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Day 1
The soil remediation workshop was organised by the Microbiology and Environmental
Biotechnology Research Group of the Agricultural Research Council-Institute for Soil, Climate and Water, led by Dr Rasheed Adeleke. The main objective of this workshop was to seek sustainable ways to mitigate soil related contaminations and pollutions. It was the first soil remediation workshop organised by ARC-ISCW (ARC-ISCW). The two day workshop was attended by 64 registered participants cutting across a broad-spectrum of stakeholders spanning from researchers in the academia, scientists, industrialists and government parastatal. The following institutions/ organisations were represented: University of Pretoria;
North West University; University of KwaZuluNatal; Department of Agriculture, Forestry and fishery (DAFF); ARC – ISCW; ARC-API, ARC-OVI; CSIR; DPO; SASOL; ESKOM; Omnia Fertilizer;
Envirosoil and Bioboer CC. There were also 2 international facilitators/participants.
The workshop was formally opened at 08h38 by Dr Rasheed Adeleke welcoming participants and introducing the objective of the workshop. He mentioned that the workshop was not meant to generate funds but to create awareness on soil pollution trends and to also provide a platform for deliberations and discussions on sustainable mitigating approaches to soil remediation issues. Dr Cyril Nwangburuka, took over the anchor of programmes and ushered in Dr Jasper Rees who presented an overview of the vision and mission of ARC. Presenters of the day included Professor Damase Khasa of the Centre for Forest Research and Institute for
Integrative and Systems Biology, Université Laval in Québec, Canada. His presentation centred on the general overview of bioremediation approaches. He defined bioremediation as “The use of microbes (bacteria and fungi) and plants to break down or degrade toxic chemical compounds that have accumulated in the environment into less toxic or non-toxic substances”. He classified environmental contaminants as pollutants (crude oil, refined oil, phosphates, and heavy metals) and xenobiotics (pesticides, herbicides and plastic). Prof
Damase also talked about the sources of contamination, types of treatment technologies in use to remove contaminants from the environment as well as advantages of bioremediation

over other remediation techniques. He, however, identified the challenges of bioremediation as high toxic concentrations of contaminants and limited supply of nutrients that facilitate degradation through microorganisms and plants. He made specific reference to the phytoremediation of oil sand tailings in Canada where Alder plants colonized by actinorhizal
Frankia species were used in bioremediation.
After a brief tea break, Prof. Don Cowan, the director of the Centre for Microbial Ecology and
Genomics (CMEG) at the University of Pretoria, gave a scintillating and expository presentation on bioremediation, microbial ecology and functional metagenomics. He gave an overview of the CMEG which focuses on research on extreme environment metagenomics with the core technologies being microbial phylogenetics, quantitative microbial ecology, genome sequencing, functional metagenomics, gene discovery, gene cloning and expression as well as protein chemistry and enzymology. He talked on the application principles of bioremediation and further defined metagenomics as the total genome content in an environmental sample. Prof. Cowan emphasized that metagenomics contribute to monitoring insitu bioremediation performance, assist in selection of functional strains/communities and drive synthetic biology.
Dr Eric Igbinigie of the Coastal and Environmental Services in Grahamstown, Rhodes followed with a presentation that explored the “Relevance of Contaminated Land Assessment in South
Africa” He talked on legislative requirements, offences, penalties and international best practices regarding contaminated land as well as the steps in conducting an environmental site assessment (also called environmental due diligence). He presented the provisions of the constitution which states that” a safe and healthy environment is a basic right” therefore it is our responsibility to protect the environment for future generations.
Professor Khasa gave his second talk titled “Phytoremediation in Agroforestry” where he gave the potential uses of phytoremediation in agroforestry using riparian buffer systems, intercropping systems and woodlot management/soil sanitation short rotation woody crop
(SRWC) fallow systems. He defined agroforestry as a dynamic ecologically based natural resource management system, where the integration of woody perennials on farms and other landscapes, diversifies and increases production and promotes socio-economic and

environmental benefits for land users. He also mentioned that ectomycorrhizal fungi in
Agroforestry act as biofilters sequestering pollution within them.
Dr. Dirk Swanevelder of the ARC Biotechnology Platform (ARC-BTP) talked on the
Biotechnology platform in ARC and the society at large. He stated the vision of the ARC-BTP as to create a world class biotechnology platform to lead agricultural research in Africa. The
ARC-BTP has the following technology focused units: Genomics, Proteomics, bioinformatics, marker assisted breeding, plant phenotyping and functional genomics and offer the following services: Next Generation Sequencing (NGS), genotyping, automation, informatics and sample preparation. He chronicled the progression of the genotyping platforms since 2011 from the Illumina HiScanSQ through Illumina MiSeq in 2012, and illumina HiSeq2500 in 2014 stating the improved efficiency through the progression.
After each presentation, questions were asked by participants followed by responses from presenters. There was a special interactive session for thorough integration and exchange of ideas among participants anchored by Prof. Cowan. This provided an opportunity for each representative organization/institution to give a brief overview of their mandate and what they do. Other highlights of the first day’s session include group photographs, identifying research collaboration interests, tea breaks and a sumptuous lunch.
Day 2
The second day’s workshop kicked off on a welcome note by Dr. Rasheed Adeleke. The programme anchor person for the day, Ms Adele Wolmarans called on Prof. Cowan to give the first talk. His lecture focused on the roles of microbial communities in the bioremediation of organic and inorganic contaminated effluents in wetlands giving the case study of a natural wetland which is operational, at a Stellenbosch winery. He concluded his presentation by taking questions from participants.
Dr. Eric Igbinigie gave the second talk. He presented a practical case study of an environmental site assessment (ESA), also called environmental due diligence (EDD), of a former brick company proposed to be used as a green environment. The American Society of
Testing and Materials (ASTM) standard practice approach was employed by conducting the study in three phases. Phase 1 was the preliminary assessment of the condition of the

property, phase 2 involved sampling and laboratory analyses while phase 3 was the in-depth studies on degree of contamination and clean up. He illustrated how to carry out an ESA/EDD complying with legislative requirements and international best practices. He however noted some challenges that came up during the assessment and how they were overcame. There was also room for questions and answer after this presentation.
Next was Professor Jannie Maree of the Department of Environment, Water and Earth
Science, Tshwane University of Technology who presented a talk on using neutralised acid mine water for irrigation. He stated that high sulphate concentrations in mine wastes have caused animal deaths in the Kruger National Park and also birth defects have been observed more frequently due to acid mine drainage. He maintained that the neutralisation of acid mine drainage (AMD) water is a safe treatment of AMD to be used for irrigation water in agriculture.
As a follow up of Prof. Maree’s presentation, His post graduate student, Mr Peter Mohasoa, presented his proposed study on using reactivated acid mine drainage (AMD) for irrigation purposes and stressed the fact that South Africa is a water-scarce area and AMD or other aquatic pollutions should be remediated. Participants were availed the opportunity for questions and comments.
The afternoon session for day 2 commenced with a presentation by Professor Mark Maboeta, an environmental ecotoxicologist from the Unit for Environmental Science of the North West
University. His presentation focused on the use of vermitechnology in dealing with soil ecotoxicology. He further illustrated how soil biological parameters can be used to assess and improve soil health. He concluded by responding to questions from participants. There was also a forum for general discussion and reflections on each presentation of the day ably coordinated by Prof Khasa. Each participant had ample opportunity to ask their questions with corresponding satisfactory response by presenters.
The concluding feature of the workshop was the special presentation on Next generation sequencing (NGS) by Professor Charlie Johnson who is the director of Genomics and
Bioinformatics at Texas A&M AgriLife, College Station. He is also an associate director for the
Texas A&M Center for Bioinformatics and Genomic Systems Engineering (CBGSE). He talked about the composition and facilities available at CBGSE. He further stated the vision of CBGSE

as “becoming the leading genomic and bioinformatics academic service provider through superior quality service, innovation, and technical excellence, meeting the needs of scientists
across the Texas A&M System, Texas and world”. Prof. Johnson highlighted their projects on human and animal health, plant pathogens research , plant and animal breeding , sequencing of over 3500 bacterial genomes , 1 st Quarter horse sequencing , 1 st Scarlet Macaw sequencing and
1 st Pacific Shrimp sequencing. He outlined the runs of the illumina sequencers as MiSeq having
15Gb/run, NextSeq500 having 120Gb/run, HiSeq2500 having 1000Gb/run and HiSeqX having
1800Gb/run. He further stated that 18000 individuals’ genomes can be analysed per year on a
HiSeqX sequencer. He also highlighted the NGS applications in De novo sequencing , resequencing , targeted resequencing , m etagenomics , genotyping/breeding (RAD-Seq), g ene expression profiling, small RNAs and whole transcriptome. Other applications of NGS were highlighted as single cell seq (cancer cell evolution), ancient DNA (sequencing highly fragmented DNA from recovered samples), non-coding rna-seq (identify novel non-coding
RNAs, disease and other biomarkers), FFPE-seq (sequencing of isolated nucleic acids from formalin-fixed and paraffin embedded tissues). He mentioned that applications can be customised to meet clients’ needs. Prof. Johnson gave clarification to questions arising from his presentation.
Other memorable moments of the day were the presentation of certificate for facilitating/ participation to facilitators and participants as well as presentations of corporate gift items to the facilitators by the workshop convener, Dr Rasheed Adeleke.
The 2-day workshop eventually came to an end, as Dr. Adeleke thanked all sponsors, facilitators, collaborators, participants as well as members of his research team that constituted the organizing committee.

Memorable moments at the workshop
Above from top: Dr Rasheed Adeleke presenting the welcome address while Dr Jasper Rees, was giving an overview of the research mandate of ARC.

Above from left: Profs Damase Khasa and Don Cowan making their presentations

Above from left: Dr. Eric Igbinigie and Prof. Jannie Maree making their presentations

From left: Prof Mark Maboeta and Mr Peter Mohasoa giving their talk

Above: Group photograph of participants at the soil remediation workshop
Interactive session of the participants at the soil remediation workshop

Participants having a Tea/coffee break

Workshop registration centre