Halobacterium sp. SP1(1) as a starter culture for accelerating fish sauce fermentation

Recent advances in the production, properties and applications of haloextremozymes protease and lipase from haloarchaea

Proteases and lipases are significant groups of enzymes for commercialization at the global level. Earlier, the industries depended on mesophilic proteases and lipases, which remain nonfunctional under extreme conditions. The discovery of extremophilic microorganisms, especially those belonging to haloarchaea, paved a new reserve of industrially competent extremozymes. Haloarchaea or halophilic archaea are polyextremophiles of domain Archaea that grow at high salinity, elevated temperature, pH range (pH 6-12), and low aw. Interestingly, haloarchaeal proteolytic and lipolytic enzymes also perform their catalytic function in the presence of 4-5 M NaCl in vivo and in vitro. Also, they are of great interest to study due to their capacity to function and are active at elevated temperatures, tolerance to pH extremes, and in non-aqueous media. In recent years, advances have been achieved in various aspects of genomic/molecular expression methods involving homologous and heterologous processes for the overproduction of these extremozymes and their characterization from haloarchaea. A few protease and lipase extremozymes have been successfully expressed in prokaryotic systems, especially E.coli, and enzyme modification techniques have improved the catalytic properties of the recombinant enzymes. Further, in-silico methods are currently applied to elucidate the structural and functional features of salt-stable protease and lipase in haloarchaea. In this review, the production and purification methods, catalytic and biochemical properties and biotechnological applications of haloextremozymes proteases and lipases are summarized along with recent advancements in overproduction and characterization of these enzymes, concluding with the directions for further in-depth research on proteases and lipases from haloarchaea.

Marine enzymes: Classification and application in various industries

Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.

Comparative Genomics of Halobacterium salinarum Strains Isolated from Salted Foods Reveals Protechnological Genes for Food Applications

Archaeal cell factories are becoming of great interest given their ability to produce a broad range of value-added compounds. Moreover, the Archaea domain often includes extremophilic microorganisms, facilitating their cultivation at the industrial level under nonsterile conditions. Halophilic archaea are studied for their ability to grow in environments with high NaCl concentrations. In this study, nine strains of Halobacterium salinarum were isolated from three different types of salted food, sausage casings, salted codfish, and bacon, and their genomes were sequenced along with the genome of the collection strain CECT 395. A comparative genomic analysis was performed on these newly sequenced genomes and the publicly available ones for a total of 19 H. salinarum strains. We elucidated the presence of unique gene clusters of the species in relation to the different ecological niches of isolation (salted foods, animal hides, and solar saltern sediments). Moreover, genome mining at the single-strain level highlighted the metabolic potential of H. salinarum UC4242, which revealed the presence of different protechnological genes (vitamins and myo-inositol biosynthetic pathways, aroma- and texture-related features, and antimicrobial compounds). Despite the presence of genes of potential concern (e.g., those involved in biogenic amine production), all the food isolates presented archaeocin-related genes (halocin-C8 and sactipeptides).

Changes in protease activity during fermentation of fish sauce and their correlation with antioxidant activity

BACKGROUND

Antioxidant activity has been found in fermented fish sauce. In this experiment, the properties of endogenous protease and antioxidant activity were studied in anchovy sauce during fermentation. The correlation between protease activity and antioxidant activity in fermented anchovy sauce was analyzed using the partial least squares (PLS) method.

RESULTS

The results showed that at least four proteases were present in the endogenous enzyme solution, and the optimum pH values were 2.5, 5.5, 9.0, and 12.5, respectively. The maximum inhibition rate of endogenous protease, from high to low, was: serine protease inhibitor > trypsin inhibitor > aspartic protease inhibitor (pepsin inhibitor) > cysteine protease inhibitor > metalloprotease inhibitor. At the sixth month of fermentation, fish sauce had stronger trypsin, pepsin-like activity, and antioxidant activity. At the ninth month of fermentation, the cathepsin activity was greater. A model correlating changes in protease activity with antioxidant activity suggested that the trypsin and serine protease were the main factors affecting antioxidant activity.

CONCLUSION

This study reports a model correlating changes in protease activity with the antioxidant activity of fish sauce. It lays a foundation for further exploration of the formation of antioxidant substances and antioxidant effects during the process of fish sauce fermentation. © 2021 Society of Chemical Industry.

Rice flour powder carrying mixed starter culture of Lactiplantibacillus plantarum KU-LM173 and Pediococcus acidilactici KU-LM145 for fermented mussel, Perna viridis Linnaeus 1758

AIMS

To develop a dried rice flour powder (DP) formulation to contain a lactic acid bacterial starter culture for fermenting mussel meat (FM).

METHODS AND RESULTS

Lactiplantibacillus plantarum KU-LM173 (LP), Enterococcus hirae KU-LM174 and Pediococcus acidilactici KU-LM145 (PA) were selected from commercial FMs and identified to have high acid and protease production. Mixed culture between LP, for high acid production, and PA, for the flavour, was the best for DP and had greater organoleptic properties than a single starter fermentation. The best ratio of DP for production was 1% of the mussel weight, while the highest numeric scoring of the organoleptic test between 3% and 6%. The starter culture fermentation accelerated over the natural (wild) fermentation and ended at day 3. The shelf life of the product was at least 30 days at 30-35°C with no pathogens detected. The shelf life of DP at 4°C was 10 weeks.

CONCLUSIONS

DP with the best strains and long shelf life promoted safety of FM and reduced the processing time. High consumer acceptance, protease and acid production and flavour were unique product characteristics.

SIGNIFICANCE AND IMPACT OF STUDY

Accelerated commercial FMs with effective DP formulation for the industrial sector may be plausible.

Genome sequencing of cold-adapted Planococcus bacterium isolated from traditional shrimp paste and protease identification

BACKGROUND

Psychrophiles have evolved to adapt to freezing environments, and cold-adapted enzymes from these organisms can maintain high catalytic activity at low temperature. The use of cold-adapted enzymes has great potential for the revolution of food and molecular biology industries.

RESULTS

In this study, four different strains producing protease were isolated from traditional fermented shrimp paste, one of which, named Planococcus maritimus XJ11 by 16S rRNA nucleotide sequence analysis, exhibited the largest protein hydrolysis clear zone surrounding the colonies. Meanwhile, the strain P. maritimus XJ11 was selected for further investigation because of its great adaptation to low temperature, low salinity and alkaline environment. The enzyme activity assay of P. maritimus XJ11 indicated that the optimum conditions for catalytic activity were pH 10.0 and 40 °C. Moreover, the enzyme also showed an increasing activity with temperatures from 10 to 40 °C and retained more than 67% activity of the maximum over a broad range of salinity (50-150 g L^-1 ). Genome sequencing analysis revealed that strain XJ11 possessed one circular chromosome of 3 282 604 bp and one circular plasmid of 67 339 bp, with a total number of 3293 open reading frames (ORFs). Besides, 21 genes encoding protease, including three serine proteases, were identified through the NR database.

CONCLUSION

Cold-adapted bacterium P. maritimus XJ11 was capable of producing alkaline proteases with high catalytic efficiency at low or moderate temperatures. Furthermore, the favorable psychrophilic and enzymatic characters of strain P. maritimus XJ11 seem to have a promising potential for industrial application. © 2020 Society of Chemical Industry.

Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments

As a group, the halophilic archaea (class Halobacteria) are the most salt-requiring and salt-resistant microorganisms within the domain Archaea. Halophilic archaea flourish in thalassohaline and athalassohaline environments and require over 100-150 g/L NaCl for growth and structural stability. Natural hypersaline environments vary in salt concentration, chemical composition and pH, and occur in climates ranging from tropical to polar and even under-sea. Accordingly, their resident haloarchaeal species vary enormously, as do their individual population compositions and community structures. These diverse halophilic archaeal strains are precious resources for theoretical and applied research but assessing their taxonomic and metabolic novelty and diversity in natural environments has been technically difficult up until recently. Environmental DNA-based high-throughput sequencing technology has now matured sufficiently to allow inexpensive recovery of massive amounts of sequence data, revealing the distribution and community composition of halophilic archaea in different hypersaline environments. While cultivation of haloarchaea is slow and tedious, and only recovers a fraction of the natural diversity, it is the conventional means of describing new species, and provides strains for detailed study. As of the end of May 2020, the class Halobacteria contains 71 genera and 275 species, 49.8% of which were first isolated from the marine salt environment and 50.2% from the inland salt environment, indicating that both thalassohaline and athalassohaline environments contain diverse halophilic archaea. However, there remain taxa that have not yet been isolated in pure culture, such as the nanohaloarchaea, which are widespread in the salt environment and may be one of the hot spots in the field of halophilic archaea research in the future. In this review, we focus on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00087-3.

The life and times of yeasts in traditional food fermentations

Yeasts are eukaryotic microorganisms which have a long history in the biotechnology of food production, as they have been used since centuries in bread-making or in the production of alcoholic beverages such as wines or beers. Relative to this importance, a lot of research has been devoted to the study of yeasts involved in making these important products. The role of yeasts in other fermentations in association with other microorganisms - mainly lactic acid bacteria - has been relatively less studied, and often it is not clear if yeasts occurring in such fermentations are contaminants with no role in the fermentation, spoilage microorganisms or whether they actually serve a technological or functional purpose. Some knowledge is available for yeasts used as starter cultures in fermented raw sausages or in the production of acid curd cheeses. This review aimed to summarize the current knowledge on the taxonomy, the presence and potential functional or technological roles of yeasts in traditional fermented plant, dairy, fish and meat fermentations.

Dynamic Changes in the Bacterial Community During the Fermentation of Traditional Chinese Fish Sauce (TCFS) and Their Correlation with TCFS Quality

This study revealed for the first time the dynamic changes of the bacterial community during the fermentation of traditional Chinese fish sauce (TCFS) using high-throughput sequencing. In the early phase of TCFS fermentation, Shewanella (approximately 90%) within Proteobacteria was the dominant bacteria. Then, Halanaerobium (3%-86%) within Firmicutes rapidly replaced Shewanella as the dominant genus until the 12th month. Lactococcus (3.31%) and Bacillus (45.56%) belonging to Firmicutes were detected abundantly in the 3rd and 9th months after fermentation, respectively. In the late phase (12-15 months), Tetragenococcus within Firmicutes replaced Halanaerobium as the most dominant bacteria (29.54%). Many other genera including Pseudomonas, Psychrobacter, Tissierella, Carnobacterium and Gallicola were abundantly present in the 15th month after fermentation. Furthermore, the relationships between the bacterial community and major functional substances of TCFS, including amino nitrogen (AAN), free amino acids (FAAs), total soluble nitrogen (TSN), and trimethylamine (TMA), were investigated by partial least squares regression (PLSR). Tetragenococcus was positively correlated with the formation of TMA, while Halanaerobium showed the opposite result, suggesting that Tetragenococcus might be a good starter for TCFS fermentation. These results contribute to our knowledge about bacterial participation in the process of TCFS fermentation and will help improve the quality of fermented seafood.

Alkaline and Halophilic Protease Production by Bacillus luteus H11 and Its Potential Industrial Applications

This paper presents the results of the study on the production of protease by Bacillus luteus H11 isolated from an alkaline soda lime. B. luteus H11 was identified as an alkalohalophilic bacterium, and its extracellular serine endoprotease also showed an extreme alkali- and halotolerance. It was remarkably stable in the presence of NaCl up to 5 M. The enzyme was active in a broad range of pH values and temperatures, with an optimum pH of 10.5 and a temperature of 45 °C. It had a molecular mass of about 37 kDa and showed activity against azocasein and a synthetic substrate for the subtilisin-like protease, N-succinyl-l-phenylalanine-p-nitroanilide. The halo-alkaline protease produced by B. luteus H11 seems to be significant from an industrial perspective because of its tolerance towards high salinity and alkalinity as well as its stability against some organic solvents, surfactants and oxidants. These properties make the protease suitable for applications in food, detergent and pharmaceutical industries, and also in environmental bioremediation.

Halobacterium salinarum storage and rehydration after spray drying and optimization of the processes for preservation of carotenoids

Spray drying is appropriate for the preservation of halophilic microorganisms due to the nature of these microorganisms, as they survive in adverse environmental conditions by being encapsulated in salt crystals. Artificial neural networks were in this study used to optimize practically significant spray-drying regimes of the C₅₀-carotenoids producer Halobacterium salinarum. Immediately after drying, the samples contained up to 54% halobacterial biomass and less than 5% moisture, and the level of preservation of carotenoids was 95-97%. The storage of biomass at 4 °C resulted in the gradual degradation of the carotenoids, which reached 58-64% in the best samples after 1 year. A comprehensive study of changes in halobacteria biomass after spray drying and the nature of the damage provided new data on the survival and preservation of cells and biologically active substances in the various spray-drying regimes and at different storage times.

Isolation, characterization and exploring biotechnological potential of halophilic archaea from salterns of western India

Thirteen halophilic archaea were isolated from Kandla and Bhayander salt pans. These isolates were grouped into three different genera Halobacterium, Haloferax and Haloarcula based on morphological and biochemical characterization, polar lipid analysis, Amplified 16S rDNA restriction analysis (ARDRA) and 16S rDNA sequence analysis. Biochemical characterization suggested the ability of isolates to produce protease, amylase and poly-hydroxybutyrate (PHB) indicating their biotechnological potential. The isolates were further screened for the amount of extracellular protease produced. Halobacterium sp. SP1(1) showed significant protease production compared to other isolates. Protease producing ability of the isolate was influenced by several factors such as NaCl concentration, type of protein source, metal ions and surfactants, and presence of amino acid supplements in the production medium. Soybean flour, FeCl₃ and dicotylsulfosuccinate were found to increase protease production by 2.36, 1.54 and 1.26 folds, respectively compared to production in basal medium. Effect of organic solvents used in paints (n-decane, n-undecane and n-dodecane) was also investigated on protease production by the isolate. Protease production by Halobacterium sp. SP1(1) was enhanced by 1.2 folds in presence of n-decane compared to control. Furthermore, the ability of isolate to hydrolyse fish protein was investigated using three different edible fishes (Pomfret, Flat fish and Seer fish) as sole protein source. Pomfret was found to be a good protein source for protease production by the isolate. These results revealed that Halobacterium sp. SP1(1) may have potential for paint-based antifouling coating preparations and fish sauce preparation by virtue of its extracellular protease.

Quality improvement on half-fin anchovy (Setipinna taty) fish sauce by Psychrobacter sp. SP-1 fermentation

BACKGROUND

A method of improving fish sauce quality during fermentation was investigated. Psychrobacter sp. SP-1, a halophilic protease-producing bacterium, was isolated from fish sauce with flavor-enhancing properties and non-biogenic amine-producing activity. The performance of Psychrobacter sp. SP-1 in Setipinna taty fish sauce fermentation was investigated further.

RESULTS

The inoculation of Psychrobacter sp. SP-1 did not significantly affect pH or NaCl concentration changes (P > 0.05), although it significantly increased total moderately halophilic microbial count, protease activity, total soluble nitrogen content and amino acid nitrogen content, and also promoted the umami taste and meaty aroma (P < 0.05). Furthermore, the inoculation of Psychrobacter sp. SP-1 significantly decreased total volatile basic nitrogen content and biogenic amines content (P < 0.05), which were regarded as harmful compounds in foods.

CONCLUSION

The results of the present study demonstrate that Psychrobacter sp. SP-1 can be used as a potential starter culture for improving fish sauce quality by fermentation. © 2017 Society of Chemical Industry.

Haloarchaea: worth exploring for their biotechnological potential

Halophilic archaea are unique microorganisms adapted to survive under high salt conditions and biomolecules produced by them may possess unusual properties. Haloarchaeal metabolites are stable at high salt and temperature conditions that are useful for industrial applications. Proteins and enzymes of this group of archaea are functional under salt concentrations at which bacterial counterparts fail to be active. Such properties makes haloarchaeal enzymes suitable for salt-based applications and their use under dehydrating conditions. For example, bacteriorhodopsin or the purple membrane protein present in halophilic archaea has the most recognizable applications in photoelectric devices, artificial retinas, holograms etc. Haloarchaea are also useful for bioremediation of polluted hypersaline areas. Polyhydroxyalkanoates and exopolysccharides produced by these microorganisms are biodegradable and have the potential to replace commercial non-degradable plastics and polymers. Moreover, halophilic archaea have excellent potential to be used as drug delivery systems and for nanobiotechnology by virtue of their gas vesicles and S-layer glycoproteins. Despite of possible applications of halophilic archaea, laboratory-to-industrial transition of these potential candidates is yet to be established.

Purification and characterisation of a salt-stable protease from the halophilic archaeon Halogranum rubrum

BACKGROUND

Because proteases play an important role in the fermentation of fish sauce, the purification and characterisation of an extracellular protease from the halophilic archaeon Halogranum rubrum was investigated.

RESULTS

The molecular mass of the protease was estimated to be approximately 47 kDa based on sodium dodecyl sulfate-polyacrylamide gel electropheresis (SDS-PAGE) and native-PAGE analysis. The optimum conditions for catalytic activity were pH 8.0 and 50°C. The protease showed alkaline stability (pH 7.0-10.0). The protease also exhibited novel catalytic ability over a broad range of salinity (NaCl 0-3 mol L^-1 ). Calcium ion enhanced the proteolytic activity of the enzyme. The K_m and V_max values of the purified protease for casein were calculated to be 4.89 mg mL^-1 and 1111.11 U mL^-1 , respectively. The protease was strongly inhibited by ethylenediamine tetraacetic acid (EDTA) and phenylmethanesulfonyl fluoride (PMSF). Meanwhile, the protease was stable in the presence of Triton X-100, isopropanol, ethanol or dithio-bis-nitrobenzoic (DTNB), but was inhibited by sodium dodecyl sulfate (SDS), dimethyl sulfoxide (DMSO) or methanol. MALDI -TOF/TOF MS analysis revealed that the protease shared some functional traits with protease produced by Halogranum salarium. Furthermore, it exhibited high hydrolytic activity on silver carp myosin protein.

CONCLUSION

The protease is an alkaline and salt-tolerant enzyme that hydrolyses silver carp myosin with high efficiency. These excellent characteristics make this protease an attractive candidate for industrial use in low-salt fish sauce fermentation. © 2016 Society of Chemical Industry.

Composition and Metabolic Activities of the Bacterial Community in Shrimp Sauce at the Flavor-Forming Stage of Fermentation As Revealed by Metatranscriptome and 16S rRNA Gene Sequencings

The bacterial community and the metabolic activities involved at the flavor-forming stage during the fermentation of shrimp sauce were investigated using metatranscriptome and 16S rRNA gene sequencings. Results showed that the abundance of Tetragenococcus was 95.1%. Tetragenococcus halophilus was identified in 520 of 588 transcripts annotated in the Nr database. Activation of the citrate cycle and oxidative phosphorylation, along with the absence of lactate dehydrogenase gene expression, in T. halophilus suggests that T. halophilus probably underwent aerobic metabolism during shrimp sauce fermentation. The metabolism of amino acids, production of peptidase, and degradation of limonene and pinene were very active in T. halophilus. Carnobacterium, Pseudomonas, Escherichia, Staphylococcus, Bacillus, and Clostridium were also metabolically active, although present in very small populations. Enterococcus, Abiotrophia, Streptococcus, and Lactobacillus were detected in metatranscriptome sequencing, but not in 16S rRNA gene sequencing. Many minor taxa showed no gene expression, suggesting that they were in dormant status.

Extracellular proteases of Halobacillus blutaparonensis strain M9, a new moderately halophilic bacterium

Halophilic microorganisms are source of potential hydrolytic enzymes to be used in industrial and/or biotechnological processes. In the present study, we have investigated the ability of the moderately halophilic bacterium Halobacillus blutaparonensis (strain M9), a novel species described by our group, to release proteolytic enzymes. This bacterial strain abundantly proliferated in Luria-Bertani broth supplemented with 2.5% NaCl as well as secreted proteases to the extracellular environment. The production of proteases occurred in bacterial cells grown under different concentration of salt, ranging from 0.5% to 10% NaCl, in a similar way. The proteases secreted by H. blutaparonensis presented the following properties: (i) molecular masses ranging from 30 to 80 kDa, (ii) better hydrolytic activities under neutral-alkaline pH range, (iii) expression modulated according to the culture age, (iv) susceptibility to phenylmethylsulphonyl fluoride, classifying them as serine-type proteases, (v) specific cleavage over the chymotrypsin substrate, and (vi) enzymatic stability in the presence of salt (up to 20% NaCl) and organic solvents (e.g., ether, isooctane and cyclohexane). The proteases described herein are promising for industrial practices due to its haloalkaline properties.

Function and biotechnology of extremophilic enzymes in low water activity

Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology.

Could halophilic archaea improve the traditional salted anchovies (Engraulis encrasicholus L.) safety and quality?

AIMS

The positive influence of two selected extremely halophilic archaea strains in the production of salted anchovies (Engraulis encrasicolus, L., 1758) was highlighted.

METHODS AND RESULTS

Anchovies produced with salt artificially contaminated with halophiles exhibited lower loads of staphylococci, Enterobacteriaceae and lactic acid bacteria, and a reduced content of histamine as well as an improved organoleptic acceptance.

CONCLUSIONS

The findings of this survey are expected to enhance the safety of salted anchovies, with regard to the histamine formation during ripening, and to improve the sensory attributes of this product.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study represents the first report on the positive influence of halophilic archaea in traditional salted anchovies production, thus suggesting new perspectives about a conscious employment of properly selected haloarchaea strains in this traditional manufacture.

A novel organic solvent tolerant protease from a newly isolated Geomicrobium sp. EMB2 (MTCC 10310): production optimization by response surface methodology

Thirty-eight haloalkaliphilic bacterial strains were isolated from Sambhar Salt Lake, India and screened for their ability to secrete haloalkaliphilic proteases. Among them, a moderately halophilic, mesophilic and alkaliphilic potent strain Geomicrobium sp. EMB2 produced an extracellular protease, which was remarkably stable in organic solvents, salt, surfactants, detergents and alkaline pH. Statistically based experimental designs were applied to study the interactions and optimization of medium constituents for efficient protease production by Geomicrobium sp. EMB2. An overall 20-fold increase in protease production was achieved in the optimized medium (721 U/ml) as compared with the unoptimized medium (37 U/ml). The high production level coupled with novel properties makes it a prospective industrial enzyme. The Geomicrobium sp. EMB2 isolate is deposited in Microbial Type Culture Collection, Chandigarh, India with accession number MTCC 10310.