Applied Soil Ecology 15 2000 25–36
Methods for assessing the composition and diversity of soil microbial communities
G.T. Hill
a,∗
, N.A. Mitkowski
a
, L. Aldrich-Wolfe
b
, L.R. Emele
a
, D.D. Jurkonie
a
, A. Ficke
a
, S. Maldonado-Ramirez
a
, S.T. Lynch
a
, E.B. Nelson
a
a
Department of Plant Pathology, Cornell University, Ithaca, NY 14853, USA
b
Department of Ecology and Systematics, Cornell University, Ithaca, NY 14853, USA
Abstract
Soil microorganisms play important roles in soil quality and plant productivity. The development of effective methods for studying the diversity, distribution, and behavior of microorganisms in soil habitats is essential for a broader understanding
of soil health. Traditionally, the analysis of soil microbial communities has relied on culturing techniques using a variety of culture media designed to maximize the recovery of diverse microbial populations. However, only a small fraction 0.1
of the soil microbial community has been accessible with this approach. To overcome these problems, other methods such as the analysis of phospholipid fatty acids and community-level physiological profiles have been utilized in an attempt to
access a greater proportion of the soil microbial community. In recent years, molecular methods for soil microbial community analysis have provided a new understanding of the phylogenetic diversity of microbial communities in soil. Among the most
useful of these methods are those in which small subunit rRNA genes are amplified from soil-extracted nucleic acids. Using these techniques, it is possible to characterize and study soil microbes that currently cannot be cultured. Microbial rRNA
genes can be detected directly from soil samples and sequenced. These sequences can then be compared with those from other known microorganisms. Additionally, group- and taxon-specific oligonucleotide probes can be developed from these
sequences making direct visualization of microorganisms in soil habitats possible. The use of these techniques provides new ways of assessing soil microbial diversity and ultimately, a more complete understanding of the potential impacts of
environmental processes and human activities on responses of soil microorganisms. Information gained from such studies will have direct impacts on our understanding of the role of microbial processes in soil health. © 2000 Published by Elsevier
Science B.V.
Keywords: Soil ecology; Molecular microbial ecology; Soil health; Soil quality; PLFA analysis; Community-level physiological profiles;
FISH; SSU rRNA; rDNA
1. Introduction
Microbial characteristics of soils are being evalu- ated increasingly as sensitive indicators of soil health
because of the clear relationships between microbial diversity, soil and plant quality, and ecosystem sus-
tainability Doran et al., 1994. While the understand-
∗
Corresponding author.
ing of microbial properties such as biomass, activity, and diversity are important to scientists in furthering
knowledge of the factors contributing to soil health, results of such analyses may also be useful to exten-
sion personnel and farmers in devising practical mea- sures of soil quality.
Studies of soil microbial properties have been com- monly conducted at the process level, where biomass,
respiration rates, and enzyme activities have been
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26 G.T. Hill et al. Applied Soil Ecology 15 2000 25–36
examined. Less attention has been given to community- level or organism-level responses to changes in soil
properties or management. Although these process- level measurements provide an important understand-
ing of gross microbial processes and their potential role in soil health, they tell us little about quali-
tative community-level changes because any given microbial process may be carried out by diverse taxa.
Furthermore, these process-level measurements are limited in their ability to describe a particular
microbial ecosystem.
Community-level microbial interactions are com- plex, with individual species relying on the presence,
function, and interaction of many other species. There- fore, quantitative and qualitative changes in the com-
position of soil microbial communities may serve as important and sensitive indicators of both short and
long-term changes in soil health. The analysis of soil microbial communities should involve not only deter-
minations of microbial biomass and diversity, but also determinations of microbial growth, distribution, func-
tion, and, if possible, the nature of interactions among species.
Two of the longstanding challenges in soil mi- crobiology have been the development of effective
methods to 1 determine which microorganisms are present in soil and 2 determine microbial function
in situ. These challenges have been exacerbated by the difficulties of separating microorganisms from the
soil matrix and from plant tissues, the morphological similarities among many organisms found in soils,
and changing microbial taxonomies. Furthermore, the microscopic size of soil microorganisms has made
direct visualization more difficult than with macro- organisms.
Over the past 10 years, the approach to analyzing soil microbial communities has changed dramatically.
Many new methods and approaches are now avail- able, allowing soil microbiologists to gain access
to more of the microorganisms residing in soil and allowing for better assessments of microbial diver-
sity. In this review, we briefly discuss some of the more important approaches for studying soil micro-
bial communities, describing their strengths as well as their weaknesses. Our goal is to place the newer
culture-independent methods in perspective with the traditional culture-based approaches for assessing
microbial diversity.
2. Culture-dependent methods of community analysis
