Soil bacterial influence on alfalfa growth and health

2013 Spring.Includes bibliographical references.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

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3

Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO2 and O3

Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes

While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats

The increased risk for cardiometabolic disease with the onset of menopause is widely studied and likely precipitated by the decline in endogenous estradiol (E2), yet the precise mechanisms are unknown. The gut microbiome is involved in estrogen metabolism and has been linked to metabolic disease, suggesting its potential involvement in the postmenopausal phenotype. Furthermore, menopause‐associated risk factors, as well as gut ecology, are altered with exercise. Therefore, we studied microbial changes in an ovariectomized (OVX vs. Sham) rat model of high (HCR) and low (LCR) intrinsic aerobic capacity (n = 8–10/group) in relation to changes in body weight/composition, glucose tolerance, and liver triglycerides (TG). Nine weeks after OVX, HCR rats were moderately protected against regional adipose tissue gain and liver TG accumulation (P < 0.05 for both). Microbial diversity and number of the Bacteroidetes phylum were significantly increased in LCR with OVX, but unchanged in HCR OVX relative to Sham. Plasma short‐chain fatty acids (SCFA), produced by bacteria in the gut and recognized as metabolic signaling molecules, were significantly greater in HCR Sham relative to LCR Sham rats (P = 0.05) and were decreased with OVX in both groups. These results suggest that increased aerobic capacity may be protective against menopause‐associated cardiometabolic risk and that gut ecology, and production of signaling molecules such as SCFA, may contribute to the mediation.We have demonstrated modest protection from the metabolic effects of surgical menopause (ovariectomy, OVX) in rats with increased aerobic capacity (high running capacity, HCR) relative to those with low aerobic capacity (low running capacity, LCR). These results are associated with significant differences in gut microbiota and their products (short chain fatty acids) between the two groups.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/113123/1/phy212488.pd

Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes

While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile

Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for salicylic acid biosynthesis

Sorghum (Sorghum bicolor [L.] Moench) is the fifth most productive cereal crop worldwide with some hybrids having high biomass yield traits making it promising for sustainable, economical biofuel production. To maximize biofuel feedstock yields, a more complete understanding of metabolic responses to low nitrogen (N) will be useful for incorporation in crop improvement efforts. In this study, 10 diverse sorghum entries (including inbreds and hybrids) were field-grown under low and full N conditions and roots were sampled at two time points for metabolomics and 16S amplicon sequencing. Roots of plants grown under low N showed altered metabolic profiles at both sampling dates including metabolites important in N storage and synthesis of aromatic amino acids. Complementary investigation of the rhizosphere microbiome revealed dominance by a single operational taxonomic unit (OTU) in an early sampling that was taxonomically assigned to the genus Pseudomonas. Abundance of this Pseudomonas OTU was significantly greater under low N in July and was decreased dramatically in September. Correlation of Pseudomonas abundance with root metabolites revealed a strong negative association with the defense hormone salicylic acid (SA) under full N but not under low N, suggesting reduced defense response. Roots from plants with N stress also contained reduced phenylalanine, a precursor for SA, providing further evidence for compromised metabolic capacity for defense response under low N conditions. Our findings suggest that interactions between biotic and abiotic stresses may affect metabolic capacity for plant defense and need to be concurrently prioritized as breeding programs become established for biofuels production on marginal soils

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3

Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO2 and O3

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3.

Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO2 and O3