PROKARYOTIC COMMUNITIES ASSOCIATED WITH THE EARTHWORM Lumbricus rubellus AND THE AGRICULTURAL SOIL IT INHABITS by DAVID RICHARD SINGLETON (Under the direction of WILLIAM B. WHITMAN) ABSTRACT 16S ribosomal RNA (rRNA) gene clone libraries were constructed from the casts of the earthworm Lumbricus rubellus and the agricultural soil it inhabits. Both samples were very diverse and contained a large number of bacterial taxa. However, increased numbers of sequences belonging to the Actinobacteria, Firmicutes, and Pseudomonas taxa, in addition to decreased numbers of one phylogenetically deep unknown taxon were found in the cast library. To examine if these differences were statistically significant, a novel method of comparing 16S rRNA clone libraries was developed (LIBSHUFF). This analysis showed that the cast sample was significantly different from the soil sample, and that the differences in abundance of all four of the previously named taxa were responsible for the difference. The analysis also suggested that the cast bacterial population was derived from the soil population. Archaeal diversity was low in both the soil and cast samples and consisted of sequences from a common soil archaeal lineage. To examine the possibility of an indigenous intestinal community, earthworms were collected, the intestines dissected and washed, and 16S rRNA clone libraries constructed from DNA extracted from the intestinal material. A significant number of prokaryotes remained attached to the intestine after washing. At least three taxa, belonging to the Acidobacteria, Firmicutes, and one deep Mycoplasma-associated lineage were found in high numbers in the intestine libraries, and were not found in clone libraries made from the cast material or the surrounding soil. An additional taxon, belonging to the β-proteobacteria was also detected in signficant numbers in the intestine of earthworms as well as cast material. With the exception of the β-proteobacteria, none of the taxa were found in all of the earthworms screened, suggesting that while these sequences may represent intestine-associated organisms, they are not necessarily stable in the L. rubellus population. An organism isolated from the burrow of an earthworm, which represents the type strain in a novel genus (Solirubrobacter) was characterized. This organism represents only the third cultured species in the Rubrobacteridae subclass of the Actinobacteria phylum and bears similarity to a number of clones recovered from soils around the world. INDEX WORDS: Lumbricus rubellus, Earthworm cast, Earthworm intestine, Soil, 16S rRNA, LIBSHUFF, Solirubrobacter PROKARYOTIC COMMUNITIES ASSOCIATED WITH THE EARTHWORM Lumbricus rubellus AND THE AGRICULTURAL SOIL IT INHABITS by DAVID RICHARD SINGLETON B.A., Illinois Wesleyan University, 1996 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS, GEORGIA 2002 2002 David Richard Singleton All Rights Reserved PROKARYOTIC COMMUNITIES ASSOCIATED WITH THE EARTHWORM Lumbricus rubellus AND THE AGRICULTURAL SOIL IT INHABITS by DAVID RICHARD SINGLETON Approved: Major Professor: William B. Whitman Committee Members: David C. Coleman Paul F. Hendrix Mary Ann Moran Eric V. Stabb Electronic Version Approved: Gordhan L. Patel Dean of the Graduate School The University of Georgia May 2002 DEDICATION To Amy, for her love and patience. ACKNOWLEDGEMENTS I would like to thank Dr. William B. Whitman for all of his help, in all of its forms, throughout my graduate school career. I would also like to thank Dr. David C. Coleman, who helped a beginning graduate student get his bearings and find a project. I would like to thank Dr. Michelle A. Furlong, for beginning the project that led to my experiments. I would also like to acknowledge Dr. Paul F. Hendrix and Dr. Mary Ann Moran for sharing their expertise on earthworms and microbial ecology, respectively. I would also like to thank Dr. Mark A. Schell who gave a great many suggesions during the course of my work, and Dr. Eric V. Stabb who came to my rescue when I needed someone. And of course, I thank my lab mates, who not only made graduate school tolerable, but occassionally enjoyable. v TABLE OF CONTENTS Page ACKNOWLEDGMENTS ..................................................................................................v CHAPTER I. INTRODUCTION AND LITERATURE REVIEW .......................................... 1 II. QUANTITATIVE COMPARISONS OF 16S rDNA SEQUENCE LIBRARIES FROM ENVIRONMENTAL SAMPLES ................................. 36 III. MOLECULAR BASED ANALYSES OF PROKARYOTIC COMMUNITIES FROM AN AGRICULTURAL SOIL AND CASTS OF THE EARTHWORM Lumbricus rubellus ...................................................... 49 IV. BACTERIAL COMMUNITIES ASSOCIATED WITH THE INTESTINE OF THE EARTHWORM Lumbricus rubellus ............................................... 96 96 V. Solirubrobacter paulii GEN. NOV., SP. NOV., A MESOPHILIC BACTERIUM WITHIN THE Rubrobacteridae RELATED TO COMMON SOIL CLONES........................................................................... 136 VI. CONCLUSIONS .......................................................................................... 155 vi CHAPTER I INTRODUCTION AND LITERATURE REVIEW 1 1. Introduction - Soil prokaryotes An estimated 4-6 x 1030 prokaryotes inhabit the earth, and a large percentage of these (2.6 x 1029) are found in soil (Whitman et al., 1998). Direct counts of bacteria in soil samples are typically 109-1010 cells per gram (dry weight) of soil (e.g. Skinner et al., 1952; Øvreås and Torsvik, 1998). Using DNA reassociation curves of genomic DNA extracted from soil, Torsvik et al. (1991) estimated 4000 unique genomes in a soil sample. Later tests on a variety of soils using similar techniques revealed as few as 1000 genomes in a sandy agricultural soil and as many as 6000 genomes in a forest soil (Torsvik et al., 1996). Using the definition of a bacterial species as two genomes with less than 70% DNA reassociation (Wayne et al., 1987), Dykhuizen (1998) projected as many as 109 – 1012 different species of bacteria may exist on the planet. Given these estimates, soil microorganisms not only represent a sizable percentage of life in the biosphere, but the diversity of these prokaryotic communities is enormous. 2. Molecular microbial ecology The study of soil bacterial and archaeal communities requires a means by which the majority of the population can be observed. When studies were limited to traditional culture-based methods, the cultivated fraction of the bacterial community was often less than 1% of the total number of cells (e.g. Skinner et al., 1952). The advent of molecular techniques has allowed researchers to bypass the requirement for a pure culture in the laboratory by permitting direct examination of an organism’s DNA. In particular, the relative ease of polymerase chain reaction (PCR) amplification and sequencing of 2 specific genes has resulted in the development of a variety of molecular techniques to study prokaryotic populations, including as-of-yet uncultured organisms. Most of the molecular techniques commonly used involve the analysis of the ribosomal RNA (rRNA) genes. In bacteria and archaea, the 16S rRNA gene is most commonly used, although sequence data for the 23S and 5S rRNA genes of many organisms are also available. The 16S rRNA gene was first identified as a molecular chronometer (reviewed in Woese 1987) and was used to help define the now familiar three domain theory of phylogeny (bacteria, archaea, and eucarya). Researchers have since applied the gene to resolve the phylogeny of existing taxonomic groups as well as to identify uncultivated organisms by their 16S rRNA gene sequence similarity to known organisms. An especially beneficial property of the 16S rRNA was the presence of multiple conserved regions found in the genes of nearly all prokaryotes, which allowed the development of PCR primers and specific oligonucleotide probes, that are now the basis for many molecular microbial ecology techniques. Although molecular studies allow examination of uncultured organisms, a number of factors must be taken into account that may influence the representation of various organisms in the analysis. One concern is the extraction of DNA from soil microorganisms and whether or not all of the different cell types present in soil are lysed equally. Typically, DNA is recovered from a soil sample by lysis of the organisms in the soil followed by recovery of the nucleic acids, although the removal of cells from the soil matrix prior to DNA recovery has also been examined. A variety of chemical (e.g. phenol, sodium dodecyl sulfate [SDS]), enzymatic (e.g. lysozyme incubation), and physical treatments (e.g. freeze-thawing, bead-beating, sonication) have been developed 3 for DNA extraction from environmental samples and compared (Frostegård et al., 1999; Martin-Laurent et al., 2001; Miller et al., 1999). Of special interest in DNA extraction are endospores and other resilient cell types, which may be present in fairly high numbers in soils and are highly resistant to environmental stress. Physical disruption by a process such as bead-beating has been found to be the most effective in recovering DNA from these cell types (Moré et al., 1994). Failure to recover DNA from one or more groups of organisms can lead to an underestimation of community diversity and non-detection of potentially abundant or physiologically important groups of organisms. 2.1 PCR amplification