Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T))

Effects of 3D-printed bulking agent on microbial community succession and carbohydrate-active enzymes genes during swine manure composting

The bulking agent plays an important role in aerobic composting, but their shape, porosity, and homogeneity need to be optimized. In the present work, a bulking agent with a uniform shape was prepared by 3D printing to explore its influence on physicochemical parameters, microbial community succession, and gene abundance of carbohydrate-active enzymes (CAZymes) in swine manure aerobic composting. The results showed that adding 3D-printed bulking agents can increase maximum temperature, prolong the thermophilic period, and improve the degradation rate of volatile solids, which was attributed to ameliorative air permeability by the porous 3D-printed bulking agent. The abundances of some pathogenic bacteria decreased and CAZymes genes increased respectively in response to the addition of the 3D-printed bulking agent, implying it has a certain positive effect on improving the safety of compost products and promoting the degradation of organic matter. In summary, the 3D-printed bulking agent has good application potential in laboratory-scale aerobic composting.

Three-dimensional printed bulking agents reduce antibiotic resistance genes in swine manure aerobic composting by regulating oxygen concentration to alter host microorganisms and mobile genetic elements

Antibiotic resistance genes (ARGs) in manure aerobic composting are a potential environmental pollutant. Therefore, reducing the abundance of ARGs is crucial. The effects of adding three-dimensional printed bulking agents (3DBAs) on ARGs in aerobic composting of swine manure were investigated in this study. Compared with the control group, 3DBAs with different addition dosages can greatest reduce the total ARGs by 5.98%, tetracycline resistance genes by 14.02%, macrolide resistance genes by 9.65%, and sulfonamide resistance genes by 20.59%. By further combining physicochemical parameters, host microorganisms, and mobile genetic elements (MGEs) for analysis, it was found that oxygen concentration was vital for ARGs reduction, and 3DBAs with regular porosity and uniform size indirectly regulate the activity of host microorganisms and MGEs abundance by changing the oxygen consumption, finally reducing vertical or horizontal ARGs transfer risks. Overall, 3DBAs addition is an effective strategy to reduce the abundance of ARGs in aerobic composting.

Bacterial dynamics for gaseous emission and humification in bio-augmented composting of kitchen waste

Using high-throughput sequencing and Functional Annotation of Prokaryotic Taxa (FAPROTAX), this study aimed to elucidate the effect of bacterial dynamics on gaseous emission and humification of kitchen and garden wastes during composting augmented with microbial inoculants. Microbial inoculant addition at up to 0.9% resulted in a diverse bacterial community with more functional bacteria to amend gaseous emission and enhance humification. Microbial inoculation facilitated the enrichment of aerobic bacteria (e.g. the genus Bacillus and Thermobifida) to enhance cellulolysis and ligninolysis to advance organic humification. By contrast, several bacteria, such as the genus Weissella and Pusillimonas were inhibited by microbial inoculation to weaken fermentation and nitrate respiration. As such, bio-augmented composting with 0.9% microbial inoculant reduced the emission of methane by 11-20% and nitrogen oxide by 17-54%. On the other hand, ammonia and hydrogen sulphide emissions increased by 26-62% and 5-23%, respectively, in bio-augmented composting due to the considerable proliferation of the genus Bacillus and Desulfitibacter to enhance ammonification and sulphur-related respiration. Results from this study highlight the need to further develop efficient and multifunctional microbial inoculants that promote humification and deodorization for bio-augmented composting of kitchen waste as well as other carbon and nutrient rich organic wastes.

Metagenomic Analysis of the Microbial Diversity in Solid Waste from Okhla Landfill, New Delhi, India

The Okhla landfill site is consistently in the news for having pollution levels higher than the city average. Here, we report the taxonomic characterization of the microbial diversity of Okhla landfill solid waste. The metagenome analyses revealed the microbial and metabolic diversity of the site.

Structural and functional comparison of Saccharomonospora azurea strains in terms of primycin producing ability

Emerging and re-emerging microbial pathogens, together with their rapid evolution and adaptation against antibiotics, highlight the importance not only of screening for new antimicrobial agents, but also for deepening knowledge about existing antibiotics. Primycin is a large 36-membered non-polyene macrolide lactone exclusively produced by Saccharomonospora azurea. This study provides information about strain dependent primycin production ability in conjunction with the structural, functional and comparative genomic examinations. Comparison of high- and low-primycin producer strains, transcriptomic analysis identified a total of 686 differentially expressed genes (DEGs), classified into diverse Cluster of Orthologous Groups. Among them, genes related to fatty acid synthesis, self-resistance, regulation of secondary metabolism and agmatinase encoding gene responsible for catalyze conversion between guanidino/amino forms of primycin were discussed. Based on in silico data mining methods, we were able to identify DEGs whose altered expression provide a good starting point for the optimization of fermentation processes, in order to perform targeted strain improvement and rational drug design.

Two new secondary metabolites, saccharochlorines A and B, from a marine bacterium Saccharomonospora sp. KCTC-19160

Two new chlorinated secondary metabolites, saccharochlorines A and B (1 and 2), were isolated from the saline cultivation of a marine-derived bacterium Saccharomonospora sp. (KCTC-19160). The chemical structures of the saccharochlorines were elucidated by 2D NMR and MS spectroscopic data. Saccharochlorines A and B (1 and 2) exhibit weak inhibition of β-secretase (BACE1) in biochemical inhibitory assay, but they induced the release of Aβ (1-40) and Aβ (1-42) in H4-APP neuroglial cells. This discrepancy might be derived from the differences between the cellular and sub-cellular environments or the epigenetic stimulation of BACE1 expression.

Cloning and functional analysis of a laccase gene during fruiting body formation in Hypsizygus marmoreus

The Hypsizygus marmoreus laccase gene (lcc1) sequence was cloned and analyzed. The genomic DNA of lcc1 is 2336 bp, comprising 13 introns and 14 exons. The 1626-bp full-length cDNA encodes a mature laccase protein containing 542 amino acids, with a 21-amino acid signal peptide. Phylogenetic analysis showed that the lcc1 amino acid sequence is homologous to basidiomycete laccases and shares the highest similarity with Flammulina velutipes laccase. A 2021-bp promoter sequence containing a TATA box, CAAT box, and several putative cis-acting elements was also identified. To study the function of lcc1, we first overexpressed lcc1 in H. marmoreus and found that the transgenic fungus producing recombinant laccase displayed faster mycelial growth than the wild-type (wt) strain. Additionally, primordium initiation was induced 3-5 days earlier in the transgenic fungus, and fruiting body maturation was also promoted approximately five days earlier than in the wt strain. Furthermore, we detected that lcc1 was sustainably overexpressed and that laccase activity was also higher in the transgenic strains compared with the wt strain during development in H. marmoreus. These results indicate that the H. marmoreus lcc1 gene is involved in mycelial growth and fruiting body initiation by increasing laccase activity.

Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T))

Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T))

Saccharomonospora marina Liu et al. 2010 is a member of the genus Saccharomonospora, in the family Pseudonocardiaceae that is poorly characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Here we describe the features of this organism, together with the complete genome sequence (permanent draft status), and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).