Proceedings of the Soil Remediation Workshop (With special

presentation on Nextgen sequencing) held at the ARC – Central

Office on May 27th and 28th, 2014.

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, 1st Quarter horse sequencing, 1st Scarlet Macaw

sequencing and 1st 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, metagenomics,

genotyping/breeding (RAD-Seq), gene 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