Draft Genome Sequence of Dyella sp. Strain C9, Isolated from a Malaysian Tropical Peat Swamp Forest.
Ontology highlight
ABSTRACT:
SUBMITTER: Too CC
PROVIDER: S-EPMC6256697 | biostudies-literature | 2018 Sep
REPOSITORIES: biostudies-literature
Publications
Draft Genome Sequence of Dyella sp. Strain C9, Isolated from a Malaysian Tropical Peat Swamp Forest.
Too Chin Chin CC Ong Kuan Shion KS Lee Sui Mae SM Yule Catherine M CM Keller Alexander A
Microbiology resource announcements 20180927 12
The bacterium Dyella sp. strain C9 was isolated from North Selangor Peat Swamp Forest, Malaysia, and studied using whole-genome sequencing. The putative genes involved in biogeochemical processes were annotated, and the genome sequence is publicly available in the NCBI database. ...[more]
Similar Datasets
Project description:We report the draft genome sequences of two antimicrobial-producing isolates, Burkholderia sp. strains MSh1 and MSh2, which were isolated from tropical peat swamp forest soil. Putative genes related to different antimicrobial production have been annotated in both genome sequences.
| S-EPMC4192393 | biostudies-literature
Project description:Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.
| S-EPMC6288306 | biostudies-literature
Project description:Emergence of antimicrobial resistance coupled with the slowdown in discovery of new antimicrobial compounds points to serious consequences for human health. Therefore, scientists are looking for new antimicrobial compounds from unique and understudied ecosystems such as tropical peat swamp forests. Over the course of isolating antimicrobial producing bacteria from North Selangor tropical peat swamp forest, Malaysia, a Gram variable, rod shaped, endospore forming, facultative anaerobic novel strain MSt1(T) that exerts potent and broad spectrum antimicrobial activity was isolated. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MSt1(T) belonged to the genus Paenibacillus with the highest similarity to Paenibacillus elgii SD17(T) (99.5%). Whole genome comparison between strain MSt1(T) with its closely related species using average nucleotide identity (ANI) revealed that similarity between strain MSt1(T) with P. elgii B69 (93.45%) and Paenibacillus ehimensis A2 (90.42%) was below the recommended threshold of 95%. Further analysis using in silico pairwise DDH also showed that similarity between strain MSt1(T) with P. elgii B69 (55.4%) and P. ehimensis A2 (43.7%) was below the recommended threshold of 70%. Strain MSt1(T) contained meso-diaminopilemic acid in the cell wall and MK-7 as the major menaquinone. The major fatty acids of strain MSt1(T) were anteiso-C15:0 (48.2%) and C16:0 (29.0%) whereas the polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unknown lipid, two unknown glycolipids, and one unknown phospholipid. Total DNA G+C content of strain MSt1(T) was 51.5 mol%. The extract from strain MSt1(T) exerted strong antimicrobial activity against Escherichia coli ATCC 25922 (MIC = 1.5 μg/mL), MRSA ATCC 700699 (MIC = 25 μg/mL) and Candida albicans IMR (MIC = 12.5 μg/mL). Partially purified active fraction exerted a strong effect against E. coli ATCC 25922 resulting in cell rupture when viewed with SEM. Based on distinctive taxonomic differences between strain MSt1(T) when compared to its closely related type species, we propose that strain MSt1(T) represents a novel species within the genus of Paenibacillus, for which the name Paenibacillus tyrfis sp. nov. (= DSM 100708(T) = MCCC 1K01247(T)) is proposed.
| S-EPMC4771734 | biostudies-literature
Project description:We previously identified and presented the draft genome of a Xanthomonadaceae bacterial strain Dyella japonica A8 which shows quorum-quenching activity. Here, we report the complete, closed genome sequence of this bacterium. This complete genome may help to further investigate the comparative quorum-quenching activity among D. japonica strains.
| S-EPMC4241664 | biostudies-literature
Project description:We studied the relationship between the coexistence of tree species and the dynamics of organic matter in forests. A tropical peat swamp forest was selected as a model ecosystem, where abiotic factors, such as geological topography or parent rock types, are homogeneous and only biological processes create habitat heterogeneity. The temporal or spatial variation of the ground elevation of peat soils is mainly caused by changes in the balance between organic matter inputs to soils and decomposition, which is affected by the growth and death of influential trees. To clarify the processes of elevation dynamics, we measured the microtopography around some tree groups, estimated organic matter (in the form of litter and roots) in soils under three kinds of microtopographic conditions, measured decomposition rates and detected dominant species' shifting distribution patterns in different stages of growth in relation to the locations of tree groups creating specific microtopographic conditions. We found that growth or death of buttressed trees has the greatest effects on the rising or sinking of ground surfaces through changes in litter supply and root production. We discuss here the possibility of extending our model to other forest types.
| S-EPMC1559832 | biostudies-literature
Project description:A novel Gram negative rod-shaped bacterium, designated strain MSh1T, was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (>10.0%) were C16:0 (31.7%), C17:0 cyclo (26.6%), and C19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1T belongs to the genus Burkholderia. The type strain MSh1T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA-DNA relatedness values between strain MSh1T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1T, it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1T (= DSM 100703T = MCCC 1K01245T). The dichloromethane extract of MSh1T exhibited antimicrobial activity against four Gram positive bacteria (Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria (Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E. faecalis strains with MIC-values of 3.13 μg/ml and 6.26 μg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis, however further work has to be done.
| S-EPMC5174137 | biostudies-literature
Project description:1. The coastal peat swamp forests of Sarawak, Malaysian Borneo, are undergoing rapid conversion, predominantly into oil palm plantations. This wetland ecosystem is assumed to have experienced insignificant disturbance in the past, persisting under a single ecologically-stable regime. However, there is limited knowledge of the past disturbance regime, long-term functioning and fundamentally the resilience of this ecosystem to changing natural and anthropogenic perturbations through time. 2. In this study, long-term ecological data sets from three degraded peatlands in Sarawak were collected to shed light on peat swamp forest dynamics. Fossil pollen and charcoal were counted in each sedimentary sequence to reconstruct vegetation and investigate responses to past environmental disturbance, both natural and anthropogenic. 3. Results demonstrate that peat swamp forest taxa have dominated these vegetation profiles throughout the last c. 2000-year period despite the presence of various drivers of disturbance. Evidence for episodes of climatic variability, predominantly linked to ENSO events, and wildfires is present throughout. However, in the last c. 500 years, burning and indicators of human disturbance have elevated beyond past levels at these sites, concurrent with a reduction in peat swamp forest pollen. 4. Two key insights have been gained through this palaeoecological analysis: (i) peat swamp forest vegetation has demonstrated resilience to disturbance caused by burning and climatic variability in Sarawak in the late Holocene, however (ii) coincident with increased fire combined with human impact c. 500 years ago, these communities started to decline. 5.Synthesis. Sarawak's coastal peat swamps have demonstrated resilience to past natural disturbances, with forest vegetation persisting through episodes of fire and climatic variability. However, palaeoecological data presented here suggest that recent, anthropogenic disturbances are of a greater magnitude, causing the observed decline in the peat swamp forest communities in the last c. 500 years and challenging the ecosystem's persistence. This study greatly extends our knowledge of the ecological functioning of these understudied ecosystems, providing baseline information on the past vegetation and its response to disturbance. This understanding is central to developing management strategies that foster resilience in the remaining peat swamp forests and ensure continued provision of services, namely carbon storage, from this globally important ecosystem.
| S-EPMC4477911 | biostudies-literature
Project description:This study presents the genome sequence of Synechococcus sp. strain C9 (= CCMEE 5213 = ATCC 700244), a thermophilic unicellular cyanobacterium that was originally isolated from a thermal pool at Octopus Spring, Yellowstone National Park, USA. The genome consists of a 2,958,309-bp chromosome with a GC content of 52.9% and 2,854 protein-coding sequences.
| S-EPMC9387270 | biostudies-literature
Project description:We report the 3.7-Mb genome sequence of Oribacterium sp. strain C9, isolated from the rumen of a steer grazing on Rhodes grass in Rockhampton, Queensland, Australia. This draft genome consists of 3,720,024 bp with a 42.8% G+C content, 3,130 predicted coding DNA sequences (CDSs), and 67 RNAs.
| S-EPMC6439248 | biostudies-literature
Project description:Actinomycetes, especially the genus Streptomyces, are one of the most promising sources of bioactive natural products. In this study, a novel Streptomyces strain, RCU-064T, was isolated from a soil sample collected from a peat swamp forest in Thailand. Strain RCU-064T showed the highest 16S rRNA gene sequence similarity (99.06%) with Streptomyces malaysiensis NBRC 16446T. Based on a polyphasic approach, strain RCU-064T represents a novel species of the genus Streptomyces, for which the name Streptomyces rugosispiralis sp. nov. is proposed. The chemical isolation of the crude ethyl acetate extracts of the strain led to the isolation of six compounds: (1) geldanamycin, (2) 17-O-demethylgeldanamycin, (3) reblastatin, (4) 17-demethoxyreblastatin, (5) nocardamine, and (6) dehydroxynocardamine. These compounds were evaluated for their biological activities. All compounds showed no antimicrobial activity against tested microorganisms used in this study. Compounds (1)-(4) displayed cytotoxic activity against the NCI-H187 cell line, with IC50 values ranging from 0.045-4.250 µg/mL. Cytotoxicity against the MCF-7 cell line was found in compounds (1) and (3) with IC50 values of 3.51 and 1.27 µg/mL, respectively. Compounds (5) and (6) exhibited cytotoxicity only against Vero cells (IC50 of 16.57 µg/mL) and NCI-H187 cells (IC50 of 13.96 µg/mL), respectively. These results indicate that peat swamp forest soil remains a promising reservoir of novel actinomycetes capable of producing bioactive natural products.
| S-EPMC10525797 | biostudies-literature