At the Frontline of Soil Microbiology and Sustainable Development

Mary Scholes

School of Animal, Plant and Environmental Sciences

University of the Witwatersrand, Johannesburg

South Africa

Brief history of soil microbiology

• Chinese – Yao Chinese dynasty – “angels of the earth”• Fungi – well know from fermentation Egyptian walls 2400BC• Van Leewenhoek - 1700s bacteria and simple microscope• Hooke – 1700s advanced Van Leewenhoek “cells”• Pasteur - 1850s pasteurization• Koch – 1910 microbial culture techniques – Koch’s postulates• Winogradsky - 1950s “Father of Soil Mircobiology” Nitrogen

and Sulfur cycles• Beijerinck – 1930s nitrogen fixing bacteria – “Everything is

everywhere and the environment selects”• Fleming - 1950s antibiotics and Penicillium• Waksman – 1970s – Soil actinomycete – Streptomyces

• Brief history of soil chemistry, soil physics and soil biology

Integrated System

Scholes and Scholes (2013), Science 342

Sustainable Development Goals –offer improvement over the MDGs – address some of the systemic barriers to SD and a better balance between social, economic and

environmental for all countries.

SDG 2 – End hunger, achieve food security and improved nutrition and promote sustainable agriculture.

SDG 15 – Protect restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification and halt and reverse land degradation and halt biodiversity loss.

“The successor to GDP should be a new set of metrics that integrates current knowledge of how ecology, economics, psychology and sociology collectively contribute to establishing and measuring sustainable wellbeing” (Costanza 2014b).

Rockström et al. (2009); Bennett et al. (in prep.)

Global freshwater use

Change in land use

Biodiversity loss

Phosphorus cycle

Nitrogen cycle

Ocean acidification

Climate change

Safe operating space

Ecosystem Services Framework

Schematic representation of where soil carbon, nutrient and water cycles, and soil biota underpin ecosystem services

(adapted from Smith et al., 2014).

Role in underpinning each ecosystem service shown by C = soil carbon, N = soil nutrients, W = soil water, B = soil biota.

A new view of roots

Display at the US Botanic Garden in Washington DC

Land Institute in Salinas, Kansas, Dr Jerry Glover 2015

Root sheaths and Phosphorus uptake

Bailey and Scholes, 1997

Bailey and Scholes, 1997

Bailey and Scholes 1997

130 species reviewed (23 did not have sheaths )

80% sand 30% sand

Grass species Sheath extent

Root hairs/ cm

Sheath extent

Root hairs/ cm

Anthephora pubescens 5 75 2 55Eragrostis pallens 5 100 2 45Digiteria eriantha 3 11 1 5

Bailey and Scholes, 1997

Frontiers in Soil Microbiology- classical culturing techniques and the new world of “omnics”

Soil as a complex biological system (the next 50-100 yrs) Microbial – host interactions: rhizosphere and functional genomics

Proteomics and Proteogenomics: genomes, proteins and complexity Metatransciptomics: gene expression of a microbial community in a

particular environment Metagenomics: collective genomes of the microbiota in an entire

environment – links between diversity and function – phylogenetic and functional markers

Soil Volatilomics VOCs produced by the plant or microbe

Key findings using “omics techniques”

Metatranscriptomics – preparation of cDNA and high throughput sequencing (Warnecke and Hess, (2009) J.Biotech 142: 91-95

These processes used for the efficient production of biocatalysts for biofuels from lignocellulolytic biomass

Key findings using omics techniques

Metagenomics analysis of a number of soils under different tillage and crop- management regimes (Souza et al, 2015 Appl. Soil Ecology 106-112)

Analysis of the number of sequences associated with each soil and treatment – conventionally tilled soils showed more sequences related to carbohydrate metabolism – possibly linked to lower soil organic matter and the need to metabolize a broader range of C sources

Crop rotation – different amino acid sequences

High level of functional diversity

Key findings using omics techniques

Soil Volatilomics -

Analyzed the VOC emitted from different soils by using Proton-transfer reaction time of flight mass spectrometry (PTR-TOR-MS).

Suitable technique for this application- able to discriminate soils and correlate VOC evolution, microbial biomass and enzyme activities.

Active metabolic pathways and specific enzyme activities – applications to reduce GHG emissions and the pesticide persistence

(Mancuso et al 2015 Appl Soil Ecology 86 182-191).

Soil additives(context specific)

Major advances in the use of biochar as a management additive and the reduction in ammonia volatilization (Mandal et al, 2015 Chemosphere (in press))

Soil erosion (context specific)

Climate Smart Agriculture Takes into account: food security, adaptation and

ecological footprint Foremost about development itself and address

smallholder concerns Crucial to deal with trade-offs Context matters: CSA differs widely Development & ecological footprint → green economy

Investment opportunities

Policy, landscape approaches, incentives to farmers and new technologies within a shared vision of sustainable development

Thank you