Pedobacter indicus sp. nov., isolated from deep-sea sediment

He, Xiaoyan; Li, Na; Chen, Xiu-Lan; Zhang, Yuzhong; Zhang, Xiying; Song, Xin

doi:10.1007/s10482-019-01346-9

“…Interestingly, the number of genomes that could be taxonomically classified at the species level was significantly decreased in all samples, suggesting that most MAGs herein reconstructed belong to undiscovered species, which require future endeavors to prompt their taxonomic classification. However, 7 species were assigned to the 9 MAGs and most of them were previously isolated from extreme environments, such as geothermal resources, R. marinus (Alfredson et al 1988 ); deep-water/coastal areas, P. indicus (He et al 2020 ), G. marinus (Li et al 2013 ), and B. sediminis (Wang et al 2015 ); and municipal solid waste landfills, L. defluvii (Yassin et al 2007 ). In addition, the species L. defluvii (Hayat et al 2013 ), G. marinus (Ballardo et al 2020 ), P. alcaliphilus (Tian et al 2013 ), R. marinus (Braga et al 2021 ), and P. gallinarii (Song et al 2015 ) are already related to biomass-degradation processes, namely, composting.…”

Section: Discussionmentioning

confidence: 99%

Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples

Santos-Pereira

¹

,

Sousa

²

,

Costa

³

et al. 2023

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples’ microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. Key points • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.

show abstract

“…At the time of writing, this genus has been amended eight times and comprises 87 validly published species (https://lpsn.dsmz.de/genus/pedobacter). Members of the genus Pedobacter are widely distributed in various environments, such as soil, drinking water, deep-sea sediment and plant roots [2–7]. Some strains of the genus Pedobacter can even exist under extreme environmental conditions, such as alpine glacier cryoconite [8].…”

Section: Full-textmentioning

confidence: 99%

Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila

Peng

¹

,

Jiang

²

,

Seo

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

An aerobic, Gram-stain-negative, weak-motile, short-rod-shaped bacterial strain, designated JBR3-12T, was isolated from halophyte Carex pumila plants, and its taxonomic position was investigated by using a polyphasic taxonomic approach. The strain produced a pink pigment on tryptic soy agar and grew optimally at 25 °C, pH 8 and in the presence of 3 % (w/v) NaCl. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain JBR3-12T formed a lineage within the genus Pedobacter and was most closely related to Pedobacter sandarakinus DS-27T (98.0 %) and Pedobacter agri PB92T (97.6 %). The DNA G+C content of the genome was 41.3 mol%; the whole genome length was 5 426 070 bp. The major fatty acids of JBR3-12T were iso-C15 : 0, summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH. The predominant polar lipid was phosphatidylethanolamine. The predominant quinone was menaquinone-7. Based on its phenotypic, phylogenetic and genotypic features, strain JBR3-12T is proposed to represent a novel species of the genus Pedobacter , for which the name is Pedobacter endophyticus sp. nov. The type strain is JBR3-12T (=KCTC 82363T=NBRC 114901T).

show abstract

“…The members in the genus are strictly aerobic, non-motile or motile by gliding, rod-shaped and have MK-7 as the major menaquinone and DNA G+C contents of 33.8–44.2 mol% [10, 11]. Members of the genus Pedobacter have been isolated from diverse terrestrial and aquatic habitats, such as Arctic and Antarctic regions [12–15], plant root [10, 16, 17], ginseng field [18, 19], sediment [20], activated sludge [21], and freshwater [22–24].…”

Section: Full-textmentioning

confidence: 99%

Pedobacter riviphilus sp. nov., isolated from stream sediment

Im

¹

,

Joung

²

,

Lee

³

2021

International Journal of Systematic and Evolutionary Microbiology

7

0

View full text Add to dashboard Cite

A Gram-stain-negative, aerobic, motile by gliding, rod-shaped and pink-coloured bacterium, designated strain SW-16T, was isolated from the sediment of small stream in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SW-16T formed a lineage within the genus Pedobacter of the family Sphingobacteriaceae . Phylogenetic analysis also showed that strain SW-16T was most closely related to Pedobacter soli 15-51T (98.0% 16S rRNA gene sequence similarity), Pedobacter humicola R135T (97.5%), Pedobacter suwonensis 15-52T (97.4%), Pedobacter sandarakinus DS-27T (97.0%) and Pedobacter kyungheensis THG-T17T (97.0%). Growth was observed at 10–37 °C (optimum at 30 °C), pH 6–8 (optimum at pH 7) and with 0–2.0 % NaCl (optimum at 0%). The major fatty acids of the bacterial strain were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). The predominant respiratory quinone was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified amino lipids, one unidentified phospholipid and three unidentified lipids. The genome size of strain SW-16T was 5.8 Mbp and the G+C content was 38.5 mol%. Based on the results of phenotypic, genomic and phylogenetic analyses, strain SW-16T represents a novel species of the genus Pedobacter , for which the name Pedobacter riviphilus sp. nov. is proposed. The type strain is SW-16T (=KEMB 1602–396T=KCTC 82079T=JCM 34181T).

show abstract

Pedobacter indicus sp. nov., isolated from deep-sea sediment

Cited by 12 publications

References 29 publications

Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples

Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples

Pedobacter endophyticus sp. nov., an endophytic bacterium isolated from Carex pumila

Pedobacter riviphilus sp. nov., isolated from stream sediment

Contact Info

Product

Resources

About