Repository logo

Soil bacterial influence on alfalfa growth and health




Sheflin, Amy M., author
Vivanco, Jorge, advisor
Weir, Tiffany, committee member
Badri, Dayakar, committee member
Manter, Dan, committee member
Paschke, Mark, committee member

Journal Title

Journal ISSN

Volume Title


Soil microbial communities have demonstrated enormous potential for promotion of plant health and productivity. In particular, the diversity of the soil community may play an important role for increased plant growth. However, previous research has focused on soil fungal diversity and neglected the role that diversity of soil bacteria may play in influencing plant growth. Therefore, a greenhouse study was conducted to determine if soil bacterial community structure influences alfalfa productivity. Prior to setup, nine soils with varying physico-chemical and microbiological profiles were chemically and biologically characterized. Soil physico-chemical factors for experimental soils were quantified via standard methods of soil nutrient testing. In addition, soil microbiology was characterized using 454 pyrosequencing to determine soil diversity indices and taxonomic classification of the soil bacterial community. These microbial communities were extracted into soil suspensions and transplanted to alfalfa plants growing in a sterile substrate. Filtered (soil microorganisms removed) and non-filtered (soil microorganisms retained) soil suspensions were applied to separate soil chemical and microbiological effects. Alfalfa plants were grown in a greenhouse for 60 days post germination; then roots and shoots were harvested, dried and weighed. This experimental setup was used to answer two distinct research questions. In the first study, alfalfa biomass was correlated with both soil physico-chemical and bacterial measures to determine which soil factors influenced plant productivity. For four soils, a biologically inactive (filtered) extract included unidentified chemical factors that had a negative effect on plant biomass production. However, in two of these cases inclusion of soil microbes counteracted this negative effect and restored plant growth to a level equal to the non-amended control. Among bacterial classes, the relative abundance of Deltaproteobacteria in soils was significantly correlated with plant productivity. Correlations between plant productivity and soil bacterial richness, diversity and evenness were marginally significant and more highly correlated than soil physico-chemical factors. Results suggest that soil microbiology can compensate for negative effects on plant growth due to soil chemistry, potentially due to microbial remediation of organic soil chemical residues such as herbicides. Also, in this study, relative abundance of specific bacterial taxa was more highly correlated than bacterial diversity indices with improved plant productivity. Many species of bacteria, referred to collectively as plant growth promoting rhizobacteria (PGPR), are known to be particularly beneficial to plant health and yield. However, inconsistency in establishment of PGPR inoculants has limited their practical use in the field. While PGPR inoculation failures have been partially attributed to competition with the indigenous soil community, studies focusing on the role that indigenous soil bacteria play on the establishment of PGPR inoculants are rare. Soil bacterial diversity is known to prevent establishment of fungal pathogens and may inhibit PGPR establishment as well. Therefore a second study was conducted using four of the nine original experimental soils, which were selected to represent the largest variety of US locale and management types from collected soils. Including four soils allowed for expansion beyond previous bacterial diversity research, which utilized only one soil type, while simultaneously including inoculation treatments of two different organisms. The same experimental setup was utilized except that either a PGPR (Pseudomonas putida) or a pathogenic microorganism (Phytophthora medicaginis) was introduced for comparison to non-amended controls. Subsequently, effects on alfalfa biomass production and disease were measured. In addition, PGPR colonization by P. putida KT2440 was quantified using qPCR via detection of the gfp gene carried on the KT2440 plasmid. Results from the second study showed increases in alfalfa productivity with added PGPR were significantly larger in soils with higher soil microbial diversity. However, no differences in PGPR root colonization were observed among non-filtered treatment groups. These results suggest that the increased effectiveness of the PGPR in high diversity communities was due to increased effectiveness of other beneficial soil microorganisms. Indeed, several native PGPR and N cycling species were correlated with shoot biomass increases when adding PGPR. Conversely, disease incidence and severity caused by "P. medicaginis" was not significantly associated with soil bacterial diversity. These results emphasize the role of soil microbial community composition and its functional relationship with the invading organism in predicting effects of an introduced PGPR inoculant or soil pathogen. In conclusion, both soil chemical and biological qualities were evaluated to lend confidence that observed effects on alfalfa biomass and microbial invasion were due to biological rather than chemical influences. Soil bacteria were found to influence plant productivity by counteracting other soil factors with negative effects on plant growth. In addition, soil community diversity played a less consequential role in these experiments than the specific taxonomical and functional bacterial members. Furthermore, soil bacterial diversity significantly improved the beneficial effects of PGPR inoculants, but was not shown to significantly reduce disease incidence or severity.


Rights Access


soil bacterial diversity
Pseudomonas putida
Phytophthora medicaginis
plant growth


Associated Publications