Microbiology.

[7]  Filipa L. Sousa,et al.  Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism , 2020, Nature Microbiology.

[8]  Joey R. Bernhardt,et al.  Life in fluctuating environments , 2020, Philosophical Transactions of the Royal Society B.

[9]  H. Gohlke,et al.  Promiscuous esterases counterintuitively are less flexible than specific ones , 2020, bioRxiv.

[10]  Patrick C. F. Buchholz,et al.  The modular structure of α/β‐hydrolases , 2020, The FEBS journal.

[11]  C. Guerra,et al.  Global projections of the soil microbiome in the Anthropocene , 2020, Global ecology and biogeography : a journal of macroecology.

[12]  T. Bell,et al.  Bacterial adaptation is constrained in complex communities , 2020, Nature Communications.

[13]  Holger Gohlke,et al.  Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A , 2020, J. Chem. Inf. Model..

[14]  D. Warner,et al.  Ecologically relevant thermal fluctuations enhance offspring fitness: biological and methodological implications for studies of thermal developmental plasticity , 2020, Journal of Experimental Biology.

[15]  D. Warner,et al.  Ecologically relevant thermal fluctuations enhance offspring fitness: biological and methodological implications for studies of thermal developmental plasticity , 2020, Journal of Experimental Biology.

[16]  B. Jones,et al.  Temporal evolution of temperatures in the Red Sea and the Gulf of Aden based on in situ observations (1958–2017) , 2019 .

[17]  Ellen Willis-Norton,et al.  Ecological change in dynamic environments: Accounting for temporal environmental variability in studies of ocean change biology , 2019, Global change biology.

[18]  M. Ferrer,et al.  Functional microbiome deficits associated with ageing: Chronological age threshold , 2019, Aging cell.

[19]  R. Bandopadhyay,et al.  Emergent climate change impact throughout the world: call for “Microbiome Conservation” before it’s too late , 2019, Biodiversity and Conservation.

[20]  D. Daffonchio,et al.  Oxygen supersaturation protects coastal marine fauna from ocean warming , 2019, Science Advances.

[21]  F. Bozinovic,et al.  Thermal performance across levels of biological organization , 2019, Philosophical Transactions of the Royal Society B.

[22]  Justin V Remais,et al.  Climate change microbiology — problems and perspectives , 2019, Nature Reviews Microbiology.

[23]  A. Lorz,et al.  Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity , 2019, Nature Communications.

[24]  T. Ravasi,et al.  Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change , 2019, Philosophical Transactions of the Royal Society B.

[25]  M. Desvaux,et al.  Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan , 2019, Front. Microbiol..

[26]  T. Crowther,et al.  Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation , 2018 .

[27]  M. Bradford,et al.  Soil microbial respiration adapts to ambient temperature in global drylands , 2018, Nature Ecology & Evolution.

[28]  M. Ferrer,et al.  Bioprospecting Reveals Class III ω-Transaminases Converting Bulky Ketones and Environmentally Relevant Polyamines , 2018, Applied and Environmental Microbiology.

[29]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[30]  A. D. Mazaris,et al.  Biologists ignore ocean weather at their peril , 2018, Nature.

[31]  I. Oliver,et al.  Effects of climate legacies on above‐ and belowground community assembly , 2018, Global change biology.

[32]  Jianjian Zhuang,et al.  Study on the Correlation between Gene Expression and Enzyme Activity of Seven Key Enzymes and Ginsenoside Content in Ginseng in Over Time in Ji’an, China , 2017, International journal of molecular sciences.

[33]  Jürgen Pleiss,et al.  Determinants and Prediction of Esterase Substrate Promiscuity Patterns. , 2017, ACS chemical biology.

[34]  Michael D. Lee,et al.  Comment on “The complex effects of ocean acidification on the prominent N2-fixing cyanobacterium Trichodesmium” , 2017, Science.

[35]  Vito M. R. Muggeo,et al.  Interval estimation for the breakpoint in segmented regression: a smoothed score‐based approach , 2017 .

[36]  K. Tait,et al.  Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments , 2017, Front. Microbiol..

[37]  I. Hoteit,et al.  Decadal trends in Red Sea maximum surface temperature , 2017, Scientific Reports.

[38]  N. Fierer,et al.  Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities , 2017, Nature Ecology & Evolution.

[39]  Christian A Hanke,et al.  Rigidity theory for biomolecules: concepts, software, and applications , 2017 .

[40]  J. Pinhassi,et al.  Marine Bacterioplankton Seasonal Succession Dynamics. , 2017, Trends in microbiology.

[41]  R. Kopp,et al.  IPCC reasons for concern regarding climate change risks , 2016 .

[42]  C. Voolstra,et al.  Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea , 2016, PloS one.

[43]  E. van Sebille,et al.  Drift in ocean currents impacts intergenerational microbial exposure to temperature , 2016, Proceedings of the National Academy of Sciences.

[44]  Antonín Pavelka,et al.  CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules , 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[45]  Holger Gohlke,et al.  Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis , 2016, PLoS Comput. Biol..

[46]  Yun‐wei Dong,et al.  The importance of thermal history: costs and benefits of heat exposure in a tropical, rocky shore oyster , 2016, Journal of Experimental Biology.

[47]  M. Ferrer,et al.  Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases , 2016, Applied and Environmental Microbiology.

[48]  Holger Gohlke,et al.  Trading off stability against activity in extremophilic aldolases , 2016, Scientific Reports.

[49]  Rafael Bargiela,et al.  Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends , 2015, Microbial biotechnology.

[50]  G. Pesole,et al.  Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase , 2015, Applied Microbiology and Biotechnology.

[51]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[52]  Holger Gohlke,et al.  Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis , 2015, PloS one.

[53]  Z. Johnson,et al.  Thermally adaptive tradeoffs in closely related marine bacterial strains. , 2015, Environmental microbiology.

[54]  Luis Pedro Coelho,et al.  Structure and function of the global ocean microbiome , 2015, Science.

[55]  A. Roitberg,et al.  Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. , 2015, Journal of chemical theory and computation.

[56]  Jed A. Fuhrman,et al.  Marine microbial community dynamics and their ecological interpretation , 2015, Nature Reviews Microbiology.

[57]  T. Nechitaylo,et al.  Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics , 2015, Applied and Environmental Microbiology.

[58]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[59]  A. Boetius,et al.  Bacterial taxa–area and distance–decay relationships in marine environments , 2014, Molecular ecology.

[60]  M. Bradford Thermal adaptation of decomposer communities in warming soils , 2013, Front. Microbiol..

[61]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.

[62]  H. Heipieper,et al.  Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica , 2013, Nature Communications.

[63]  Ruth M. Potrafka,et al.  Temperature Drives the Continental-Scale Distribution of Key Microbes in Topsoil Communities , 2013, Science.

[64]  Ibrahim Hoteit,et al.  Remote Sensing the Phytoplankton Seasonal Succession of the Red Sea , 2013, PloS one.

[65]  Holger Gohlke,et al.  CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function , 2013, Nucleic Acids Res..

[66]  Holger Gohlke,et al.  Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function , 2013, J. Chem. Inf. Model..

[67]  Andreas W. Götz,et al.  SPFP: Speed without compromise - A mixed precision model for GPU accelerated molecular dynamics simulations , 2013, Comput. Phys. Commun..

[68]  Holger Gohlke,et al.  Global and local indices for characterizing biomolecular flexibility and rigidity , 2013, J. Comput. Chem..

[69]  L. Riemann,et al.  Effect of resource availability on bacterial community responses to increased temperature , 2013 .

[70]  Joanna R. Bernhardt,et al.  Resilience to climate change in coastal marine ecosystems. , 2013, Annual review of marine science.

[71]  Antonín Pavelka,et al.  CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures , 2012, PLoS Comput. Biol..

[72]  A. Libchaber,et al.  Pressure and temperature dependence of growth and morphology of Escherichia coli: experiments and stochastic model. , 2012, Biophysical journal.

[73]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[74]  Holger Gohlke,et al.  Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio. , 2012, Journal of biotechnology.

[75]  Charles Troupin,et al.  Bio‐ORACLE: a global environmental dataset for marine species distribution modelling , 2012 .

[76]  Ibrahim Hoteit,et al.  Abrupt warming of the Red Sea , 2011 .

[77]  Holger Gohlke,et al.  Protein rigidity and thermophilic adaptation , 2011, Proteins.

[78]  A. Hoffmann,et al.  Climate change and evolutionary adaptation , 2011, Nature.

[79]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[80]  H. Pörtner,et al.  Oxygen- and capacity-limitation of thermal tolerance: a matrix for integrating climate-related stressor effects in marine ecosystems , 2010, Journal of Experimental Biology.

[81]  G. Somero,et al.  The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine ‘winners’ and ‘losers’ , 2010, Journal of Experimental Biology.

[82]  A. Farrell,et al.  Physiology and Climate Change , 2008, Science.

[83]  H. Gohlke,et al.  Exploiting the Link between Protein Rigidity and Thermostability for Data‐Driven Protein Engineering , 2008 .

[84]  T. Cheatham,et al.  Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations , 2008, The journal of physical chemistry. B.

[85]  W. Thuiller Biodiversity: Climate change and the ecologist , 2007, Nature.

[86]  Alan Y. Chiang,et al.  Generalized Additive Models: An Introduction With R , 2007, Technometrics.

[87]  R. Redman,et al.  A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance , 2007, Science.

[88]  C. Pace,et al.  Measuring the conformational stability of a protein by NMR. , 2006, CSH protocols.

[89]  S. Wood Generalized Additive Models: An Introduction with R , 2006 .

[90]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[91]  M. Thorpe,et al.  Protein flexibility using constraints from molecular dynamics simulations , 2005, Physical biology.

[92]  C. S. Holling,et al.  Regime Shifts, Resilience, and Biodiversity in Ecosystem Management , 2004 .

[93]  G. Feller,et al.  Psychrophilic enzymes: hot topics in cold adaptation , 2003, Nature Reviews Microbiology.

[94]  Marti J. Anderson,et al.  CANONICAL ANALYSIS OF PRINCIPAL COORDINATES: A USEFUL METHOD OF CONSTRAINED ORDINATION FOR ECOLOGY , 2003 .

[95]  Neo D. Martinez,et al.  Food-web structure and network theory: The role of connectance and size , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[96]  D. Jacobs,et al.  Protein flexibility predictions using graph theory , 2001, Proteins.

[97]  P. Casper,et al.  Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples. , 2000, Journal of microbiological methods.

[98]  J. Richardson,et al.  Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. , 1999, Journal of molecular biology.

[99]  V. Riis,et al.  Extraction of microorganisms from soil: evaluation of the efficiency by counting methods and activity measurements , 1998 .

[100]  S. L. Mayo,et al.  Automated design of the surface positions of protein helices , 1997, Protein science : a publication of the Protein Society.

[101]  C. Pace,et al.  How to measure and predict the molar absorption coefficient of a protein , 1995, Protein science : a publication of the Protein Society.

[102]  R. Rosson,et al.  Improved Method of Enumeration of Attached Bacteria for Study of Fluctuation in the Abundance of Attached and Free-Living Bacteria in Response to Diel Variation in Seawater Turbidity , 1990, Applied and environmental microbiology.

[103]  G. Somero,et al.  Biochemical Adaptation: Mechanism and Process in Physiological Evolution , 1984 .

[104]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[105]  E. Borer,et al.  Biodiversity change is uncoupled from species richness trends: Consequences for conservation and monitoring , 2018 .

[106]  Scott T. Bates,et al.  Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. , 2015, Ecology letters.

[107]  G. Somero The physiology of global change: linking patterns to mechanisms. , 2012, Annual review of marine science.

[108]  M. Angilletta Thermal Adaptation: A Theoretical and Empirical Synthesis , 2009 .

[109]  W. W. Lathem,et al.  A Virus in a Fungus in a Plant : Three-Way Symbiosis Required for Thermal Tolerance , 2007 .

[110]  G. Somero,et al.  Proteins and temperature. , 1995, Annual review of physiology.

[111]  P. Privalov,et al.  Stability of protein structure and hydrophobic interaction. , 1988, Advances in protein chemistry.