• Clomburg J.M.
• et al.

Industrial biomanufacturing: the future of chemical production.

Science. 2017; 355aag0804

• Philp J.C.
• et al.

Biobased chemicals: the convergence of green chemistry with industrial biotechnology.

Trends Biotechnol. 2013; 31: 219-222

• Steen E.J.
• et al.

Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol.

Microb. Cell Factories. 2008; 7: 36

• Chen G.Q.
• et al.

Engineering biosynthesis mechanisms for diversifying polyhydroxyalkanoates.

Trends Biotechnol. 2015; 33: 565-574

• Fang H.
• et al.

Metabolic engineering of Escherichia coli for de novo biosynthesis of vitamin B12.

Nat. Commun. 2018; 9: 4917

• Chen G.Q.
• Jiang X.R.

Next generation industrial biotechnology based on extremophilic bacteria.

Curr. Opin. Biotechnol. 2018; 50: 94-100

• Zhang X.
• et al.

Halophiles as chassis for bioproduction.

Adv. Biosyst. 2018; 21800088

• Coker J.A.

Recent advances in understanding extremophiles.

F1000Research. 2019; 8: 1917

• Tan D.
• et al.

Engineering Halomonas TD01 for the low-cost production of polyhydroxyalkanoates.

Metab. Eng. 2014; 26: 34-47

• Tao W.
• et al.

Engineering Halomonas species TD01 for enhanced polyhydroxyalkanoates synthesis via CRISPRi.

Microb. Cell Factories. 2017; 16: 48

• Ye J.
• et al.

Pilot scale-up of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) production by Halomonas bluephagenesis via cell growth adapted optimization process.

Biotechnol. J. 2018; 13e1800074

• Sarilmiser H.K.
• et al.

Effective stimulating factors for microbial levan production by Halomonas smyrnensis AAD6T.

J. Biosci. Bioeng. 2015; 119: 455-463

• Obruca S.
• et al.

Polyhydroxyalkanoates synthesis by halophiles and thermophiles: towards sustainable production of microbial bioplastics.

Biotechnol. Adv. 2022; 58107906

Polyhydroxyalkanoate biosynthesis at the edge of water activity-Haloarchaea as biopolyester factories.

Bioengineering (Basel). 2019; 6: 34

• Krulwich T.A.
• et al.

Molecular aspects of bacterial pH sensing and homeostasis.

Nat. Rev. Microbiol. 2011; 9: 330-343

• Toivari M.
• et al.

Low pH D-xylonate production with Pichia kudriavzevii.

Bioresour. Technol. 2013; 133: 555-562

• Xiao H.
• et al.

Exploiting Issatchenkia orientalis SD108 for succinic acid production.

Microb. Cell Factories. 2014; 13: 121

• Park H.J.
• et al.

Low-pH production of d-lactic acid using newly isolated acid tolerant yeast Pichia kudriavzevii NG7.

Biotechnol. Bioeng. 2018; 115: 2232-2242

• Sousa J.A.
• et al.

Ecology and application of haloalkaliphilic anaerobic microbial communities.

Appl. Microbiol. Biotechnol. 2015; 99: 9331-9336

• Pikuta E.V.
• et al.

Microbial extremophiles at the limits of life.

Crit. Rev. Microbiol. 2007; 33: 183-209

• Zhu D.
• et al.

Recent development of extremophilic bacteria and their application in biorefinery.

Front Bioeng. Biotechnol. 2020; 8: 483

• Wernick D.G.
• et al.

Sustainable biorefining in wastewater by engineered extreme alkaliphile Bacillus marmarensis.

Sci. Rep. 2016; 6: 20224

• Bhandiwad A.
• et al.

Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production.

Metab. Eng. 2014; 21: 17-25

• Tian L.
• et al.

Metabolic engineering of Clostridium thermocellum for n-butanol production from cellulose.

Biotechnol. Biofuels. 2019; 12: 186

• Khongto B.
• et al.

Fermentation process development of recombinant Hansenula polymorpha for gamma-linolenic acid production.

J. Microbiol. Biotechnol. 2010; 20: 1555-1562

• Löbs A.K.
• et al.

CRISPR-Cas9-enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in Kluyveromyces marxianus.

Biotechnol. Biofuels. 2017; 10: 164

• Atalah J.
• et al.

Thermophiles and the applications of their enzymes as new biocatalysts.

Bioresour. Technol. 2019; 280: 478-488

• Giovanella P.
• et al.

Metal and organic pollutants bioremediation by extremophile microorganisms.

J. Hazard. Mater. 2020; 382121024

• Gabani P.
• Singh O.V.

Radiation-resistant extremophiles and their potential in biotechnology and therapeutics.

Appl. Microbiol. Biotechnol. 2013; 97: 993-1004

• Shukla M.
• et al.

Multiple-stress tolerance of ionizing radiation-resistant bacterial isolates obtained from various habitats: correlation between stresses.

Curr. Microbiol. 2007; 54: 142-148

• Ye J.W.
• Chen G.Q.

Halomonas as a chassis.

Essays Biochem. 2021; 65: 393-403

• Lan L.H.
• et al.

Engineering Halomonas spp. as a low-cost production host for production of bio-surfactant protein PhaP.

Biotechnol. J. 2016; 11: 1595-1604

• Xu T.
• et al.

Deficiency of exopolysaccharides and O-antigen makes Halomonas bluephagenesis self-flocculating and amenable to electrotransformation.

Commun. Biol. 2022; 5: 623

• Baker T.A.
• Wickner S.H.

Genetics and enzymology of DNA replication in Escherichia coli.

Annu. Rev. Genet. 1992; 26: 447-477

• Chung D.
• et al.

Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus.

PLoS One. 2013; 8e62881

• Li T.
• et al.

Engineering of core promoter regions enables the construction of constitutive and inducible promoters in Halomonas sp.

Biotechnol. J. 2016; 11: 219-227

• Zhao H.
• et al.

Novel T7-like expression systems used for Halomonas.

Metab. Eng. 2017; 39: 128-140

• Shen R.
• et al.

Promoter engineering for enhanced P(3HB-co-4HB) production by Halomonas bluephagenesis.

ACS Synth. Biol. 2018; 7: 1897-1906

• Spath K.
• et al.

Direct cloning in Lactobacillus plantarum: electroporation with non-methylated plasmid DNA enhances transformation efficiency and makes shuttle vectors obsolete.

Microb. Cell Factories. 2012; 11: 141

• Martínez-García E.
• et al.

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts.

Nucleic Acids Res. 2020; 48: 1164-1170

• Lammens E.M.
• et al.

SEVAtile: a standardised DNA assembly method optimised for Pseudomonas.

Microb. Biotechnol. 2022; 15: 370-386

• Klapatch T.R.
• et al.

Restriction endonuclease activity in Clostridium thermocellum and Clostridium thermosaccharolyticum.

Appl. Microbiol. Biotechnol. 1996; 45: 127-131

• Clifton K.P.
• et al.

The genetic insulator RiboJ increases expression of insulated genes.

J. Biol. Eng. 2018; 12: 23

• Olson D.G.
• et al.

Identifying promoters for gene expression in Clostridium thermocellum.

Metab. Eng. Commun. 2015; 2: 23-29

• Luo Y.
• et al.

Systematic identification of a panel of strong constitutive promoters from Streptomyces albus.

ACS Synth. Biol. 2015; 4: 1001-1010

• Zhang Y.
• et al.

A promoter engineering-based strategy enhances polyhydroxyalkanoate production in Pseudomonas putida KT2440.

Int. J. Biol. Macromol. 2021; 191: 608-617

• Sun W.
• et al.

Integration of metabolic pathway manipulation and promoter engineering for the fine-tuned biosynthesis of malic acid in Bacillus coagulans.

Biotechnol. Bioeng. 2021; 118: 2597-2608

• Lammens E.M.
• et al.

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria.

Nat. Commun. 2020; 11: 5294

• Hueso-Gil A.
• et al.

Multiple-site diversification of regulatory sequences enables interspecies operability of genetic devices.

ACS Synth. Biol. 2020; 9: 104-114

• Meyers A.
• et al.

Cell density-dependent auto-inducible promoters for expression of recombinant proteins in Pseudomonas putida.

Microb. Biotechnol. 2019; 12: 1003-1013

• Wang X.
• et al.

Reversible thermal regulation for bifunctional dynamic control of gene expression in Escherichia coli.

Nat. Commun. 2021; 12: 1411

• Qin Q.
• et al.

CRISPR/Cas9 editing genome of extremophile Halomonas spp.

Metab. Eng. 2018; 47: 219-229

• Zhao C.
• et al.

Engineered Halomonas spp. for production of L-lysine and cadaverine.

Bioresour. Technol. 2022; 349126865

• Yin J.
• et al.

Development of an enhanced chromosomal expression system based on porin synthesis operon for halophile Halomonas sp.

Appl. Microbiol. Biotechnol. 2014; 98: 8987-8997

• Wang L.J.
• et al.

Engineering Halomonas bluephagenesis via small regulatory RNAs.

Metab. Eng. 2022; 73: 58-69

• Yin J.
• et al.

Effects of chromosomal gene copy number and locations on polyhydroxyalkanoate synthesis by Escherichia coli and Halomonas sp.

Appl. Microbiol. Biotechnol. 2015; 99: 5523-5534

• Marx C.J.
• Lidstrom M.E.

Broad-host-range cre-lox system for antibiotic marker recycling in Gram-negative bacteria.

Biotechniques. 2002; 33: 1062-1067

• Weinstock M.T.
• et al.

Vibrio natriegens as a fast-growing host for molecular biology.

Nat. Methods. 2016; 13: 849-851

• Xu T.
• et al.

Efficient genome editing in Clostridium cellulolyticum via CRISPR-Cas9 nickase.

Appl. Environ. Microbiol. 2015; 81: 4423-4431

• Walker J.E.
• et al.

Development of both type I-B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum.

Metab. Eng. Commun. 2020; 10e00116

• Shi F.
• et al.

Ribosomal binding site sequences and promoters for expressing glutamate decarboxylase and producing γ-aminobutyrate in Corynebacterium glutamicum.

AMB Express. 2018; 8: 61

• Stiller L.M.
• et al.

Engineering the salt-inducible ectoine promoter region of Halomonas elongata for protein expression in a unique stabilizing environment.

Genes (Basel). 2018; 9: 184

• Ye J.
• et al.

Stimulus response-based fine-tuning of polyhydroxyalkanoate pathway in Halomonas.

Metab. Eng. 2020; 57: 85-95

• Yu L.P.
• et al.

Biosynthesis of functional polyhydroxyalkanoates by engineered Halomonas bluephagenesis.

Metab. Eng. 2020; 59: 119-130

• Ma H.
• et al.

Rational flux-tuning of Halomonas bluephagenesis for co-production of bioplastic PHB and ectoine.

Nat. Commun. 2020; 11: 3313

• Chen Y.
• et al.

Chromosome engineering of the TCA cycle in Halomonas bluephagenesis for production of copolymers of 3-hydroxybutyrate and 3-hydroxyvalerate (PHBV).

Metab. Eng. 2019; 54: 69-82

• Du H.
• et al.

Engineering Halomonas bluephagenesis for L-threonine production.

Metab. Eng. 2020; 60: 119-127

• Gupta A.
• et al.

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit.

Nat. Biotechnol. 2017; 35: 273-279

• Ma Y.
• et al.

Engineering an oleic acid-induced system for Halomonas, E. coli and Pseudomonas.

Metab. Eng. 2022; 72: 325-336

• Jiang X.R.
• et al.

Controlling cell volume for efficient PHB production by Halomonas.

Metab. Eng. 2017; 44: 30-37

• Wang Z.
• et al.

Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties.

Metab. Eng. 2021; 67: 53-66

• Ouyang P.
• et al.

Increasing oxygen availability for improving poly(3-hydroxybutyrate) production by Halomonas.

Metab. Eng. 2018; 45: 20-31

• Ling C.
• et al.

Engineering self-flocculating Halomonas campaniensis for wastewaterless open and continuous fermentation.

Biotechnol. Bioeng. 2019; 116: 805-815

• Ling C.
• et al.

Engineering NADH/NAD⁺ ratio in Halomonas bluephagenesis for enhanced production of polyhydroxyalkanoates (PHA).

Metab. Eng. 2018; 49: 275-286

• Liu X.
• et al.

Identification of genome integration sites for developing a CRISPR-based gene expression toolkit in Yarrowia lipolytica.

Microb. Biotechnol. 2022; 15: 2223-2234

• Liu X.
• et al.

Rapid quantification of polyhydroxyalkanoates accumulated in living cells based on green fluorescence protein-labeled phasins: the qPHA method.

Biomacromolecules. 2022; 23: 4153-4166

• Wang B.L.
• et al.

Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption.

Nat. Biotechnol. 2014; 32: 473-478

• Schulze S.
• et al.

The archaeal proteome project advances knowledge about archaeal cell biology through comprehensive proteomics.

Nat. Commun. 2020; 11: 3145

• Mori Y.
• Shirai T.

Designing artificial metabolic pathways, construction of target enzymes, and analysis of their function.

Curr. Opin. Biotechnol. 2018; 54: 41-44

• Zhao Q.
• et al.

High ectoine production by an engineered Halomonas hydrothermalis Y2 in a reduced salinity medium.

Microb. Cell Factories. 2019; 18: 184

• Liu M.
• et al.

Identification of the biosynthetic pathway of glycine betaine that is responsible for salinity tolerance in halophilic Thioalkalivibrio versutus D301.

Front. Microbiol. 2022; 13875843

• Ram S.
• et al.

Bacteria as an alternate biofactory for carotenoid production: a review of its applications, opportunities and challenges.

J. Funct. Foods. 2020; 67103867

• Zhang Y.
• et al.

Systems metabolic engineering of Vibrio natriegens for the production of 1,3-propanediol.

Metab. Eng. 2021; 65: 52-65

• Elleuche S.
• et al.

Extremozymes-biocatalysts with unique properties from extremophilic microorganisms.

Curr. Opin. Biotechnol. 2014; 29: 116-123

• Lee S.Y.
• et al.

A comprehensive metabolic map for production of bio-based chemicals.

Nat. Catal. 2019; 2: 18-33

• Keasling J.
• et al.

Microbial production of advanced biofuels.

Nat. Rev. Microbiol. 2021; 19: 701-715

• Meng W.
• et al.

Non-sterilized fermentation of 2,3-butanediol with seawater by metabolic engineered fast-growing Vibrio natriegens.

Front Bioeng. Biotechnol. 2022; 10955097

• Ibrahim M.H.
• Steinbüchel A.

High-cell-density cyclic fed-batch fermentation of a poly(3-hydroxybutyrate)-accumulating thermophile, Chelatococcus sp. strain MW10.

Appl. Environ. Microbiol. 2010; 76: 7890-7895

• Peleg M.
• et al.

The Arrhenius equation revisited.

Crit. Rev. Food Sci. Nutr. 2012; 52: 830-851

• Blum P.
• et al.

Experimental microbial evolution of extremophiles.

in: Rampelotto P.H. Biotechnology of Extremophiles. Springer, 2016: 619-636

• Wang Y.
• et al.

Microbial engineering for easy downstream processing.

Biotechnol. Adv. 2019; 37107365

• Shen R.
• et al.

Manipulation of polyhydroxyalkanoate granular sizes in Halomonas bluephagenesis.

Metab. Eng. 2019; 54: 117-126

• Do D.T.H.
• et al.

Organic wastes as feedstocks for non-conventional yeast-based bioprocesses.

Microorganisms. 2019; 7: 229

• Mohanty S.S.
• et al.

A critical review on various feedstocks as sustainable substrates for biosurfactants production: a way towards cleaner production.

Microb. Cell Factories. 2021; 20: 120

• Lopes M.
• et al.

Microbial valorization of waste cooking oils for valuable compounds production – a review.

Crit. Rev. Environ. Sci. Technol. 2019; 50: 2583-2616

• Chavan S.
• et al.

A review on production of polyhydroxyalkanoate (PHA) biopolyesters by thermophilic microbes using waste feedstocks.

Bioresour. Technol. 2021; 341125900

• Li M.
• et al.

Tailor-made polyhydroxyalkanoates by reconstructing Pseudomonas entomophila.

Adv. Mater. 2021; 33e2102766

• Lin Y.
• et al.

Engineering Halomonas bluephagenesis as a chassis for bioproduction from starch.

Metab. Eng. 2021; 64: 134-145

• Van Dyk J.S.
• Pletschke B.I.

A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes – factors affecting enzymes, conversion and synergy.

Biotechnol. Adv. 2012; 30: 1458-1480

• Zhao Z.
• et al.

Biochemical routes for uptake and conversion of xylose by microorganisms.

Biotechnol. Biofuels. 2020; 13: 21

• Tiso T.
• et al.

Towards bio-upcycling of polyethylene terephthalate.

Metab. Eng. 2021; 66: 167-178

• Trotsenko Y.A.
• Khmelenina V.N.

Biology of extremophilic and extremotolerant methanotrophs.

Arch. Microbiol. 2002; 177: 123-131

• Gurdo N.
• et al.

Merging automation and fundamental discovery into the design–build–test–learn cycle of nontraditional microbes.

Trends Biotechnol. 2022; 40: 1148-1159

• Zhang X.
• et al.

Response surface methodology for the optimization of ultrasound-assisted extraction of tetrodotoxin from the liver of Takifugu pseudommus.

Toxins (Basel). 2018; 10: 529

• Costello Z.
• Martin H.G.

A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data.

NPJ Syst. Biol. Appl. 2018; 4: 19

• Scheper T.
• et al.

Digitalization and bioprocessing: promises and challenges.

Adv. Biochem. Eng. Biotechnol. 2021; 176: 57-69

• Darlington A.P.S.
• Bates D.G.

Architectures for combined transcriptional and translational resource allocation controllers.

Cell Syst. 2020; 11: 382-392

• Zhu J.
• et al.

Factors for promoting polyhydroxyalkanoate (PHA) synthesis in bio-nutrient-removal and recovery system.

IOP Conf. Ser. Earth Environ. Sci. 2018; 178012021

• Lo T.M.
• et al.

A two-layer gene circuit for decoupling cell growth from metabolite production.

Cell Syst. 2016; 3: 133-143

• Quillaguaman J.
• et al.

Poly(beta-hydroxybutyrate) production by a moderate halophile, Halomonas boliviensis LC1 using starch hydrolysate as substrate.

J. Appl. Microbiol. 2005; 99: 151-157

• Yue H.
• et al.

A seawater-based open and continuous process for polyhydroxyalkanoates production by recombinant Halomonas campaniensis LS21 grown in mixed substrates.

Biotechnol. Biofuels. 2014; 7: 108

• Tan D.
• et al.

Unsterile and continuous production of polyhydroxybutyrate by Halomonas TD01.

Bioresour. Technol. 2011; 102: 8130-8136

• Ye J.
• et al.

Engineering of Halomonas bluephagenesis for low cost production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) from glucose.

Metab. Eng. 2018; 47: 143-152

• Wang Z.
• et al.

Hyperproduction of PHA copolymers containing high fractions of 4-hydroxybutyrate (4HB) by outer membrane-defected Halomonas bluephagenesis grown in bioreactors.

Microb. Biotechnol. 2022; 15: 1586-1597

• Jiang X.R.
• et al.

Hyperproduction of 3-hydroxypropionate by Halomonas bluephagenesis.

Nat. Commun. 2021; 12: 1513

• Fu X.Z.
• et al.

Development of Halomonas TD01 as a host for open production of chemicals.

Metab. Eng. 2014; 23: 78-91

• Erkorkmaz B.A.
• et al.

Development of a cost-effective production process for Halomonas levan.

Bioprocess Biosyst. Eng. 2018; 41: 1247-1259

• Hannya A.
• et al.

Efficient production and secretion of oxaloacetate from Halomonas sp. KM-1 under aerobic conditions.

AMB Express. 2017; 7: 209

• Kawata Y.
• et al.

Efficient production and secretion of pyruvate from Halomonas sp. KM-1 under aerobic conditions.

AMB Express. 2016; 6: 22

• Manfrão-Netto J.H.C.
• et al.

Advances in using Hansenula polymorpha as chassis for recombinant protein production.

Front Bioeng. Biotechnol. 2019; 7: 94

• Merino N.
• et al.

Living at the extremes: extremophiles and the limits of life in a planetary context.

Front. Microbiol. 2019; 10: 780

• Dhakar K.
• Pandey A.

Wide pH range tolerance in extremophiles: towards understanding an important phenomenon for future biotechnology.

Appl. Microbiol. Biotechnol. 2016; 100: 2499-2510

• Tsuji A.
• et al.

Establishment of genetic tools for genomic DNA engineering of Halomonas sp. KM-1, a bacterium with potential for biochemical production.

Microb. Cell Factories. 2022; 21: 122