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Soil Microbiology

Doug Nelson

Dr. Douglas Nelson

Professor, Microbiology and Molecular Genetics

University of California, Davis

Friday, January 13, 2017

Abstract:  While knowledge about diversity of bacteria in soils began with pure culture studies in the late 1800s, it has exploded in the last 30 years with the advent of molecular characterization of all life based on sequencing of SSU rRNAs (Small Subunit Ribosomal RNAs; 16S for Bacteria and Archaea; 18S for Eukarya).  Currently bacterial species and genera are defined based on clusters of SSU sequences from pure culture strains and from environmental DNA samples.  Furthermore, the sequences from genera are grouped into roughly 52 higher order groups (phyla), with half of these referred to as “candidate phyla” because there is no pure culture representative within the group. Deducing the physiological properties and environmental roles of bacteria in candidate phyla is obviously difficult, but some progress has been made and will be discussed for dominant soil groups. Groups of archaea and eucarya important in soils will also be discussed briefly. The types of bacteria that survive and proliferate in non-saturated surface soils are characterized by their ability to produce desiccation-resistant spores, the properties of which will be discussed.  Firmicutes (examples: Bacillus species and Sporosarcina pasteurii) and Actinobacteria (example: Streptomyces species) are spore-forming phyla (collectively termed Gram positive bacteria) that dominate in dry soils and are well represented in culture collections.  Manipulations of native soils, e.g. for geotechnical purposes, by addition of nutrient-rich solutions constitute “enrichments”, which favor the growth of relatively fast-growing bacteria that can typically also be coaxed into pure culture.  Saturated and nutrient-amended soils can readily become anoxic, which selects for the growth of fermentative bacteria and for those bacteria and archaea capable of using electron acceptors other than oxygen.  The predictable succession of anaerobes based on endogenous or added alternate electron acceptors (nitrate, ferric iron, sulfate, carbon dioxide, etc.) will be discussed because the waste products of these processes impact geotechnical aims.  Time permitting, the following topics will also be discussed: (1) It is a generalization in microbial ecology that, of the bacteria that can be directly counted (microscopically), approximately 1% will yield to cultivation on relatively rich media.  Soil bacteria, as compared to those from nutrient-poor aquatic environments, appear to be somewhat more cultivatable.  Why? (2) Is everything everywhere?  That is, for bacteria of interest for a specific geotechnical applications will enrichments with any type of soil be successful?

Bio:  Douglas C. Nelson is a Professor in the Microbiology and Molecular Genetics Department at the University of California, Davis.  Nelson received his PhD in Biology from the University of Oregon.   His research interests include ecology, physiology, and genetics of chemoautotrophic sulfur bacteria including impact of high in situ pressure; microbial production of methyl mercury in marine and freshwater sediments; and stimulation and augmentation promoting bacterial production of calcite for improvement of soil mechanical properties.  His teaching interests include general microbiology laboratory, microbial diversity. microbial ecology.