Ann C. Kennedy

Soil microbial diversity and the sustainability of agricultural soils

Many world ecosystems are in various states of decline evidenced by erosion, low productivity, and poor water quality caused by forest clearing, intensive agricultural production, and continued use of land resources for purposes that are not sustainable. The biological diversity of these systems is being altered. Little research has been conducted to quantify the beneficial relationships between microbial diversity, soil and plant quality, and ecosystem sustainability. Ecosystem functioning is governed largely by soil microbial dynamics. Differences in microbial properties and activities of soils have been reported but are restricted to general ecological enumeration methods or activity levels, which are limited in their ability to describe a particular ecosystem. Microbial populations and their responses to stresses have been traditionally studied at the process level, in terms of total numbers of microorganisms, biomass, respiration rates, and enzyme activities, with little attention being paid to responses at the community or the organismal levels. These process level measurements, although critical to understanding the ecosystem, may be insensitive to community level changes due to the redundancy of these functions. As microbial communities comprise complex interactions between diverse organisms, they should be studied as such, and not as a “black box” into which inputs are entered and outputs are received at measured rates. Microbial communities and their processes need to be examined in relation to not only the individuals that comprise the community, but the effect of perturbations or environmental stresses on those communities.

Bacterial diversity in agroecosystems

All life forms rely on bacterial processes for their survival. Bacterial diversity is greater than the diversity of any other group of organisms. Bacteria are responsible for diverse metabolic functions that affect soil and plant health. Nutrient cycling, organic matter formation and decomposition, soil structure formation, and plant growth promotion are among the beneficial functions that bacteria perform. Deleterious effects include plant disease promotion. As bacterial functioning is critical to soil and plant health, the objective of this manuscript was to explore bacterial diversity and bioindication in agroecosystems. Microbial research has generally involved studying bacteria that are culturable. However, it is estimated that only a small portion of all bacteria are culturable, a vast portion of soil bacterial communities remains unstudied. With molecular techniques, more information can be obtained about those bacteria that are contributing to ecosystem functioning and are viable, but not culturable. Enhancing knowledge of soil bacterial functioning and diversity will aid in the development of sustainable agroecosystems.

Fatty acid methyl ester (FAME) profiles as a tool to investigate community structure of two agricultural soils

Soil microbiological parameters may be the earliest predictors of soil quality changes. Recently, molecular techniques such as fatty acid methyl ester (FAME) profiles have been used to characterize soil microbial communities. Fatty acid methyl ester (FAME) from whole soil may be derived from live cells, dead cells, humic materials, as well as plant and root exudates. Our objective was to verify differences in FAME profiles from two agricultural soils with different plants. Soil samples were collected from Ritzville and Palouse silt loams for fatty acid analysis. Soil samples from wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), pea (Pisum sativum L.), jointed goatgrass ( Aegilops cylindrica L.) and downy brome (Bromus tectorum L.) rhizospheres were also collected for fatty acid analysis. Principal component analysis (PCA) of the two soils explained 42% of the variance on PC1, which accounted for Palouse soil. Ritzville soil accounted for 19% of the variance on PC2. Factor analysis showed that rhizosphere microbial communities from various plant species may differ depending on the plant species. Presence of Gram-positive bacteria as identified by a15:0, i15:0, a17:0 and i17:0 peaks were similar between rhizosphere and nonrhizosphere soils. Gram-negative bacteria characterized by short chain hydroxy acids (10:03OH and 12:03OH) as well as cyclopropane acids (cy17:0) were higher in rhizosphere soil than nonrhizosphere. This indicates a possible shift in the bacterial community to more Gram-negative bacteria and fewer Gram-positive bacteria in the rhizospheres of the plants species studied.

Enzyme activities and microbial community structure in semiarid agricultural soils

This study investigated the effect of management on β-glucosidase, β-glucosaminidase, alkaline phosphatase, and arylsulfatase activities and the microbial community structure in semiarid soils from West Texas, USA. Surface samples (0–5xa0cm) were taken from a fine sandy loam, sandy clay loam, and loam that were under continuous cotton ( Gossypium hirsutum L.) or in cotton rotated with peanut ( Arachis hypogaea L.), sorghum ( Sorghum bicolor L.), rye ( Secale cereale) or wheat ( Triticum aestivum L.), and had different water management (irrigated or dryland), and tillage (conservation or conventional). The enzyme activities were higher in the loam and sandy clay loam than in the fine sandy loam. Soil pH was not affected by management, but the soil organic C and total N contents were generally affected by the different crop rotations and tillage practices studied. The trends of the enzyme activities as affected by management depended on the soil, but in general crop rotations and conservation tillage increased the enzyme activities in comparison to continuous cotton and conventional tillage. The soil enzyme activities were significantly correlated with the soil organic C ( r -values up to 0.90, P< 0.001), and were correlated among each other ( r -values up to 0.90, P <0.001). There were differences in the fatty acid methyl ester profiles between the fine sandy loam and the sandy clay loam and loam, and they reflected the differences in the enzyme activities found among the soils. For example, a 15:0 ranged from 1.61±0.25% in cotton-peanut/irrigated/no-till in the fine sandy loam to 3.86±0.48% in cotton-sorghum/dryland/conservation tillage in the sandy clay loam. There were no differences due to management within the same soil.

Soil Microbial Diversity: Present And Future Considerations

Microbes are the most diverse group of soil organisms, yet very little is known about them. Until recently, research has focused on those organisms that are culturable; however, a wealth of information is now being collected from both culturable and, as yet, unculturable organisms. Functions of t

Seasonal mycorrhizal colonization of winter wheat and its effect on wheat growth under dryland field conditions

Abstractu2002A field experiment was conducted to determine the seasonal patterns of arbuscular mycorrhiza (AM) in a dryland winter wheat (Triticum aestivum L.) system and to determine wheat growth and P uptake responses to inoculation with mycorrhizal fungus. Broadcast-incorporated treatments included (1) no inoculation with mycorrhizal fungus, with and without P fertilizer, and (2) mycorrhizal fungal inoculation at a rate of 5000 spores of Glomus intraradices (Schenck and Smith), per 30u2009cm in each row, with and without fertilizer P. Winter wheat was seeded within a day after treatments were imposed, and roots were sampled at five growth stages to quantify AM. Shoot samples were also taken for determination of dry matter, grain yield and yield components, and N and P uptake. No AM infection was evident during the fall months following seeding, which was characterized by low soil temperature, while during the spring, the AM increased gradually. Increases in wheat grain yields by enhanced AM were of similar magnitude to the response obtained from P fertilization. However, responses differed at intermediate growth stages. At the tillering stage, P uptake was mainly increased by P fertilization but not by fungal inoculation. At harvest, enhanced AM increased P uptake regardless of whether or not fertilizer P was added. The AM symbiosis increased with rising soil temperatures in the spring, in time to enhance late-season P accumulation and grain production.

Soil carbon pools and fluxes after land conversion in a semiarid shrub-steppe ecosystem

Worldwide soil carbon (C) losses associated with agricultural expansion and intensification have contributed significantly to increased atmospheric CO2. Soil disturbances resulting from land use changes were shown to modify the turnover of C and the formation of soil organic matter. A native semiarid shrub-steppe ecosystem recently converted into an irrigated agricultural development in the Columbia Basin of Washington State was evaluated for several abiotic indicators that might signal changes in an ecosystem during the initial stages of conversion and disturbance. Soil samples were collected in March of 2003 and 2004 from nine sites that included native shrub-steppe and agricultural fields converted in 2001 and 2002. Disturbance from conversion to irrigated crop production influenced total organic C and nitrogen (N) storage, C and N mineralization, and C turnover. Cultivated fields had greater concentrations of total organic C and N and higher cumulative C and N mineralization than native sites after 3xa0years of cultivation. Soil organic C was divided into three pools: an active pool (Ca) consisting of labile C (simple sugars, organic acids, the microbial biomass, and metabolic compounds of incorporated plant residues) with a mean residence time of days, an intermediate or slow pool (Cs) consisting of structural plant residues and physically stabilized C, and a resistant fraction (Cr) consisting of lignin and chemically stabilized C. Extended laboratory incubations of soil with measurements of CO2 were used to differentiate the size and turnover of the Ca and Cs functional C pools. The active pools were determined to be 4.5 and 6.5% and slow pools averaged 44 and 47% of the total C in native and cultivated fields, respectively. Cultivation, crop residue incorporation, and dairy manure compost amendments contributed to the increase in total soil C.

Rhizoplane colonization of pea seedlings by Rhizobium leguminosarum and a deleterious root colonizing Pseudomonas sp. and effects on plant growth

Some pseudomonads produce a toxin that specifically inhibits winter wheat (Triticum aestivum L.) root growth and the growth of several microorganisms. The toxin does not inhibit pea (Pisum sativum) root growth, but the organisms are aggressive root colonizers and their effect on Rhizobium leguminosarum growth, colonization, and nodulation of peas was not known. Peas were grown in Leonard jars in the greenhouse. Pea roots were inoculated with R. leguminosarum, a toxin-producing Pseudomonas sp., both, or neither (control). The Pseudomonas sp. colonized pea roots more rapidly and in greater number than R. leguminosarum after ten days. In the presence of the Pseudomonas sp., the R. leguminosarum population on the rhizoplane was less at ten days. When the roots were inoculated with both R. leguminosarum and Pseudomonas sp., the number of nodules were greater than when R. leguminosarum was inoculated alone, but nodule dry weight and pea shoot biomass were similar to plants inoculated with only R. leguminosarum. Although these results need confirmation with non-sterile soil and field studies, these preliminary results indicate that peas will not be affected by wheat root-inhibitory rhizobacteria.

Host range of a deleterious rhizobacterium for biological control of downy brome

Abstract Pseudomonas fluorescens strain D7 (P. f. D7; NRRL B-18293) is a root-colonizing bacterium that inhibits downy brome (Bromus tectorum L. BROTE) growth. Before commercialization as a biological control agent, strain D7 must be tested for host plant specificity. Agar plate bioassays in the laboratory and plant–soil bioassays in a growth chamber were used to determine the influence of P. f. D7 on germination and root growth of 42 selected weed, cultivated or native plant species common in the western and midwestern United States. In the agar plate bioassay, all accessions of downy brome were inhibited by P. f. D7. Root growth of seven Bromus spp. was inhibited an average of 87% compared with that of controls in the agar plate bioassay. Root growth of non-Bromus monocots was reduced by 0 to 86%, and only 6 out of 17 plant species were inhibited 40% or greater. Among all plant species, only downy brome root growth from two accessions was significantly inhibited by P. f. D7 in plant–soil bioassays (42 and 64%). P. f. D7 inhibited root growth and germination in agar plate bioassays more than in plant–soil bioassays. Inhibition in plant–soil bioassays was limited to downy brome, indicating promise for P. f. D7 as a biocontrol agent that will not harm nontarget species. Nomenclature:u2003Downy brome; Bromus tectorum L. BROTE; rhizobacterium; Pseudomonas fluorescens.

Soil Quality and Water Intake in Traditional-Till vs. No-Till Paired Farms in Washington's Palouse Region

Many farmers in the steeply sloped Palouse region of eastern Washington and northern Idaho practice no-till (NT) farming. Soil quality and water intake parameters were assessed in standing wheat (Triticum aestivum L.) stubble along summit, side, and toe-slope positions in a 2-yr study at three paired-farm sites using traditional tillage (TT) vs. NT management. Paired sites had similar south-facing aspect, slopes ranged from 29 to 45%, and NT fields had not been tilled from 2 to 20 yr. Soil aggregates .1000 mm were 5.4 to 9.8% higher in NT compared with TT. Soil organic carbon (SOC) in NTwas 30% greater than in TT at the toe-slope position. Dehydrogenase enzyme activity (DEA) was higher in TT, mainly due to the exposed CaCO3 layer at the side-slope position and higher pH of TT. Phospholipid fatty acid methyl ester (PLFA) analysis showed that fungal biomarkers were higher and Gram positive and Gram negative biomarkers were lower in NT compared with TT. There were no differences in over-winter soil water storage or ponded water infiltration rate in undisturbed standing wheat stubble between TT and NT, indicating soils that produce high wheat grain yield of 6 Mg ha or more have similar water intake regardless of tillage history as long as the stubble is left standing over winter. Results show long-term cumulative benefits of NT vs. TT on soil quality, but no differences in soil water intake when stubble is left standing over winter, possibly due to the high quantity of wheat root channels produced in both systems. MANY FARMERS in the Palouse region are adopting NT practices to reduce water erosion, enhance soil quality, increase water use efficiency, and improve farm economics. The Palouse region encompasses 750000 ha of cropland that is recognized for world record grain yields of dryland winter wheat that average 6.5 to 7 Mg ha. Tillage is generally intensive, with the moldboard plow historically used to completely invert the top 15 to 25 cm of soil to bury winter wheat stubble to prepare a seedbed. Water erosion rates following moldboard plowing used in past years averaged 45 Mg soil loss ha yr (USDA, 1978). Presently, more than 40% of Palouse cropland is under conservation tillage and water erosion rates are reduced from previous (USDA, 1978) levels, but still exceed the tolerable rate of 11 Mg ha yr in some areas (Renard et al., 1997). Approximately 5% of dryland crop hectares in the western USA are planted using NT (CTIC, 2002). The Palouse region receives an average of 420-to 600-mm annual precipitation with the majority occurring during the winter. Farming is performed on 8 to 45% slopes on deep loessial soils. The land was broken out of native prairie grassland for farming only 125 yr ago, but SOC has declined to half the original values of the native soil during that time (Papendick et al., 1985). Reduction or elimination of tillage will slow or halt the rate of SOC loss and is critical in the development of successful conservation tillage systems (Papendick and Parr, 1997). Research on conservation tillage and cropping systems is needed to improve soil quality, maximize overwinter soil water storage, and reduce water erosion. Potential for economic and environmental benefits is amajor driving force in the ongoing gradual shift by farmers to adopt reducedand no-till farming methods. Surface residue retention and the amount of soil disturbance are key factors in choosing management systems. Surface residue improves soil quality (Doran et al., 1996) by increasing SOC accumulation (Nyakatawa et al., 2001), fungal biomass, earthworm populations, and DEA (Holland and Coleman, 1987; Karlen et al., 1994). Changes in the soil ecology that occur with NT are dependent on many factors, such as landscape position, soil type and depth, precipitation, temperature, and residue management. Due to high residue levels and steep slopes, farmers in the Palouse region have lagged behind other areas of the USA and the world (i.e., Argentina, Brazil, and Canada) in adopting NT. The main collaborators for the study, John and Cory Aeschliman of Colfax, WA, have been leaders in the NT farming movement in the PNW for more than 20 yr (Mallory et al., 1999). The Aeschlimans have adopted NT on their family owned land and, in recent years, on land that they lease. Thus, parcels of the Aeschliman farm have been in continuous NT from 2 to 20 yr. These fields with various years into NT provided an avenue to study changes with NT compared with TT over time. In the PNW, residue burial with tillage during the fall reduces over-winter soil water storage compared with leaving stubble standing over the winter (Papendick and McCool, 1994). One of our goals was to measure the long-term cumulative effects of TT vs. NTon over-winter soil water storage and ponded water infiltration rate, thus tillage was conducted in the spring in this study. Our hypothesis for the experiment was that, as the time in NT A.C. Kennedy, USDA-ARS, 217 Johnson Hall, Washington State Univ., Pullman, WA 99164-6421; W.F. Schillinger, Dep. of Crop and Soil Sciences, Washington State Univ., Dryland Res. Stn., Lind, WA 99341. Mention of product and equipment names does not imply endorsement by the authors or by USDA-ARS and Washington State University. Received 23 May 2005. *Correspondingauthor(akennedy@