Impact of Physicochemical Parameters on the Diversity and Distribution of Microbial Communities Associated with Three South African Peatlands.

Peatlands are complex wetland-like ecosystems that harbor diverse microbial communities. In this study, the microbial communities (fungal and actinobacterial) associated with an unimpacted peatland (Vankervelsvlei; VV), an impacted peatland (Goukou River system; GK), and a developing peatland (Nuwejaars River system; NR) were determined through ITS and 16S rRNA metataxonomic analyses. Unidentified Acidimicrobiales dominated in GK and NR, unidentified Intrasporangiaceae and Solirubobacterales in NR, and Corynebacterium, Propionibacterium, and Streptomyces species in VV. The fungal phyla, Ascomycota and Basidiomycota, dominated all three sites, and harbored unique fungal taxa belonging to a wide range of fungal guilds. Physicochemical properties of the peat collected from the three sites were analyzed in association with microbial community structures in order to determine which parameters acted as the main drivers for microbial diversity. BEST analysis (linking microbial diversity patterns to environmental variables) showed that nitrogen (N), aluminum (Al), phosphorus (P), and potassium (K) were the most significant physicochemical drivers of actinobacterial community structure, while iron (Fe) and humification were the environmental parameters that affected the fungal communities the most. In conclusion, this study has provided some insight into the fungal and actinobacterial communities associated with three South African peatlands and the main environmental drivers that influence these communities.

Peroxidase-producing actinobacteria from Algerian environments and insights from the genome sequence of peroxidase-producing Streptomyces sp. S19 / Actinobacteria productora de peroxidasa de ambientes argelinos y perspectivas de la secuencia genómica de Streptomyces sp. S19

Unique environments often serve as a source of novel microorganisms with novel chemistries. In this study, telluric samples collected from different regions of Algeria were processed for the isolation of novel peroxidase-producing actinobacterial strains. An agar-based screening identified 45 isolates with the ability to produce peroxidase. The 16S rRNA gene sequencing showed that most of the strains belong to the genus Streptomyces. Optimization of cultivation conditions was performed for the top five peroxidase-producing strains. Apart from strain 36 (optimal growth temperature of 30 °C) and strain 45 (optimal medium pH of 6.0), the strains exhibited optimal peroxidase production when cultivated for 5 days at 37 °C and in a medium at pH 7.0. Extracellular peroxidase production was induced by ferulic acid in three of the five strains, while the presence of canola lignocellulosic waste (CLW) induced peroxidase production in all strains. Strain 19 (S19) was selected for further optimization and the extracellular peroxidase purified using acid and acetone precipitation, followed by size exclusion chromatography. The purified fraction showed a single band on the polyacrylamide gel with an estimated molecular weight of 21.45 kDa. Genome analysis confirmed the assignment of S19 to the genus Streptomyces, the presence of genes encoding for peroxidases, and the presence of genes encoding for carbohydrate-active enzymes. The presence of biosynthetic gene clusters potentially encoding for biosurfactants further highlighted the great biotechnological potential of the strain.(AU)

Peroxidase-producing actinobacteria from Algerian environments and insights from the genome sequence of peroxidase-producing Streptomyces sp. S19.

Unique environments often serve as a source of novel microorganisms with novel chemistries. In this study, telluric samples collected from different regions of Algeria were processed for the isolation of novel peroxidase-producing actinobacterial strains. An agar-based screening identified 45 isolates with the ability to produce peroxidase. The 16S rRNA gene sequencing showed that most of the strains belong to the genus Streptomyces. Optimization of cultivation conditions was performed for the top five peroxidase-producing strains. Apart from strain 36 (optimal growth temperature of 30 °C) and strain 45 (optimal medium pH of 6.0), the strains exhibited optimal peroxidase production when cultivated for 5 days at 37 °C and in a medium at pH 7.0. Extracellular peroxidase production was induced by ferulic acid in three of the five strains, while the presence of canola lignocellulosic waste (CLW) induced peroxidase production in all strains. Strain 19 (S19) was selected for further optimization and the extracellular peroxidase purified using acid and acetone precipitation, followed by size exclusion chromatography. The purified fraction showed a single band on the polyacrylamide gel with an estimated molecular weight of 21.45 kDa. Genome analysis confirmed the assignment of S19 to the genus Streptomyces, the presence of genes encoding for peroxidases, and the presence of genes encoding for carbohydrate-active enzymes. The presence of biosynthetic gene clusters potentially encoding for biosurfactants further highlighted the great biotechnological potential of the strain.

Production and characterisation of a novel actinobacterial DyP-type peroxidase and its application in coupling of phenolic monomers.

The extracellular peroxidase from Streptomyces albidoflavus BSII#1 was purified to near homogeneity using sequential steps of acid and acetone precipitation, followed by ultrafiltration. The purified peroxidase was characterised and tested for the ability to catalyse coupling reactions between selected phenolic monomer pairs. A 46-fold purification of the peroxidase was achieved, and it was shown to be a 46 kDa haem peroxidase. Unlike other actinobacteria-derived peroxidases, it was only inhibited (27 % inhibition) by relatively high concentrations of sodium azide (5 mM) and was capable of oxidising eleven (2,4-dichlorophenol, 2,6-dimethoxyphenol, 4-tert-butylcatechol, ABTS, caffeic acid, catechol, guaiacol, l-DOPA, o-aminophenol, phenol, pyrogallol) of the seventeen substrates tested. The peroxidase remained stable at temperatures of up to 80 °C for 60 min and retained >50 % activity after 24 h between pH 5.0-9.0, but was most sensitive to incubation with hydrogen peroxide (H2O2; 0.01 mM), l-cysteine (0.02 mM) and ascorbate (0.05 mM) for one hour. It was significantly inhibited by all organic solvents tested (p ≤ 0.05). The Km and Vmax values of the partially purified peroxidase with the substrate 2,4-DCP were 0.95 mM and 0.12 mmol min-1, respectively. The dyes reactive blue 4, reactive black 5, and Azure B, were all decolourised to a certain extent: approximately 30 % decolourisation was observed after 24 h (1 µM dye). The peroxidase successfully catalysed coupling reactions between several phenolic monomer pairs including catechin-caffeic acid, catechin-catechol, catechin-guaiacol and guaiacol-syringaldazine under the non-optimised conditions used in this study. Genome sequencing confirmed the identity of strain BSII#1 as a S. albidoflavus strain. In addition, the genome sequence revealed the presence of one peroxidase gene that includes the twin arginine translocation signal sequence of extracellular proteins. Functional studies confirmed that the peroxidase produced by S. albidoflavus BSII#1 is part of the dye-decolourising peroxidase (DyP-type) family.

Streptosporangium minutum sp. nov., isolated from garden soil exposed to microwave radiation.

The actinobacterium, strain M26T, was isolated from garden soil that was pre-treated with microwave radiation. The soil sample was collected in Roodepoort, Gauteng Province, South Africa as part of an antibiotic-screening programme. The isolate produced branched vegetative mycelium with sporangiophores bearing small sporangia ranging from 3 to 6 µm in diameter. Rapid genus identification revealed that the isolate belongs to the genus Streptosporangium. To confirm this result, the strain was subjected to polyphasic taxonomic characterisation. Chemotaxonomic characteristics were as follows: meso-DAP in the peptidoglycan, the whole-cell hydrolysate yielded madurose, predominant menaquinones were MK9 (21%), MK9(H2) (40%), MK9(H4) (31%) and MK9(H6) (3%); the polar lipid profile included an aminolipid, phosphoglycolipids, phosphatidylethanolamine, and phosphatidylmonomethylethanolamine. In addition, the fatty acid profile showed the presence of C16:0 (12.8%), C17:1ω8c (14.2%), and 10-methyl-C17:0 (15.8%). Furthermore, 16S rRNA gene sequence phylogenetic analysis showed that the strain is closely related to members of the genus Streptosporangium, which supports its classification within the family Streptosporangiaceae. Strain M26T exhibited antibiosis against a range of pathogenic bacteria, including, but not limited to Acinetobacter baumannii ATCC 19606T, Enterobacter cloacae subsp. cloacae ATCC BAA-1143, Enterococcus faecalis ATCC 51299 (vancomycin resistant), Escherichia coli ATCC 25922, Listeria monocytogenes ATCC 19111, Mycobacterium tuberculosis H37RvT, Pseudomonas aeruginosa ATCC 27853, Salmonella enterica subsp. arizonae ATCC 13314T, and the methicillin-resistant Staphylococcus aureus subsp. aureus ATCC 33591 (MRSA). The name Streptosporangium minutum is proposed with the type strain M26T (=LMG 28850T =NRRL B-65295T).

Streptomyces swartbergensis sp. nov., a novel tyrosinase and antibiotic producing actinobacterium.

As part of an antibiotic screening program, an actinobacterium, strain HMC13T, was isolated from soil collected from the banks of the Gamka River, Western Cape Province, South Africa. The isolate was found to produce branched mycelia that differentiated into spiral spore chains with spiny spores. 16S rRNA gene sequence analysis showed the strain to be closely related to Streptomyces caelestis NRRL 2418T (99.72%) and Streptomyces azureus NBRC 12744T (99.51%). Chemotaxonomic analyses confirmed the classification of the strain as a member of the genus Streptomyces: LL-DAP in the peptidoglycan, no diagnostic sugars in the whole cell sugar pattern, dominant menaquinones including MK9(H8), MK9(H6), and the polar lipids detected included phosphatidylethanolamine. The fatty acid profile revealed the presence of mostly branched, saturated fatty acids: iso-C15:0 (14.4%), anteiso-C15:0 (21.1%), iso-C16:0 (16.8%), C16:1ω7c/2-OH iso-C15:0 (5.8%), C16:0 (6.2%), iso-C17:1ω9c (5.8%), iso-C17:0 (5.9%), and anteiso-C17:0 (9.6%). Strain HMC13T is a tyrosinase producer and exhibits very strong antibiosis against Mycobacterium aurum A+ and Staphylococcus aureus subsp. aureus ATCC 33591 (methicillin resistant), while only weak activity was observed against Bacillus cereus ATCC 10876, Enterococcus faecium VanA (vancomycin resistant), Enterococcus faecalis ATCC 51299 (vancomycin resistant) and Candida tropicalis ATCC 750T. Strain HMC13T (= LMG 28849T = NRRL B-65294T) is proposed as the type strain of a new species, to be named Streptomyces swartbergensis sp. nov.

The effect of biogenic and chemically manufactured silver nanoparticles on the benthic bacterial communities in river sediments.

This study was conducted to determine and compare the effect of chemically-synthesised and biogenic silver nanoparticles on the benthic bacterial community structure in mesocosms containing sediment from three rivers in geographical sites with different population densities (low, medium, high), and therefore likely to be associated with respective low, moderate and high degrees of anthropogenic input. The nanoparticles were applied at the upper limit expected to accumulate in impacted environments (4 µg kgsed-1). The biomass, concentrations of elements, including selection metals (P, K, Na, K, Ca, Mg, Zn, Cu, Al, Ag) were all significantly higher at the high density than at the low density sites. Bacterial community profiling (terminal restriction fragment length polymorphism and amplicon sequencing) showed that the bacterial community structure in the sediments from the high population density site were resilient to environmental perturbations [adjustment from in-situ to ex-situ (laboratory) conditions], as well as to exposure to silver nanoparticles, with the converse being true for the low population density site. Results obtained from amplicon sequencing were interrogated to the lowest taxonomic level with a relative abundance >5%. Proteobacteria was the most abundant phylum in all the sediments. Notable resistance (increased relative abundance) to one or both forms of silver nanoparticles was seen in the class Thermoleophilia, and the orders Myxococcales, Bacteriodales, Pirellules CCU21 and iii 1-15 (class Acidobacteria 6). Conversely, sensitivity was demonstrated in the family Koribacteraceae and the orders Rhizobiales, Ellin 329 and Gemmatales. It is recommended that pro-active environmental monitoring is performed in aquatic systems receiving point source pollution from wastewater treatment plants in order to assess the accumulation of silver nanoparticles. If necessary, measures should be implemented to mitigate the entry of silver nanoparticles, especially into more vulnerable environments.

Draft Genome Sequence of Gordonia lacunae BS2T.

We report here the draft genome sequence of the soil bacterium Gordonia lacunae BS2T (= DSM 45085T = JCM 14873T = NRRL B-24551T), isolated from an estuary in Plettenberg Bay, South Africa. Analysis of the draft genome revealed that more than 40% of the secondary metabolite biosynthetic genes encode new compounds.