Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

Zhu, Daochen; Adebisi, Wasiu Adewale; Ahmad, Fiaz; Sethupathy, Sivasamy; Danso, Blessing; Sun, Jianzhong

doi:10.3389/fbioe.2020.00483

Cited by 116 publications

(62 citation statements)

References 183 publications

(183 reference statements)

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“…Extremophilic bacteria have proven to be an excellent source of highly resistant proteins for several industries, such as in biofuel production, biorefinery, bioremediation, or the revalorization of agricultural waste products, such as lignocellulosic material ( Zhu et al, 2020 ). However, many of these applications rely on genetic engineering techniques and synthetic biology and represent only a fraction of their possibilities.…”

Section: Discussionmentioning

confidence: 99%

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

et al. 2021

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One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.

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Section: Discussionmentioning

confidence: 99%

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

et al. 2021

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“…Acidophilic bacteria survive in acidic environments with pH 1 to 5. Their high membrane impermeability and membrane potential reversal are some of the functions that make them good prospects in industrial applications [ 45 ]. Barophilic microorganisms can live in environments with irregular pressure levels.…”

Section: Distribution Of Lignocellulolytic Bacteriamentioning

confidence: 99%

“…There are also halotolerant organisms that can grow in highly saline conditions and normal conditions as well. Lignocellulolytic enzymes like cellulase, xylanase, and laccase, used in the production of biofuel, when derived from halophilic and halotolerant sources are very stable [ 45 ].…”

Section: Distribution Of Lignocellulolytic Bacteriamentioning

confidence: 99%

“…Bioenergy comprises various forms of energy sources, whether they are liquid, gaseous, or solid. These arise from a bio-refinery which is a platform that employs the use of biomass to produces bioenergy [ 45 ]. The saccharification of lignocellulose biomass leads to a release of sugars which can be used for downstream production of useful products [ 48 ].…”

Section: Bio-refinery Productsmentioning

confidence: 99%

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A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products

Chukwuma

Rafatullah

Tajarudin

et al. 2021

IJERPH

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Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.

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“…This may alleviate, to significant extent, scale up problems of mixing and aeration and enable greater substrate loadings. Elevated temperatures can also enable more costeffective recovery of volatile products by distillation (preferably continuous) or gas stripping that would reduce inhibition of products, therefore, prolonging the fermenting life of cultures and resulting in increased yields 26,27 . Despite their potential, no examples of industrial microbial production using thermophilic organisms exist on a commercial scale.…”

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confidence: 99%

Efficient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant

Adalsteinsson

Kristjansdottir

Merre

et al. 2021

Sci Rep

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Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. We identified CaldoCas9 and designed an associated guide RNA and showed that the pair have targetable nuclease activity in vitro at temperatures up to 65 °C. We performed a detailed characterization of the protospacer adjacent motif specificity of CaldoCas9, which revealed a preference for 5′-NNNNGNMA. We constructed a plasmid vector for the delivery and use of the CaldoCas9 based genome editing system in the extreme thermophile Thermus thermophilus at 65 °C. Using the vector, we generated gene knock-out mutants of T. thermophilus, targeting genes on the bacterial chromosome and megaplasmid. Mutants were obtained at a frequency of about 90%. We demonstrated that the vector can be cured from mutants for a subsequent round of genome editing. CRISPR-Cas9 based genome editing has not been reported previously in the extreme thermophile T. thermophilus. These results may facilitate development of genome editing tools for other extreme thermophiles and to that end, the vector has been made available via the plasmid repository Addgene.

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Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

Cited by 116 publications

References 183 publications

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products

Efficient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant

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