Rothamsted Research

where knowledge grows

The terrestrial nitrogen cycle: N losses from soilvOur group studies microbial communities in soil and in association with plants.

We apply metagenomic methods to establish the size and diversity of communities associated with different soils treatments, management practices and crop plants. We monitor both individual organisms and the abundance and activity of functional genes of interest, relevant to maintaining soil quality for sustainable agriculture. Currently we are determining key marker genes for active groups associated with nutrient cycling in the rhizosphere and soil, with a particular focus on nitrogen.

Introduction to soil microbial ecology and interactions in the rhizosphere

Microorganisms play an essential role in maintaining soil fertility: cycling nutrients, influencing their availability; improving soil structure; supporting healthy plant growth; degrading organic pollutants. Some soil bacteria and fungi cause plant diseases; others are antagonistic to plant pathogens and invertebrate pests.  The rhizosphere provides a region of increased microbial activity in which certain groups of bacteria and fungi are more likely to proliferate than in the bulk soil.

Some rhizosphere microorganisms originate from the seed but the majority are derived from the soil in which a plant is growing, and they will be returned to the soil, thus bulk soil and rhizosphere reciprocate impact on microbial communities. This is especially important in the case of plant pathogenic microorganisms and microbial antagonists to pests and pathogens.

Any one group of microbes is unlikely to perform with maximum efficiency under all circumstances so genetically diverse populations are needed to provide continuation of important soil processes. Since the relationship between the size, diversity and activity of microbial populations and soil 'quality' is unclear, also how these properties fluctuate throughout the seasons, with crop rotations, and the scale (temporal, spatial) on which they vary, it is difficult to predict effects of changes in agricultural practice, land use, climate, introduction of novel plants, microbial inoculants and pollution on soil quality.

Baseline studies are needed to demonstrate the significance of any observed changes in response to unusual stress. Some functions undertaken by specific groups of bacteria can be measured in situ and may indicate the size of the active population, but cannot describe its diversity or indicate if there is a related, inactive population. Advances in molecular techniques mean that more detailed examination of individual groups and of the total microbial population is possible, whether or not they can be isolated from the soil and be grown in laboratory culture. Because the genetic material defines organism identity, profiles based on DNA are the most reliable method of identification, including difficult-to-culture microbes.

Soil and rhizosphere microbial ecology

The available DNA sequence information on environmental bacteria is increasing exponentially, enabling design of many group- and species-specific primers. PCR techniques can be used to amplify sequences from individual or related strains in nucleic acids (DNA or RNA) isolated from soil providing estimates of activity, diversity and relative abundance. Quantitative PCR can estimate the frequency of sequences and reverse transcriptase PCR can amplify ribosomal sequences and functional genes identifying which populations are active. However, to assess and compare whole populations, DNA arrays offer great future possibilities.

The application of modern molecular techniques to study the ecology of soil fungi lags behind bacteria. Several groups of soil fungi are known to attack plant pathogenic nematodes, and have potential as biological control agents. To exploit fungal agents, or to manage the development of naturally suppressive soils, further understanding of fungal biology and ecology, especially genetic diversity and population dynamics, is important.

Transformation of fungi with marker genes

Transformation of fungi with marker genes offers a method for visualising hyphae on roots, nematodes and in soil and observing interactions in situ

GM Plants and soil biology

Concern that genetically modified plants could adversely impact soil biology has been expressed. 


Bacterial community structure in the rhizosphere is influenced by carbon exudation from roots - carbon availability limits microbial growth in soil.


Denitrification, the reduction of nitrate to oxides of nitrogen, arises from the activity of many different groups of bacteria in soil.

Monitoring survival and impact of bacteria

Monitoring survival and impact of bacteria introduced into the field, and their potential for gene exchange with native soil bacteria, has been the subject of a long-term study at Rothamsted. 


Metagenomics is a recently described technique for cloning functional genes.

Microbial diversity in soils

The study of microbial diversity in soil requires a wide variety of methods.  We have developed refined and applied relevant techniques to a wide range of organisms and problems in soil.  

Nematophagous fungus

The nematophagous fungus Pochonia chlamydosporia infects and destroys the eggs of root knot and cyst nematodes.


Nitrification, the conversion of ammonia to nitrate, is an important process in soils: ammonia is less soluble and so less easily lost by leaching, but is also less mobile and so less available to plants. 

Fungal interactions in the rhizosphere

Fungal interactions in the rhizosphere are difficult to monitor in situ


The genetic diversity and culturability of bacteria in archived Broadbalk soil samples has been compared, in two plots under continuous wheat, one fertilized with farmyard manure (FYM), the other with inorganic N, P, K and Mg.

Science Team

Group Leader
Penny Hirsch

Current Staff
Ian Clark
Tim Mauchline

PhD Student
Rebekah Robinson
Frances Cheesman
Daniel Morais

Visiting Workers
Rifat Hayat
Maike Rossmann
Cervin Guyomar