Kate M. Scow

Determinants of Soil Microbial Communities: Effects of Agricultural Management, Season, and Soil Type on Phospholipid Fatty Acid Profiles

A bstractPhospholipid fatty acid (PLFA) profiles were measured in soils from organic, low-input, and conventional farming systems that are part of the long term Sustainable Agriculture Farming Systems (SAFS) Project. The farming systems differ in whether their source of fertilizer is mineral or organic, and in whether a winter cover crop is grown. Sustained increases in microbial biomass resulting from high organic matter inputs have been observed in the organic and low-input systems. PLFA profiles were compared to ascertain whether previously observed changes in biomass were accompanied by a change in the composition of the microbial community. In addition, the relative importance of environmental variables on PLFA profiles was determined. Redundancy analysis ordination showed that PLFA profiles from organic and conventional systems were significantly different from April to July. On ordination plots, PLFA profiles from the low-input system fell between organic and conventional systems on most sample dates. A group of fatty acids (i14:0, a15:0, 16:1ω7c, 16:1ω5c, 14:0, and 18:2ω6c) was enriched in the organic plots throughout the sampling period, and another group (10Me16:0, 2OH 16:1 and 10Me17:0) was consistently lower in relative abundance in the organic system. In addition, another group (15:0, a17:0, i16:0, 17:0, and 10Me18:0) was enriched over the short term in the organic plots after compost incorporation. The relative importance of various environmental variables in governing the composition of microbial communities could be ranked in the order: soil type > time > specific farming operation (e.g., cover crop incorporation or sidedressing with mineral fertilizer) > management system > spatial variation in the field. Measures of the microbial community and soil properties (including microbial biomass carbon and nitrogen, substrate induced respiration, basal respiration, potentially mineralizable nitrogen, soil nitrate and ammonium, and soil moisture) were seldom associated with the variation in the PLFA profiles.

Impacts of Carbon and Flooding on Soil Microbial Communities: Phospholipid Fatty Acid Profiles and Substrate Utilization Patterns

A bstractPhospholipid fatty acid (PLFA) profiles provide a robust measure that can be used to fingerprint the structure of soil microbial communities, and measure their biomass. A replicated field trial, with gradients in substrate and O2 availability created by straw incorporation and flooding was used to test the ability of PLFA to discriminate soil microbial communities in different management regimes. Another objective was to test the usefulness, on a large scale, of some of the proposed interpretations of PLFA biomarkers. Using a direct gradient statistical analysis method, PLFA profiles were found to be very sensitive to flooding and straw treatments. Relative abundances of monounsaturated fatty acids were reduced with flooding and increased with added carbon, consistent with their proposed interpretations as indicators of aerobic conditions and high substrate availability. The cyclopropyl fatty acids were not useful as taxonomic indicators of respiratory type, although their responses were consistent with their proposed use as growth condition indicators. Branched fatty acids decreased, as a group, in response to high substrate conditions. A specific biomarker for Type II methanotrophs was not found in this rice soil, even under high carbon, low O2 conditions, which resulted in methane exposure in the soil. Direct comparison of PLFA and substrate utilization patterns indicated that Biolog patterns are highly selective, and do not reflect compositional changes in soil communities.

Application of Real-Time PCR To Study Effects of Ammonium on Population Size of Ammonia-Oxidizing Bacteria in Soil

ABSTRACT Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and has a large global impact. In the past, the ecology and physiology of AOB were not well understood because these organisms are notoriously difficult to culture. Recent applications of molecular techniques have advanced our knowledge of AOB, but the necessity of using PCR-based techniques has made quantitative measurements difficult. A quantitative real-time PCR assay targeting part of the ammonia-monooxygenase gene (amoA) was developed to estimate AOB population size in soil. This assay has a detection limit of 1.3 × 105 cells/g of dry soil. The effect of the ammonium concentration on AOB population density was measured in soil microcosms by applying 0, 1.5, or 7.5 mM ammonium sulfate. AOB population size and ammonium and nitrate concentrations were monitored for 28 days after (NH4)2SO4 application. AOB populations in amended treatments increased from an initial density of approximately 4 × 106 cells/g of dry soil to peak values (day 7) of 35 × 106 and 66 × 106 cells/g of dry soil in the 1.5 and 7.5 mM treatments, respectively. The population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) remained between 0.7 × 109 and 2.2 × 109 cells/g of soil, regardless of the ammonia concentration. A fertilization experiment was conducted in a tomato field plot to test whether the changes in AOB density observed in microcosms could also be detected in the field. AOB population size increased from 8.9 × 106 to 38.0 × 106 cells/g of soil by day 39. Generation times were 28 and 52 h in the 1.5 and 7.5 mM treatments, respectively, in the microcosm experiment and 373 h in the ammonium treatment in the field study. Estimated oxidation rates per cell ranged initially from 0.5 to 25.0 fmol of NH4+ h−1 cell−1 and decreased with time in both microcosms and the field. Growth yields were 5.6 × 106, 17.5 × 106, and 1.7 × 106 cells/mol of NH4+ in the 1.5 and 7.5 mM microcosm treatments and the field study, respectively. In a second field experiment, AOB population size was significantly greater in annually fertilized versus unfertilized soil, even though the last ammonium application occurred 8 months prior to measurement, suggesting a long-term effect of ammonium fertilization on AOB population size.

Soil microbial community composition and land use history in cultivated and grassland ecosystems of coastal California

Phospholipid ester-linked fatty acid (PLFA) profiles were used to evaluate soil microbial community composition for 9 land use types in two coastal valleys in California. These included irrigated and non-irrigated agricultural sites, non-native annual grasslands and relict, never-tilled or old field perennial grasslands. All 42 sites were on loams or sandy loams of similar soil taxa derived from granitic and alluvial material. We hypothesized that land use history and its associated management inputs and practices may produce a unique soil environment, for which microbes with specific environmental requirements may be selected and supported. We investigated the relationship between soil physical and chemical characteristics, management factors, and vegetation type with microbial community composition. Higher values of total soil C, N, and microbial biomass (total PLFA) and lower values of soil pH occurred in the grassland than cultivated soils. The correspondence analysis (CA) of the PLFA profiles and the canonical correspondence analysis (CCA) of PLFA profiles, soil characteristics, and site and management factors showed distinct groupings for land use types. A given land use type could thus be identified by soil microbial community composition as well as similar soil characteristics and management factors. Differences in soil microbial community composition were highly associated with total PLFA, a measure of soil microbial biomass, suggesting that labile soil organic matter affects microbial composition. Management inputs, such as fertilizer, herbicide, and irrigation, also were associated with the distinctive microbial community composition of the different cultivated land use types.

Soil Water Content and Organic Carbon Availability Are Major Determinants of Soil Microbial Community Composition

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (–C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.

Wet-dry cycles affect dissolved organic carbon in two California agricultural soils

Abstract During Californias hot, dry summers, irrigated soils are subjected to frequent wet–dry cycles and surface layers dry to near air–dry conditions between irrigations. We investigate whether wet–dry cycles enhance soil dissolved organic carbon (DOC) concentrations. This research follows up on previous observations of higher DOC concentrations in the surface (0–2 cm) than deeper (2–15 cm) soil layer late in the growing season, even when soils were moist throughout the profile. We also investigate whether DOC contents correspond to other measures of C available to microorganisms. All measurements were made on soils stabilized at −0.03 MPa water potential for 48 h at 25°C to avoid the initial pulse of microbial activity which follows re-wetting of dry soils. After 3 months during the summer field season, DOC concentrations increased 2.5-fold in the surface 0–2 cm layer and 1.20 to 1.35-fold in the 2–15 cm layer in soils under both organic (N inputs of cover crop and manure) and conventional (inorganic N inputs) management for irrigated tomatoes. In microcosms exposed to wet–dry cycles for 3 months, DOC concentrations increased by 70%, while in microcosms maintained at −0.03 MPa for 3 months DOC remained constant. The increase in DOC in both field and microcosm soils exposed to wet–dry cycles indicates that wet–dry cycles contribute to higher background DOC contents. The greater DOC increase in the field than microcosms may be due to evaporation causing upward movement of water and concentrating DOC at the soil surface, or to greater C availability in the field due to the presence of plant roots. Respiration and microbial biomass C (MBC) remained constant or declined slightly in both soil layers and microcosm treatments over the growing season, counter to the trends in DOC concentration. Therefore DOC contents measured under moist soil conditions do not appear to consistently indicate C availability to microorganisms. The percentage of labile DOC, as measured by a bioassay, declined in the surface layer of the organic field soil and in organic and conventional soils in both microcosm treatments over the 3 month experiment, possibly indicating that roots were a continuing source of labile DOC in the lower field layers. Reflecting the higher organic inputs to the organic than conventional soil, DOC, MBC and respiration rates were 2–2.5 times higher in the organic than conventional soil throughout the experiments, however the percentage of labile DOC was approximately twice as high in the conventional soil as in organic soil.

Rapid response of soil microbial communities from conventional, low input, and organic farming systems to a wet/dry cycle

Soil microbial communities may be strongly influenced by agricultural practices which change the soil environment. One such practice is the use of organic amendments and cover crops which increase carbon availability to microorganisms. Another is irrigation which, in California’s hot, rain-free growing season, can cause severe wet/dry cycles. We investigated (i) long-term diAerences in amounts of organic inputs using soils from organic, low input, and conventional farming systems, and (ii) diAerences in severity of soil drying following irrigation, using soil from two depths, 0‐3 and 3‐15 cm. All soils were air-dried and re-wetted, and we measured short-term changes in microbial biomass carbon (MBC), dissolved organic carbon (DOC), respiration, and phospholipid ester-linked fatty acid (PLFA) composition before and for 27 h after re-wetting. Respiration rates were fit to a two-first-order-component model. Carbon respired from the more slowly utilized C pool of the two-component model, MBC, and DOC increased with increasing amounts of organic inputs, and PLFA composition of the organic and conventional soils clearly diAered in their mole percentages of numerous fatty acids when analyzed by principal components analysis and redundancy analysis. Despite these diAerences, the response of microbial communities in the three farming systems to soil drying and re-wetting was similar. For example, the relative increase in MBC following soil re-wetting did not diAer among the farming system soils. In contrast, the relative increase in MBC after re-wetting was greater, and the respiratory response to soil re-wetting was more rapid in the surface (0‐3 cm) than deeper (3‐15 cm) layer. Higher ratios of cyclopropyl fatty acids to their precursors suggested greater stress to bacteria in the deep than surface layer, and these ratios declined more rapidly after re-wetting in the deep than surface layer. This study suggested that adaptation to wet/dry cycles by surface microorganisms had occurred during the 3-month growing season, leading to changes in both microbial process rates and community composition. # 1999 Published by Elsevier Science Ltd. All rights reserved.

On-Farm Assessment of Soil Quality in California's Central Valley

Program, 1990; Mitchell et al., 1999). Mitchell et al. (1999) also reported a perceived decline in soil quality The high-value, large-scale crop production systems in the San among producers. As a result of these concerns, many Joaquin Valley (SJV) of California typically entail intensive tillage and large fertilizer and water inputs but few C additions to the soil. SJV producers have begun to question the long-term Such practices often contribute to a decline in soil quality. Our objecsustainability of their intensively managed agricultural tive for this participatory study was to examine the effects of supplesystems. mental C management practices (SCMPs) on various soil quality To help farmers in the SJV evaluate the soil quality indicators. To increase farmer participation, we conducted the study effects of alternative soil management practices, the West on farms using a variety of SCMPs, including cover crops, compost and Side On-Farm Demonstration Project (WSD) was conmanure amendments, and several different crop rotations common ducted from 1995 to 1998. This participatory research to the region. The SCMPs significantly changed a number of soil and extension program originally included 11 large-scale properties, including soil organic matter (SOM); total Kjeldahl N; SJV row-crop producers, University of California Coopmicrobial biomass C and N; exchangeable K; Olsen P; and extractable erative Extension researchers, USDA Natural Resources Fe, Mn, and Zn. A comparison including previously established, adjacent organic, conventional, and transitional fields in addition to the Conservation Service (NRCS) conservationists, USDAtreatment fields at one farm revealed significant differences in 16 of ARS scientists, and private-sector consultants. 18 soil quality indicators. A soil quality index computed for this farm Developing science-based guidelines to quantify imscored the established organic system significantly higher than the pacts of routinely used organic inputs in this region was conventional system. Our results suggest that significant changes in identified as an important priority among the project’s several soil quality indicators occur with a variety of SCMPs. This is farmer participants (Mitchell and Goodell, 1996). A especially noteworthy considering the intensive tillage, irrigation, and brief, written survey of 15 participants, conducted durhot, semiarid environment of the SJV, California, where increases in ing a routine project meeting, invited input about their SOM and related soil properties are generally not expected in a 3-yr interest in an indexing tool to evaluate soil quality (sensu study. Andrews and Carroll, 2001; Karlen et al., 1998). Fourteen of the respondents indicated that a soil quality assessment tool would be useful to compare manageW Fresno County in the San Joaquin Valley ment alternatives (one blank response) (S.S. Andrews, (SJV) of California is one of the world’s most J.P. Mitchell, and D.L. Karlen, unpublished data, 1999). productive agricultural regions. Farmers in this area Based on that level of participatory support, our project produce more than one-third of the county’s annual

Responses of soil microbial processes and community structure to tillage events and implications for soil quality

3 objectives were to (i) facilitate information exchange billion agricultural output, making it the highest reveamong farmers, consultants, and researchers regarding nue-producing county in the USA (California Dep. of these soil management practices; (ii) monitor and evaluFood and Agric., 1997). Dominant crop rotations inate on-farm, side-by-side comparisons of various SCMPs; clude annual crops (Mitchell et al., 1999) such as proand (iii) demonstrate the use of a soil quality index cessing tomato (Lycopersicon esculentum L.), cotton (SQI) for the region. (Gossypium hirsutum L.), onion (Allium cepa L.), garlic (A. sativum L.), cantaloupe (Cucumis melo L. var. reticulatus Naud.), wheat (Triticum aestivum L.), sugarbeet MATERIALS AND METHODS (Beta vulgaris L.), and lettuce (Lactuca sativa L.). Site Descriptions The intense production practices used in this region Side-by-side comparisons of conventional and organicinclude frequent and intensive tillage, irrigation, and based production systems were established on 11 farms in extensive use of fertilizers and pesticides but few addiautumn 1995. The farms were located in the western SJV tions of organic amendments to the soil (Mitchell et al., between Mendota and Huron, CA. At the beginning of the 1999). These intensive practices have raised concerns project, we randomly designated adjacent fields at each farm about resource management and water consumption as to receive either conventional or alternative treatments. The well as environmental concerns such as fugitive dust, fields varied in size but generally ranged from 30 to 60 ha ground water quality, and food safety (SJV Drainage Abbreviations: BD, bulk density; CEC, cation exchange capacity; S.S. Andrews and D.L. Karlen, USDA-ARS, Natl. Soil Tilth Lab., EC, electrical conductivity; MBN, microbial biomass nitrogen; MDS, Ames, IA 50011; J.P. Mitchell and T.K. Hartz, Dep. of Vegetable minimum data set; NRCS, Natural Resources Conservation Service; Crops and Weed Sci., and W.R. Horwath, G.S. Pettygrove, and K.M. PC, principal component; PCA, principal component analysis; PMN, Scow, Dep. of Soils and Biogeochem., Univ. of California, Davis, CA potentially mineralizable nitrogen; SAFS, Sustainable Agriculture 95616; R. Mancinelli, Dep. of Crop Prod., Univ. of Tuscia, 01100, Farming Systems (Project); SAR, sodium adsorption ratio; SCMPs, Viterbo, Italy; and D.S. Munk, Univ. of California Coop. Ext., 1720 supplemental carbon management practices; SJV, San Joaquin Valley; S. Maple Ave., Fresno, CA 93702. Received 22 May 2000. *CorreSOM, soil organic matter; SQI, soil quality index; TKN, total Kjeldahl sponding author (andrews@nstl.gov). nitrogen; WSA, water-stable aggregates; WSD, West Side On-Farm Demonstration Project; x-K, exchangeable potassium. Published in Agron. J. 94:12–23 (2002).

Changes in microbial biomass and community composition, and soil carbon and nitrogen pools after incorporation of rye into three California agricultural soils

The short-term responses of soil microbial processes and community structure to perturbation constitute one aspect of soil quality. Such responses are often associated with an increase in the emissions of greenhouse gases (i.e., CO2, NO, or N2O) and the accumulation and potential loss of nitrate by leaching. Here we describe our recent work on responses of soil carbon and nitrogen dynamics, microbial biomass, and microbial community structure to a tillage event in intensively managed vegetable crop systems in California. Our results indicate that CO2 emission is high for the first day after tillage, but respiration declines or remains constant, suggesting that physical processes are responsible for the high flux from the soil surface. Net mineralization and nitrate accumulation increase for several days after tillage, and this can be accompanied by higher denitrification rates. Tillage causes immediate changes in microbial community structure, based on phospholipid fatty acid (PLFA) analysis, but little concomitant change in total microbial biomass. Tillage events contribute to decreased soil quality by increasing emissions of greenhouse gases, and increasing the potential for nitrate leaching to groundwater, and these negative aspects must be weighed against the benefits of tillage for increasing the health and productivity of some crops. D 2003 Elsevier Science B.V. All rights reserved.