Metagenomic exploration of cold-active enzymes for detergent applications: Characterization of a novel, cold-active and alkali-stable GH8 endoglucanase from ikaite columns in SW Greenland.

Microbial communities from extreme environments are largely understudied, but are essential as producers of metabolites, including enzymes, for industrial processes. As cultivation of most microorganisms remains a challenge, culture-independent approaches for enzyme discovery in the form of metagenomics to analyse the genetic potential of a community are rapidly becoming the way forward. This study focused on analysing a metagenome from the cold and alkaline ikaite columns in Greenland, identifying 282 open reading frames (ORFs) that encoded putative carbohydrate-modifying enzymes with potential applications in, for example detergents and other processes where activity at low temperature and high pH is desired.

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland.

The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column.

The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome.

The Greenland Ice Sheet is a biome which is mainly microbially driven. Several different niches can be found within the glacial biome for those microbes able to withstand the harsh conditions, e.g.

Complete genome sequence of "Bacillaceae sp. strain IKA-2": a cold-active, amylase-producing bacterium from ikaite columns in SW Greenland.

Bacillaceae sp. strain IKA-2 is a bacterium isolated from the permanently cold and alkaline ikaite columns in the Ikka Fjord in SW Greenland (61°12'05″N; 48°00'50″W). The bacterium grows well at 10°C in a substrate buffered to pH 10.

Plant-Root Exudate Analogues Influence Activity of the 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Gene in G20-18.

Plants exposed to abiotic stress such as drought and salinity produce 1-aminocyclopropane-1-carboxylic acid (ACC) that is converted into the stress hormone ethylene. However, plant growth-promoting bacteria (PGPB), which synthesize the enzyme ACC deaminase, may lower the ACC concentration thereby reducing the concentration of ethylene and alleviating the abiotic stress. The PGPB G20-18 (previously named G20-18) harbors the genes and that encode regulation and synthesis of ACC deaminase, respectively.

sp. nov., a plant hormone producing bacterium isolated from Arctic grass, Ellesmere Island, Canada.

Bacterial strain G20-18 was previously isolated from the rhizosphere of an Arctic grass on Ellesmere Island, Canada and was characterized and described as . However, new polyphasic analyses coupled with phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 5-25 °C (optimum, 20-25 °C), at pH 5-9 (optimum, pH 6-7) and with 0-4 % NaCl (optimum, 2 % NaCl).

Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches.

The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats.

Constructing Marine Bacterial Metabolic Chassis for Potential Biorefinery of Red Algal Biomass and Agaropectin Wastes.

Marine red algal biomass is a promising feedstock for sustainable production of value-added chemicals. However, the major constituents of red algal biomass, such as agar and carrageenan, are not easily assimilated by most industrial metabolic chassis developed to date. Synthetic biology offers a solution by utilizing nonmodel organisms as metabolic chassis for consolidated biological processes.

Characterization of a novel cold-adapted intracellular serine protease from the extremophile Or1.

The enzymes of microorganisms that live in cold environments must be able to function at ambient temperatures. Cold-adapted enzymes generally have less ordered structures that convey a higher catalytic rate, but at the cost of lower thermodynamic stability. In this study, we characterized P355, a novel intracellular subtilisin protease (ISP) derived from the genome of Or1, which is a bacterium metabolically active down to -25°C.

sp. nov. isolated from a suppressive potato field in Greenland.

The bacterial strain In5 was previously isolated from a suppressive potato field in southern Greenland and has been characterized and described as . However, the results of new polyphasic analyses coupled with those of phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 4-28 °C (optimum temperature 20-25 °C) and at pH 5-9 (optimum pH 6-7).

Enzymatic Process for the Carrageenolytic Bioconversion of Sulfated Polygalactans into β-Neocarrabiose and 3,6-Anhydro-d-galactose.

Oligosaccharides and anhydro-sugars derived from carrageenan have great potential as functional foods and drugs showing various bioactivities, including antioxidant, anti-inflammatory, antiviral, antitumor, and cytotoxic activities. Although preparation of sulfated carrageenan oligosaccharides by chemical and enzymatic processes has been widely reported, preparation of nonsulfated β-neocarrabiose (β-NC2) and the rare sugar 3,6-anhydro-d-galactose (d-AHG) was not reported in the literature. Based on the carrageenan catabolic pathway in marine heterotrophic bacteria, an enzymatic process was designed and constructed with recombinant κ-carrageenase, GH127/GH129 α-1,3 anhydrogalactosidase, and cell-free extract from marine carrageenolytic bacteria A3.

Characterization of five marine family 29 glycoside hydrolases reveals an α-L-fucosidase targeting specifically Fuc(α1,4)GlcNAc.

$\text{L} $ -Fucose is the most widely distributed $\text{L} $-hexose in marine and terrestrial environments and presents a variety of functional roles. $\text{L} $-Fucose is the major monosaccharide in the polysaccharide fucoidan from cell walls of brown algae and is found in human milk oligosaccharides (HMOs) and the Lewis blood group system, where it is important in cell signaling and immune response stimulation. Removal of fucose from these biomolecules is catalyzed by fucosidases belonging to different carbohydrate-active enzyme (CAZy) families.

A Novel Auxiliary Agarolytic Pathway Expands Metabolic Versatility in the Agar-Degrading Marine Bacterium Colwellia echini A3.

Marine microorganisms encode a complex repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of algal cell wall polysaccharides. While the core enzyme cascade for degrading agar is conserved across agarolytic marine bacteria, gain of novel metabolic functions can lead to the evolutionary expansion of the gene repertoire. Here, we describe how two less-abundant GH96 α-agarases harbored in the agar-specific polysaccharide utilization locus (PUL) of Colwellia echini strain A3 facilitate the versatility of the agarolytic pathway.

Fungal-Associated Molecules Induce Key Genes Involved in the Biosynthesis of the Antifungal Secondary Metabolites Nunamycin and Nunapeptin in the Biocontrol Strain Pseudomonas fluorescens In5.

In5 synthesizes the antifungal cyclic lipopeptides (CLPs) nunamycin and nunapeptin, which are similar in structure and genetic organization to the pseudomonas-derived phytotoxins syringomycin and syringopeptin. Regulation of syringomycin and syringopeptin is dependent on the two-component global regulatory system GacS-GacA and the SalA, SyrF, and SyrG transcription factors, which activate syringomycin synthesis in response to plant signal molecules. Previously, we demonstrated that a specific transcription factor, NunF, positively regulates the synthesis of nunamycin and nunapeptin in In5 and that the gene is upregulated by fungal-associated molecules.

sp. nov., a new antifungal species isolated from potato ().

A novel bacterial strain, S40, with strong antifungal activity was isolated from the rhizosphere of green potato collected from Zealand, Denmark. Polyphasic analysis with a combined phenotypic, phylogenetic and genomic approach was used to characterize S40. Phylogenetic analysis based on the 16S rRNA gene and MLSA (concatenated , , and sequences) showed that strain S40 was affiliated with the genus and with PRI-2C as the closest related strain [average nucleotide identity (ANI), 99.

Identification and Characterization of a β--Acetylhexosaminidase with a Biosynthetic Activity from the Marine Bacterium S66.

β--Acetylhexosaminidases are glycoside hydrolases (GHs) acting on -acetylated carbohydrates and glycoproteins with the release of -acetylhexosamines. Members of the family GH20 have been reported to catalyze the transfer of -acetylglucosamine (GlcNAc) to an acceptor, i.e.

Discovery of a Bacterial Gene Cluster for Deglycosylation of Toxic Potato Steroidal Glycoalkaloids α-Chaconine and α-Solanine.

Potato juice is a byproduct of starch processing currently used as feed. However, potato proteins are an untapped source of high-protein food for human nutrition if harmful constituents notably glycoalkaloids (GAs) are detoxified. The two principle GAs found in potato are α-chaconine and α-solanine, both consisting of a solanidine aglycone with a carbohydrate side chain.

A Multifunctional Polysaccharide Utilization Gene Cluster in Encodes Enzymes for the Complete Degradation of κ-Carrageenan, ι-Carrageenan, and Hybrid β/κ-Carrageenan.

Algal cell wall polysaccharides constitute a large fraction in the biomass of marine primary producers and are thus important in nutrient transfer between trophic levels in the marine ecosystem. In order for this transfer to take place, polysaccharides must be degraded into smaller mono- and disaccharide units, which are subsequently metabolized, and key components in this degradation are bacterial enzymes. The marine bacterium A3 is a potent enzyme producer since it completely hydrolyzes agar and κ-carrageenan.

Transglycosylating β-d-galactosidase and α-l-fucosidase from Paenibacillus sp. 3179 from a hot spring in East Greenland.

Thermal springs are excellent locations for discovery of thermostable microorganisms and enzymes. In this study, we identify a novel thermotolerant bacterial strain related to Paenibacillus dendritiformis, denoted Paenibacillus sp. 3179, which was isolated from a thermal spring in East Greenland.

Imaging Gene Expression Dynamics in In5 duringInteractions with the Fungus PH-1.

Genomics, transcriptomics and metabolomics are powerful technologies for studying microbial interactions. The main drawback of these methods is the requirement for destructive sampling. We have established an alternative but complementary technique based on a microplate system combined with promoter fusions for visualizing gene expression in space and time.

Draft Genome Sequences of Two Glycoalkaloid-Degrading Strains Isolated from Green Potato Peel.

Here, we report the genome sequences of two sp. strains isolated from potato and capable of degrading the toxic potato-derived glycoalkaloids (GAs) α-chaconine and α-solanine. Information from the genome sequences will provide insight into the genetic mechanism of GA degradation by these isolates.

Draft Genome Sequence of a Novel sp. Strain with Antifungal Activity.

This report describes the draft genome sequence of Serratia sp. strain S40, isolated from potato; it contains 5,383,735 bp and a G+C content of 55.9% and harbors 4,875 predicted coding sequences across 29 contigs.

A Screening Method for the Isolation of Bacteria Capable of Degrading Toxic Steroidal Glycoalkaloids Present in Potato.

Potato juice, a by-product of starch processing, is a potential high-value food ingredient due to its high protein content. However, conversion from feed to human protein requires the removal of the toxic antinutritional glycoalkaloids (GAs) α-chaconine and α-solanine. Detoxification by enzymatic removal could potentially provide an effective and environmentally friendly process for potato-derived food protein production.

Discovery and screening of novel metagenome-derived GH107 enzymes targeting sulfated fucans from brown algae.

Sulfated fucans, often denoted as fucoidans, are highly variable cell wall polysaccharides of brown algae, which possess a wide range of bioactive properties with potential pharmaceutical applications. Due to their complex architecture, the structures of algal fucans have until now only been partly determined. Enzymes capable of hydrolyzing sulfated fucans may allow specific release of defined bioactive oligosaccharides and may serve as a tool for structural elucidation of algal walls.

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium S66 Encoded in a Sizeable Polysaccharide Utilization Locus.

Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. S66 is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides.