Proceedings of Soil Remediation Workshop_27-28 … Remediatio… · Web viewProceedings of the Soil...
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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.
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: Group photograph of participants at the soil remediation workshop
Interactive session of the participants at the soil remediation workshop