Studies on carbohydrate metabolism in Bifidobacterium : isolation, characterisation and regulation of a sucrose-utilisation gene cluster in Bifidobacterium lactis

Bibliography: leaves 167-195.The primary aim of the project was, therefore, to analyse carbohydrate metabolism for the identification of and/or the development of prebiotic substrates, and to provide a molecular characterisation for their utilisation. Several carbohydrates were tested for their ability to support the growth of bifidobacteria as a sole carbohydrate source. The four bifidobacterial strains, B. breve, B. bifidum, B. longum and B. lactis were able to utilise a wide variety of substrates

Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ~15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60–100%) and HMs removal (21–100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities

Genomic characterization of a prophage, Smhb1, that Infects Salinivibrio kushneri BNH isolated from a Namib Desert saline spring

Funding text 1 Funding: This work was supported by the National Research Foundation (NRF) of South Africa. Funding text 2 This work was supported by the National Research Foundation (NRF) of South Africa. We wish to thank the researcher and management of the Gobabeb Desert research station for hosting us during sample collection. We also thank Mohammed Jaffer at the Electron Microscope Unit at the University of Cape Town for helping to capture TEM images.Recent years have seen the classification and reclassification of many viruses related to the model enterobacterial phage P2. Here, we report the identification of a prophage (Smhb1) that infects Salinivibrio kushneri BNH isolated from a Namib Desert salt pan (playa). Analysis of the genome revealed that it showed the greatest similarity to P2-like phages that infect Vibrio species and showed no relation to any of the previously described Salinivibrio-infecting phages. Despite being distantly related to these Vibrio infecting phages and sharing the same modular gene arrangement as seen in most P2-like viruses, the nucleotide identity to its closest relatives suggest that, for now, Smhb1 is the lone member of the Peduovirus genus Playavirus. Although host range testing was not extensive and no secondary host could be identified for Smhb1, genomic evidence suggests that the phage is capable of infecting other Salinivibrio species, including Salinivibrio proteolyticus DV isolated from the same playa. Taken together, the analysis presented here demonstrates how adaptable the P2 phage model can be. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.National Research Foundation (NRF University of Cape Town (UCT

Antibacterial activities of bacteria isolated from the marine sponges Isodictya compressa and Higginsia bidentifera collected from Algoa Bay, South Africa

Due to the rise inmulti-drug resistant pathogens and other diseases, there is renewed interest in marine sponge endosymbionts as a rich source of natural products (NPs). The South African marine environment is rich in marine biota that remains largely unexplored and may represent an important source for the discovery of novel NPs.We first investigated the bacterial diversity associated with five South African marine sponges, whose microbial populations had not previously been investigated, and select the two sponges (Isodictya compressa and Higginsia bidentifera) with highest species richness to culture bacteria. By employing 33 different growth conditions 415 sponge-associated bacterial isolates were cultured and screened for antibacterial activity. Thirty-five isolates showed antibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implying that some of the bioactive compounds could be novel. Genome sequencing of two of these isolates confirmed that they harbour uncharacterized biosynthetic pathways that may encode novel chemical structures.IS

Do biosurfactants as anti-biofilm agents have a future in industrial water systems?

Biofilms are bacterial communities embedded in exopolymeric substances that form on the surfaces of both man-made and natural structures. Biofilm formation in industrial water systems such as cooling towers results in biofouling and biocorrosion and poses a major health concern as well as an economic burden. Traditionally, biofilms in industrial water systems are treated with alternating doses of oxidizing and non-oxidizing biocides, but as resistance increases, higher biocide concentrations are needed. Using chemically synthesized surfactants in combination with biocides is also not a new idea; however, these surfactants are often not biodegradable and lead to accumulation in natural water reservoirs. Biosurfactants have become an essential bioeconomy product for diverse applications; however, reports of their use in combating biofilm-related problems in water management systems is limited to only a few studies. Biosurfactants are powerful anti-biofilm agents and can act as biocides as well as biodispersants. In laboratory settings, the efficacy of biosurfactants as anti-biofilm agents can range between 26% and 99.8%. For example, long-chain rhamnolipids isolated from Burkholderia thailandensis inhibit biofilm formation between 50% and 90%, while a lipopeptide biosurfactant from Bacillus amyloliquefaciens was able to inhibit biofilms up to 96% and 99%. Additionally, biosurfactants can disperse preformed biofilms up to 95.9%. The efficacy of antibiotics can also be increased by between 25% and 50% when combined with biosurfactants, as seen for the V9T14 biosurfactant co-formulated with ampicillin, cefazolin, and tobramycin. In this review, we discuss how biofilms are formed and if biosurfactants, as anti-biofilm agents, have a future in industrial water systems. We then summarize the reported mode of action for biosurfactant molecules and their functionality as biofilm dispersal agents. Finally, we highlight the application of biosurfactants in industrial water systems as anti-fouling and anti-corrosion agents

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic contentmust be representative of the total microbial diversity. In this study,we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB- and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols. The SDS-based protocol enabled access to the highest sorghumendophytic diversities. Therefore, “SDS-extracted” sorghum root and stem microbiome diversities were analysed via 454 pyrosequencing, and this revealed that the two tissues harbour significantly different endophytic communities. Nevertheless, both communities are dominated by agriculturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas and Stenotrophomonas; which have previously been shown to play a role in plant growth promotion. This study shows that DNA extraction protocols introduce biases in culture-independent studies of environmental microbial communities by influencing the mDNA quality, which impacts the microbial diversity analyses and evaluation. Using the broad-spectrum SDSbased DNA extraction protocol allows the recovery of the most diverse endophytic communities associated with sorghum tissues and, as such, establishes a reliable basis for future study of endophytic communities.South African National Research Foundation (NRF) Grant No: 71081.http://www.elsevier.com/locate/jmicmeth2016-05-31hb201

Degradation of Hydrocarbons and Heavy Metal Reduction by Marine Bacteria in Highly Contaminated Sediments

Investigations on the ability of bacteria to enhance removal of hydrocarbons and reduce heavy metal toxicity in sediments are necessary to design more effective bioremediation strategies. In this study, five bacterial strains, Halomonas sp. SZN1, Alcanivorax sp. SZN2, Pseudoalteromonas sp. SZN3, Epibacterium sp. SZN4, and Virgibacillus sp. SZN7, were isolated from polluted sediments from an abandoned industrial site in the Gulf of Naples, Mediterranean Sea, and tested for their bioremediation efficiency on sediment samples collected from the same site. These bacteria were added as consortia or as individual cultures into polluted sediments to assess biodegradation efficiency of polycyclic aromatic hydrocarbons and heavy metal immobilisation capacity. Our results indicate that these bacteria were able to remove polycyclic aromatic hydrocarbons, with a removal rate up to ca. 80% for dibenzo-anthracene. In addition, these bacteria reduced arsenic, lead, and cadmium mobility by promoting their partitioning into less mobile and bioavailable fractions. Microbial consortia generally showed higher performance toward pollutants as compared with pure isolates, suggesting potential synergistic interactions able to enhance bioremediation capacity. Overall, our findings suggest that highly polluted sediments select for bacteria efficient at reducing the toxicity of hazardous compounds, paving the way for scaled-up bioremediation trials

Characterization of a highly xylose tolerant β-xylosidase isolated from high temperature horse manure compost

: There is a continued need for improved enzymes for industry. β-xylosidases are enzymes employed in a variety of industries and although many wild-type and engineered variants have been described, enzymes that are highly tolerant of the products produced by catalysis are not readily available and the fundamental mechanisms of tolerance are not well understood.: Screening of a metagenomic library constructed of mDNA isolated from horse manure compost for β-xylosidase activity identifed 26 positive hits. The fosmid clones were sequenced and bioinformatic analysis performed to identity putative β-xylosidases. Based on the novelty of its amino acid sequence and potential thermostability one enzyme (XylP81) was selected for expression and further characterization. XylP81 belongs to the family 39 β-xylosidases, a comparatively rarely found and characterized GH family. The enzyme displayed biochemical characteristics (KM—5.3 mM; Vmax—122 U/mg; kcat—107; Topt—50 °C; pHopt—6) comparable to previously characterized glycoside hydrolase family 39 (GH39) β-xylosidases and despite nucleotide identity to thermophilic species, the enzyme displayed only moderate thermostability with a half-life of 32 min at 60 °C. Apart from acting on substrates predicted for β-xylosidase (xylobiose and 4-nitrophenyl-β-D-xylopyranoside) the enzyme also displayed measurable α-Larabainofuranosidase, β-galactosidase and β-glucosidase activity. A remarkable feature of this enzyme is its ability to tolerate high concentrations of xylose with a Ki of 1.33 M, a feature that is highly desirable for commercial applications

Metaviromics of Namib desert salt pans : a novel lineage of haloarchaeal salterproviruses and a rich source of ssDNA viruses

Viral communities of two different salt pans located in the Namib Desert, Hosabes and Eisfeld, were investigated using a combination of multiple displacement amplification of metaviromic DNA and deep sequencing, and provided comprehensive sequence data on both ssDNA and dsDNA viral community structures. Read and contig annotations through online pipelines showed that the salt pans harbored largely unknown viral communities. Through network analysis, we were able to assign a large portion of the unknown reads to a diverse group of ssDNA viruses. Contigs belonging to the subfamily Gokushovirinae were common in both environmental datasets. Analysis of haloarchaeal virus contigs revealed the presence of three contigs distantly related with His1, indicating a possible new lineage of salterproviruses in the Hosabes playa. Based on viral richness and read mapping analyses, the salt pan metaviromes were novel and most closely related to each other while showing a low degree of overlap with other environmental viromes.National Research Foundation (NRF) of South Africa, Claude Leon Foundation and the Vice Chancellor’s Postdoctoral Fellowship program of the University of Pretoria.http://www.mdpi.com/journal/viruseshb201

Three novel bacteriophages isolated from the East African Rift Valley soda lakes

BACKGROUND : Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. METHODS : Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each phage in its host was investigated and the genome sequences determined and analysed by comparison with known phages. RESULTS : Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family. Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial amino acid similarity with previously described Bacillus infecting phages (Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel. CONCLUSION : The addition of these phages to current databases should help with metagenome/metavirome annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to these phages.Additional file 1: Figure S1. Whole genome alignment of phage Shbh1 with six of its closest relatives. Similarly coloured regions indicate homology or local collinear blocks (LCB) between nucleotide sequences, with the level of similarity indicated by the height of the bars within each LCB. Genome alignments were performed using MAUVE.Additional file 2: Table S1. Predicted open reading frames on Shpa and closest BLASTp hit on the NCBI database.Additional file 3: Table S2. Predicted open reading frames on Mgbh1 and closest BLASTp hit on the NCBI database.Additional file 4: Table S3. Predicted open reading frames on Shbh1 and closest BLASTp hit on the NCBI database.Additional file 5: Figure S2. GC skew analysis of the Shbh1 genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp.Additional file 6: Figure S4. GC skew analysis of the Shpa genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp.Additional file 7: Figure S3. GC skew analysis of the Mgbh1 genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp.The National Research Foundation (NRF) of South Africahttp://www.virologyj.comam2017Genetic