Mechanism of sulfur-oxidizing inoculants and nitrate on regulating sulfur functional genes and bacterial community at the thermophilic compost stage

The emission of H₂S odors predominantly occurred at the thermophilic phase of composting, which could cause odorous gas pollution and reduce the fertilizer value of composting products. And sulfur-oxidizing bacteria (SOB) possess oxidative capacities for inorganic sulfur compounds with nitrate applied as electron acceptors. Therefore, this study aimed to assess the effectiveness of combined additives (SOB inoculants and nitrate) on the bacterial community diversity, sulfur-oxidizing gene abundances, and metabolic function prediction at the thermophilic stage of sewage sludge composting. The highest sulfate contents were increased by 1.02-1.34 folds, and the abundances of the sulfur-oxidizing genes (sqr, pdo, sox, and sor) were also enhanced by adding the combined additives. Network patterns revealed a strengthened interaction of inoculants and sulfur functional genes. Microbial functional pathways predicted higher metabolic levels of carbohydrate and amino acid metabolisms with the addition of combined additives, and the predicted relative abundances of sulfur metabolism and nitrogen metabolism were increased by 19.3 ± 2.5% and 24.7 ± 4.1%, respectively. Heatmap analysis showed that the SOB might have a competitive advantage over the indigenous denitrifying bacteria in using nitrate for biochemical reactions. Correlation analyses suggested that sulfur-oxidizing efficacy could be indirectly affected by the environmental parameters through changing the structure of bacterial community. These findings provide new insights toward an optimized inoculation strategy of using SOB and nitrate to enhance sulfur preservation and modulate the bacterial communities at the thermophilic phase of sewage sludge composting.

Streptomyces sennicomposti sp. nov., an actinomycete isolated from compost of Senna siamea (Lam.)

A member of the genus Streptomyces , designated RCPT1-4T, was isolated from compost of Senna siamea (Lam.), collected from an agricultural area in Rayong province, Thailand. The spore morphology and the presence of ll-diaminopimelic acid in the peptidoglycan indicate that RCPT1-4T shows the typical properties of members of the genus Streptomyces . On the basis of the results of 16S rRNA gene sequence analysis, the strain should be classified as representing a member of the genus Streptomyces and was most closely related to Streptomyces fumigatiscleroticus NBRC 12999T with the highest 16S rRNA gene sequence similarity of 99.2 %, followed by Streptomyces spiralis NBRC 14215T (99.0 %). In addition, RCPT1-4T shared the highest average nucleotide identity by blast (ANIb) (86.0 %), and digital DNA–DNA hybridization (dDDH) (32.1 %) values with S. spiralis NBRC 14215T. Furthermore, several physiological and biochemical differences were observed between RCPT1-4T and the closely related type strains of species with validly published names. These taxonomic data indicated that RCPT1-4T could be considered to represent a novel species of the genus Streptomyces and the name Streptomyces sennicomposti sp. nov. is proposed for this strain. The type strain is RCPT1-4T (=TBRC 11260T=NBRC 114303T).

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.

Actinocrispum wychmicini gen. nov., sp. nov., a novel member of the family Pseudonocardiaceae, isolated from soil

A novel actinomycete, designated MI503-A4T, was isolated from soil. Comparative analysis of 16S rRNA gene sequences indicated that MI503-A4T was phylogenetically related to members of the family Pseudonocardiaceae. The most closely related genus was Kibdelosporangium (95.7-96.2 % sequence similarity). Substrate mycelia were branched and pale yellow to pale yellowish-brown. Straight- to zigzag-shaped aerial mycelia were observed, but Sporangium-like structures were absent. The whole-cell hydrolysate contained meso-diaminopimelic acid. The muramic acid residues in the peptidoglycan were N-acetylated. Whole-cell sugars were rhamnose, ribose, arabinose and galactose (cell wall chemotype IV). The predominant menaquinone was MK-9(H4). A small amount of MK-8(H4) was also detected. The DNA G+C content was 70.3-71.1 mol%. Polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine and hydroxyl-phosphatidylethanolamine. Cellular fatty acid analysis of MI503-A4T detected predominantly iso-C14 : 0 (11.5 %), iso-C15 : 0 (13.3 %) and iso-C16 : 0 (35.7 %). Phenotypic and phylogenetic characteristics differentiated MI503-A4T from members of all genera within the family Pseudonocardiaceae with validly published names. Therefore, MI503-A4T is proposed to be a representative of a novel species in a novel genus, Actinocrispum wychmicini gen. nov., sp. nov. The type strain of the type species is MI503-A4T (=NBRC 109632T=DSM 45934T).

Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard)

The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH, C16 : 1ω9c, iso-C16 : 1 and C16 : 0. The genomic DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204279T should be placed in the family Pseudonocardiaceae, in which the strain formed a distinct lineage next to the genus Actinophytocola. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained the Pseudonocardiaceae family-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis and phenotypic characteristics supported the conclusion that strain CPCC 204279T represents a novel species of a new genus in the family Pseudonocardiaceae, for which the name Herbihabitans rhizosphaerae gen. nov., sp. nov. is proposed. Strain CPCC 204279T (=NBRC 111774T=DSM 101727T) is the type strain of the type species.

Tamaricihabitans halophyticus gen. nov., sp. nov., an endophytic actinomycete of the family Pseudonocardiaceae

A novel actinomycete strain, designated KLBMP 1356T, was isolated from the root of halophyte Tamarix chinensis Lour. collected from the coastal area of Jiangsu province, PR China. The isolate was characterized using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequence indicated that strain KLBMP 1356T was phylogenetically related to members of the family Pseudonocardiaceae and formed a distinct monophyletic clade between the genera Amycolatopsis (93.1–94.7 % 16S rRNA gene sequence similarity), Prauserella (93.6–95.1 %) and Saccharomonospora (93.2–94.3 %). The isolate displayed long spore chains containing rod-shaped and smooth-surfaced spores. Strain KLBMP 1356T contained meso-diaminopimelic acid as the diagnostic diamino acid, and galactose, arabinose and glucose as the whole-cell sugars. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C17 : 1ω8c, C17 : 1ω6c and C17 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, unknown aminophospholipids and an unknown glycolipid. Mycolic acids were not present. The G+C content of the genomic DNA was 67.2 mol%. On the basis of the evidence from this polyphasic study, strain KLBMP 1356T is considered to represent a novel species of a new genus in the family Pseudonocardiaceae, for which the name Tamaricihabitans halophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is KLBMP 1356T ( = DSM 45765T = NBRC 109361T).

Thermophilic and alkaliphilic Actinobacteria: biology and potential applications

Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.