Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

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Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale.

Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.

The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

Soil profiles are often many meters deep, but with the majority of studies in soil microbiology focusing exclusively on the soil surface, we know very little about the nature of the microbial communities inhabiting the deeper soil horizons. We used phospholipid fatty acid (PLFA) analysis to examine the vertical distribution of specific microbial groups and to identify the patterns of microbial abundance and communitylevel diversity within the soil profile. Samples were collected from the soil surface down to 2 m in depth from two unsaturated Mollisol profiles located near Santa Barbara, CA, USA. While the densities of microorganisms were generally one to two orders of magnitude lower in the deeper horizons of both profiles than at the soil surface, approximately 35% of the total quantity of microbial biomass found in the top 2 m of soil is found below a depth of 25 cm. Principal components analysis of the PLFA signatures indicates that the composition of the soil microbial communities changes significantly with soil depth. The differentiation of microbial communities within the two profiles coincides with an overall decline in microbial diversity. The number of individual PLFAs detected in soil samples decreased by about a third from the soil surface down to 2 m. The ratios of cyclopropyl/monoenoic precursors and total saturated/total monounsaturated fatty acids increased with soil depth, suggesting that the microbes inhabiting the deeper soil horizons are more carbon limited than surface-dwelling microbes. Using PLFAs as biomarkers, we show that Gram-positive bacteria and actinomycetes tended to increase in proportional abundance with increasing soil depth, while the abundances of Gram-negative bacteria, fungi, and protozoa were highest at the soil surface and substantially lower in the subsurface. The vertical distribution of these specific microbial groups can largely be attributed to the decline in carbon availability with soil depth. q 2003 Elsevier Science Ltd. All rights reserved.

Variations in microbial community composition through two soil depth profiles

Primary productivity and herbivory were studied in the Serengeti National Park, Tanzania, and Masai Mara Game Reserve, Kenya, during the annual cycle of 1974—1975, and wet—dry season transitions in 1976—1979. Basic state variables measured were aboveground plant biomass inside permanent and temporary fences, and outside fences. Productivity was calculated as the sum of positive plant biomass increments. Control productivity (cPn) was calculated from biomass dynamics inside permanent fences. Temporary fences were moved in concert with grazing by the region's abundant ungulates to estimate actual aboveground primary productivity (aPn). Primary productivity was highly stochastic with productive periods poorly synchronized even among nearby sites. Short—term productivities could be extremely high, exceeding 30 g°m—2°d—1. Grazing animals adjusted their densities in relation to grassland productivity. The average proportion of annual aPn that was consumed by herbivores was 0.66, with a minimum of 0.15 and a maximum of 0.94. Green forage was available everywhere late in the wet season in May but was available only at high rainfall sites in the northwest late in the dry season in November. By the end of the dry season, the residual plant biomass outside fences averaged only 8% of cPn. Nomadic grazers moved seasonally in response to grassland productivity. The growing season ranged from 76 d in low rainfall areas to virtually continuous in high rainfall areas. Annual cPn was linearly related to rainfall and averaged 357 g°m—2°yr—1 over the year and 1.89 g°m—2°d—1 during the growing season. Actual aPn was substantially greater than cPn at most sites, averaging 664 g°m—2°yr—1. Growing season aPn averaged 3.78 g°m—2°d—1. Grazing stimulated net primary productivity at most locations, with the maximum stimulation at intermediate grazing intensities. Stimulation was dependent upon soil moisture status at the time of grazing. Rain had a diminishing effect on primary productivity as the wet season progressed and plant biomass accumulated. Part of the stimulation of grassland productivity by grazing was due to maintenance of the vegetation in an immature, rapidly growing state similar to that at the beginning of the rainy season. Since grazers overrode rainfall—determined productivity patterns, aPn was more closely related to grazing intensity than to ranfall. Grazing was heavier on grasslands that were intrinsically more productive. Rate of energy flow per unit of plant biomass was much higher in grazed vegetation. Grazers ate green leaves almost exclusively during the wet season, but species composition of the diets of different grazers differed markedly. Diets of nomadic grazers were very different in the wet and dry seasons. Vegetation dried out rapidly at the onset of the dry season and dry plant tissues made up a substantial proportion of ungulate dry season diets. However, green forage commonly was more abundant in diets than in the vegetation. Grazing increased both forage quality and its rate of production. Zebras supplemented a high—bulk diet by eating the seeds of awnless grasses. The foraging patterns of different grazers were differentiated by several vegetation properties, including productivity, structure, and species composition, in a manner suggesting resource partitioning. The relationship between the stability of vegetation functional properties and community species diversity was positive in five of seven tests. Greater species diversity was associated with greater biomass stability through the seasons, greater resistance to grazing by a single species of ungulate in both the wet and dry seasons, and greater resilience after grazing. Species diversity was not associated with greater resistance to grazing by several ungulate species or to plant species extinction. Specific properties of trophic web members were identified that produced greater functional stability in more diverse communities. Fire does not appear to have important effects upon the functional properties of the grasslands except for a weak stimulation of productivity in the wet season immediately following dry season burning. Fire did have an important effect upon structural properties of the vegetation that would tend to regulate ungulate feeding. The ecology of neither the plants nor the animals in the Serengeti ecosystem can be understood in isolation; many traits of both suggest coevolution among trophic web members. The functional dynamics of the trophic web suggest that the acceleration of energy and nutrient flow rates due to intense herbivory has resulted in the development of an entire consumer food web due to additive fluxes rather than mere quasi—parasitic fluxes from plants to animals.

Ecology of a Grazing Ecosystem: The Serengeti

Aboveground net primary production of grasslands is strongly influenced by the amount and distribution of annual precipitation. Analysis of data collected at 9500 sites throughout the central United States confirmed the overwhelming importance of water availability as a control on production. The regional spatial pattern of production reflected the east-west gradient in annual precipitation. Lowest values of aboveground net primary production were observed in the west and highest values in the east. This spatial pattern was shifted eastward during unfavorable years and westward during favorable years. Vari- ability in production among years was maximum in northern New Mexico and southwestern Kansas and decreased towards the north and south. The regional pattern of production was largely accounted for by annual precipitation. Production at the site level was explained by annual precipitation, soil water-holding capacity, and an interaction term. Our results support the inverse texture hypothesis. When precipitation is 370 mm/yr.

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Primary Production of the Central Grassland Region of the United States

1 The Soils Around Us 2 Formation of Soils from Parent Materials 3 Soil Classification 4 Soil Architecture and Physical Properties 5 Soil Water: Characteristics and Behavior 6 Soil and the Hydrologic Cycle 7 Soil Aeration and Temperature 8 Soil Colloids: Seat of Soil Chemical and Physical Activity 9 Soil Acidity 10 Soils of Dry Regions: Alkalinity, Salinity, and Sodicity 11 Organisms and Ecology of the Soil 12 Soil Organic Matter 13 Nitrogen and Sulfur Economy of Soils 14 Soil Phosphorus and Potassium 15 Micronutrients and Other Trace Elements 16 Practical Nutrient Management 17 Soil Erosion and Its Control 18 Soils and Chemical Pollution 19 Geographic Soils Information 20 Prospects for Global Soil Quality Appendix A Soil Classification: World Resource Base Autralian and Canadian Systems Appendix B SI Units, Conversion Factors, Periodic Table of the Elements and Scentific Names of Plants Mentioned Glossary Index

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The Nature and Properties of Soils

The soils around us -- Formation of soils from parent materials -- Soil classification -- Soil architecture and physical properties -- Soil water: characteristics and behavior -- Soil and the hydrologic cycle -- Soil aeration and temperature -- Soil colloids: seat of soil chemical and physical activity -- Soil acidity -- Soils of dry regions: alkalinity, salinity, and sodicity -- Organisms and ecology of the soil -- Soil organic matter -- Nitrogen and sulfur economy of soils -- Soil phosphorus and potassium -- Calcium, Magnesium and trace elements -- Practical nutrient management -- Soil erosion and its control -- Soils and chemical pollution -- Geographic soils information -- Prospects for global soil quality as affected by human acitvities.

The nature and properties of soils

1. The Soils Around Us. 2. Formation of Soils from Parent Materials. 3. Soil Classification. 4. Soil Architecture and Physical Properties. 5. Soil Water: Characteristics and Behavior. 6. Soil and the Hydrologic Cycle. 7. Soil Aeration and Temperature. 8. Soil Colloids: Their Nature and Practical Significance. 9. Soil Acidity, Alkalinity, and Salinity. 10. Organisms and Ecology of the Soil. 11. Soil Organic Matter. 12. Nitrogen and Sulfur Economy of Soils. 13. Soil Phosphorus, Potassium, and Micronutrients. 14. Practical Nutrient Management. 15. Soil Erosion and Its Control. Appendix A: U.S. Soil Taxonomy Suborder Map and Legend. Appendix B: Canadian and FAO Soil Classification Systems. Appendix C: SI Unit Conversion Factors and Periodic Table of the Elements. Glossary. Index.

Nyle C. Brady

Papers

The Nature and Properties of Soils

The nature and properties of soils

Elements of the Nature and Properties of Soils

The Nature and Properties of Soils, 13th Edition

The Nature and Properties of Soils. 15th edition