Search

Microaerobacter geothermalis Nad S1 T is a rare Bacillaceae thermophile that grows optimally at 55°C and circumneutral pH. Although strain Nad S1 T was discovered >10 years ago, its genome is yet to be described. The release of the Nad S1 T genome sequence serves as reference genetic information for subsequent use.

The wide use of whole-genome sequencing approach in the modern genomic era has opened a great opportunity to reveal the prospective applications of halophilic bacteria. Robertkochia marina CC-AMO-30D(T) is one of the halophilic bacteria that was previously taxonomically identified without any inspection on its biotechnological potential from a genomic aspect. In this study, we present the whole-genome sequence of R. marina and demonstrated the ability of this bacterium in solubilizing phosphate by producing phosphatase. The genome of R. marina has 3.57 Mbp and contains 3107 predicted genes, from which 3044 are protein coding, 52 are non-coding RNAs, and 11 are pseudogenes. Several phosphatases such as alkaline phosphatases and pyrophosphatases were mined from the genome. Further genomic study (phylogenetics, sequence analysis, and functional mechanism) and experimental data suggested that the alkaline phosphatase produced by R. marina could potentially be utilized in promoting plant growth, particularly for plants on saline-based agricultural land. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-020-00401-2.

Cellulomonas sp. strain PS-H5 was isolated from Sekinchan Beach in Selangor, Malaysia, using an ex situ cultivation method. The present work reports a high-quality draft annotated genome sequence of this strain and suggests its potential glycoside hydrolase enzymes for cellulose, hemicellulose, and starch degradations.

Roseovarius sp. strain PS-C2 is a bacterium that was isolated from Sekinchan Beach in Selangor, Malaysia, using an ex situ cultivation technique. Here, we present a high-quality annotated draft genome of strain PS-C2 and suggest potential applications of this bacterium.

Longimonas halophila and Longibacter salinarum are type strains of underexplored genera affiliated with Salisaetaceae. Herein, we report the draft genome sequences of two strains of these bacteria, L. halophila KCTC 42399 and L. salinarum KCTC 52045, with the intent of broadening knowledge of this family. Genome annotation and gene mining revealed that both bacteria exhibit amylolytic abilities.

The genus Meridianimaribacter is one of the least-studied genera within Cytophaga-Flavobacteria. To date, no genomic analysis of Meridianimaribacter has been reported. In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information coupled with experimental studies confirmed the ability of strain CL38 to degrade lignocellulosic biomass. Therefore, Meridianimaribacter sp. strain CL38, with its halotolerance, could be useful for seawater based lignocellulosic biorefining.

12 páginas, 4 tablas y 5 figuras, A bacterial strain designated as P08T was isolated from laboratory tap water during a water quality assessment in University of Malaya, Malaysia. The strain was a Gramnegative, rod‐shaped, nonmotile, and aerobic bacterium. Complete genome of P08T comprised of a 2,820,660 bp chromosome with a G + C content of 36.43%. Both 16S rRNA phylogeny and phylogenetic tree inferred from the core gene matrix demonstrated that P08T formed a hitherto unknown subline within the family Neisseriaceae. Ortho average nucleotide identity (OrthoANI) values and the percentage of conserved proteins (POCP) calculated from complete genome sequence indicated low relatedness between P08T and its phylogenetic neighbors. Respiratory quinone analysis revealed Q‐8 as the only detectable quinone. The predominant cellular fatty acids were identified as C14:0, iso‐C15:0, and summed feature 3 (C16:1 ω7c/C16:1 ω6c). The polar lipids consisted of uncharacterized aminolipid, phosphatidylglycerol, and phosphatidylethanolamine. All aspects of phenotypic and phylogenetic data suggested that strain P08T represents a novel genus within family Neisseriaceae, for which the name Aquella gen. nov. is proposed. The type species of the genus is Aquella oligotrophica sp. nov., and the type strain is P08T (=LMG 29629T =DSM 100970T)., This work was supported by University of Malaya—Ministry of Higher Education High Impact Research Grant (UM‐MOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/14/1, Grant No. H‐ 50001‐ A000027) and University of Malaya Research Grants (GA001‐2016, GA002‐2016) awarded to Kok‐Gan Chan and Postgraduate Research Grant (PPP) (Grant No. PG124‐2016A) awarded to Li Sin Lee. Kian Mau Goh thanks UTM GUP grant 15H50. Wah‐Seng See‐Too thanks Bright Sparks Unit of University of Malaya for the scholarship support.

The recent discovery of key methane-metabolizing genes in the genomes from the archaeal phyla Bathyarchaeota and Verstraetearchaeota has expanded our understanding of the distribution of methane metabolism outside of the phylum Euryarchaeota. Here, we recovered two near-complete crenarchaeotal metagenome-assembled genomes (MAGs) from circumneutral hot springs that contain genes for methanogenesis, including the genes that encode for the key methyl-coenzyme M reductase (MCR) complex. These newly recovered archaea phylogenetically cluster with Geoarchaeota (deep lineage of archaeal order Thermoproteales), and the MCR-encoding genes clustered with the recently reported methanogens within the Verstraetearchaeota. In addition, genes encoding hydroxybutyryl-CoA dehydratase were identified in the newly recovered methanogens, indicating they might carry out the β-oxidation process. Together, our findings further expanded the methane metabolism outside the phylum Euryarchaeota.

Thermostable cellulase plays an important role in the process of converting lignocellulosic waste to biofuel. A culture-dependent approach may not effectively discover new thermostable cellulase, hemicellulase, or lignin-acting enzymes, since many thermophiles are not culturable in general laboratory setups. Due to this limitation, culture-independent techniques—for instance, the metagenomic approach—may be a good technique for finding novel genes. This current chapter demonstrates a method to amplify complete genes from a hot spring complex metagenome without the need to isolate bacterium or perform a clonal library. To achieve this, one needs to perform sampling (water, sediment, or biofilm from hot spring), extract the environmental DNA material, and perform 16S rRNA amplicon sequencing using a next-generation sequencer. From the microbial population data, we can then identify the genera of interest and their cellulase genes, followed by the designing of specific or degenerate primers, and finally amplification of the genes of interest using conventional PCR. This methodology will likely be an economic and powerful approach to discover novel genes that are present in complex environments. This chapter also describes the challenges of using such an approach. Using this method, an interesting heat-tolerant enzyme for biomass degradation was cloned, expressed, and purified. The enzyme exhibited optimum activity at a pH of 5.5 and at 90°C, a much higher temperature than other known enzyme counterparts. This enzyme is highly active on complex polysaccharide carboxymethyl cellulose. This technique will be useful for any gene amplification from hot springs using the guidance of 16S rRNA amplicon metagenomics.

Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain.

To date, the genus Roseivirga consists of six species with one subspecies and is one of the least-studied genera among the family Flammeovirgaceae. In order to further explore this genus, the genome sequences of five Roseivirga spp. were compared and described in this study. The Roseivirga genomes have similar sizes in the range of 4.08-4.47Mb with an average of 4.22Mb. Several key proteins related to osmotic stress adaptation were identified in Roseivirga spp. including betaine transporter, choline dehydrogenase, and glutamate synthases. Significant amount of proteins associated with amino acid transport and metabolism were also present in Roseivirga genome. All five Roseivirga spp. were able to grow in medium contained casamino acids (mixture of amino acids) as sole carbon or nitrogen sources. Taken together, these findings suggested the potential role of Roseivirga in decomposing organic nitrogen matter in marine environment.

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment., Centro de Investigación y Desarrollo en Fermentaciones Industriales

Jeotgalibacillus alimentarius JY-13 T (=KCCM 80002 T = JCM 10872 T ) is a moderate halophile. In 2001, this was the first strain of the newly proposed Jeotgalibacillus genus. The draft genome of J. alimentarius was found to consist of 32 contigs ( N 50 , 315,125 bp) with a total size of 3,364,745 bp. This genome information will be helpful for studies on pigmentation as well as applications for this bacterium.

Trehalose has similar chemical formula as maltose. In terms of price, trehalose is much more expensivethan maltose. A pink-pigmented bacterium identified as Meiothermus sp. SK3-2 was found to be able to convert maltose to trehalose. Based on fatty acids analysis, the Meiothermus sp. SK3-2 may be a new strain that produce trehalose synthase (TreS). Meiothermus sp. SK3-2 achieved a better biomass growth in MM medium containing maltose. Besides that, TreS activity yield was also higher in MM medium, approximately 3.5, 1.8 and 0.3 fold than that in PY medium, thermophilic Bacillus medium and Castenholz medium, respectively. The optimum working temperature and pH for Meiothermus sp. SK3-2 TreS was 65°C and pH 6.0, respectively. Ammonium chloride at 10 mM increased the activity significantly, while calcium chloride at 5 mM decreased the activity by about 80% and the activity wasfully retarded by 10 mM CaCl2. It was found that the product specificity of this TreS was influenced by factors like temperature, pH and buffer system used. Analysis of the nucleotide sequence revealed the presence of an open reading frame of 2,890 bp which encoded a 963 amino acid protein. In conclusion, Meiothermus sp. SK3-2 TreS could serve as an alternative source to trehalose production.

Jeotgalibacillus soli , a bacterium capable of degrading N -acyl homoserine lactone, was isolated from a soil sample in Portugal. J. soli constitutes the only Jeotgalibacillus species isolated from a non-marine source. Here, the draft genome, several interesting glycosyl hydrolases, and its putative N -acyl homoserine lactonases are presented.

Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium.

Jeotgalibacillus spp. are halophilic bacteria within the family Planococcaceae. No genomes of Jeotgalibacillus spp. have been reported to date, and their metabolic pathways are unknown. How the bacteria survive in hypertonic conditions such as seawater is yet to be discovered. As only few studies have been conducted on Jeotgalibacillus spp., potential applications of these bacteria are unknown. Here, we present the complete genome of J. malaysiensis D5(T) (=DSM 28777(T) =KCTC 33350(T)), which is invaluable in identifying interesting applications for this genus.

Anoxybacillus thermarum AF/04 T was isolated from the Euganean hot springs in Abano Terme, Italy. The present work reports a high-quality draft genome sequence of strain AF/04 T . This work also provides useful insights into glycoside hydrolases, glycoside transferases, and sugar transporters that may be involved in cellular carbohydrate metabolism.

Jeotgalibacillus campisalis SF-57(T) (=KCCM 41644(T), JCM 11810(T)) is a moderate halophilic bacterium isolated from a Korean marine saltern. In this study, we describe the high-quality draft genome of strain SF-57(T), which was assembled into 24 contigs containing 3,650,490bp with a G+C content of 41.06%. Availability of the genome sequence of J. campisalis SF-57(T) will contribute to a better understanding of the genus Jeotgalibacillus.

Type strain Vitellibacter vladivostokensis KMM 3516(T) (=NBRC 16718(T)) belongs to the phylum Cytophaga-Flavobacterium-Bacteroides. To date, no genomes of the Vitellibacter spp. have been reported, and their metabolic pathways are unknown. This study reports the draft genome sequence of V. vladivostokensis. Moreover, mining of genes associated with proteolytic enzymes was performed to provide insights for further enzyme characterization.

Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism.

Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many biotechnological applications. Anoxybacillus ayderensis AB04T (= NCIMB 13972T = NCCB 100050T) was isolated from the Ayder hot spring in Rize, Turkey, and is one of the earliest described Anoxybacillus type strains. The present work reports the cellular features of A. ayderensis AB04T, together with a high-quality draft genome sequence and its annotation. The genome is 2,832,347 bp long (74 contigs) and contains 2,895 protein-coding sequences and 103 RNA genes including 14 rRNAs, 88 tRNAs, and 1 tmRNA. Based on the genome annotation of strain AB04T, we identified genes encoding various glycoside hydrolases that are important for carbohydrate-related industries, which we compared with those of other, sequenced Anoxybacillus spp. Insights into under-explored industrially applicable enzymes and the possible applications of strain AB04T were also described.