Francisco J. Calderón

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.

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

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.

Microbial responses to simulated tillage in cultivated and uncultivated soils

Tillage is known to have long-term eAects on organic matter and labile pools of nutrients in soil, but the short-term changes in microbial dynamics and activity after tillage are less well understood. We investigated the immediate eAects of simulated tillage on microbial community structure as determined by phospholipid fatty acid (PLFA) profiles, microbial activity, and carbon (C) and nitrogen (N) pools. Intact cores were obtained from Chualar sandy loam soils under grassland and vegetable production. The top 15 cm of soil was sieved to simulate tillage, then the cores were incubated in the greenhouse. Sampling took place 1 day before the tillage simulation and throughout the next 2 weeks. In the grassland soil, multivariate analysis showed changes in PLFA profiles within hours, indicating rapid changes in microbial community structure. Specific PLFA markers indicated a reduction in microeukaryotic biomass as well as an increase in a microbial stress marker after sieving. Respiration (as determined by soil incubation in sealed containers) decreased immediately after sieving and continued to decline through the next 14 days. Sieving was followed by a continuous accumulation of nitrate. In the vegetable soil, the changes in PLFA profiles were slow and gradual. The PLFA stress indicator rose only slightly. Microbial activity and biomass were low, and only small changes occurred in most variables. A decline in respiration and an increase in nitrate occurred several days after sieving. In both soils, decreased soil moisture may have contributed to changes in soil responses after sieving. Short-term responses to tillage may be less pronounced in soils with a long history of cultivation because of a relatively resilient microbial community and/or because lower initial microbial biomass and nutrient pools preclude a strong response to disturbance. 7 2000 Elsevier Science Ltd. All rights reserved.

Soil chemical insights provided through vibrational spectroscopy

Vibrational spectroscopy techniques provide a powerful approach to the study of environmental materials and processes. These multifunctional analytical tools can be used to probe molecular vibrations of solid, liquid, and gaseous samples for characterizing materials, elucidating reaction mechanisms, and examining kinetic processes. Although Fourier transform infrared (FTIR) spectroscopy is the most prominent type of vibrational spectroscopy used in the field of soil science, applications of Raman spectroscopy to study environmental samples continue to increase. The ability of FTIR and Raman spectroscopies to provide complementary information for organic and inorganic materials makes them ideal approaches for soil science research. In addition, the ability to conduct in situ, real time, vibrational spectroscopy experiments to probe biogeochemical processes at mineral interfaces offers unique and versatile methodologies for revealing a myriad of soil chemical phenomena. This review provides a comprehensive overview of vibrational spectroscopy techniques and highlights many of the applications of their use in soil chemistry research.

Diffuse-Reflectance Mid-infrared Spectral Properties of Soils under Alternative Crop Rotations in a Semi-arid Climate

We carried out mid-infrared (mid-IR) spectral interpretation of soils 0–5 and 5–15 cm deep in selected alternative crop rotations (ACR) treatments and an adjacent native prairie soil. Ashing and spectral subtraction shows that absorbance at 3700–2850 and 1700–1550 cm−1 indicates organic absorbance. Prairie soils, with their greater carbon (C) content, have different spectral properties from the cropped soils. Prairie soils have greater absorbance at the 2950–2870 cm−1 and the 1230 cm−1 CH bands. The soils from the different depths had different spectral properties, with the soils 0–5 cm deep having stronger absorbance at the 1055 cm−1 carbohydrate band, at 1270–1460 cm−1, and at the 1730 cm−1 ester band. The soils 5–15 cm deep are characterized by greater absorbance at the clay band. Soil C and nitrogen (N) correlated negatively with the 3700 cm−1 clay band and the 1830 cm−1 quartz band and correlated positively with the 2920 cm−1 because of aliphatic CH absorbance.

Quantification and FTIR characterization of dissolved organic carbon and total dissolved nitrogen leached from litter: a comparison of methods across litter types

Background and aimsQuantification and characterization of dissolved organic matter (DOM) leached from leaf litter in the laboratory may well depend on the method used to leach the litter. However, we lack a comparative assessment of the available methods. Here, we test how: i) four commonly used methods to leach plant litter, ii) cutting of the litter, and iii) litter species affect the quantity and composition of dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) leached using fourier transform mid-infrared spectroscopy (FTIR).MethodsWe tested how soaking litter in water, dripping water over litter, and shaking litter in two different volumes of water affected leaching of both cut and whole leaves of alfalfa (Medicago sativa), ash (Fraxinus excelsior), big bluestem grass (Andropogon gerardii), oak (Quercus macrocarpa) and pine (Pinus ponderosa) litter. We measured DOC and TDN on the leachate to quantify how much DOM was leached by each method. We used the DOC:TDN ratio and FTIR to analyze the composition of the DOM leached.ResultsThe leaching method and cutting had an impact on the amount of DOM leached from the litter. The amount of DOM leached was also affected by the litter species and its interaction with leaching method and cutting. FTIR analysis identified the same main functional groups of plant litter leachates across all of the litter species. Leaching method, cutting and litter type affected the concentration of the leachate and the resolution of the FTIR spectral data but not the relative contribution of the main functional groups.ConclusionsMethods of leaching should be chosen consistently with experimental objectives and type of litter examined. The leaching method, cutting of the litter and litter species should be taken into consideration when comparing data on DOM amounts obtained from different leaching methods but the leachate consists of similar functional group components across method, cutting and litter species.

Pyrosequencing Reveals Bacteria Carried in Different Wind-Eroded Sediments

Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. The novel technique of pyrosequencing promises to expand our understanding of the microbial diversity of soils and eroded sediments because it can sequence 10 to 100 times more DNA fragments than previous techniques, providing enhanced exploration into what microbes are being lost from soil due to wind erosion. Our study evaluated the bacterial diversity of two types of wind-eroded sediments collected from three different organic-rich soils in Michigan using a portable field wind tunnel. The wind-eroded sediments evaluated were a coarse sized fraction with 66% of particles >106 μm (coarse eroded sediment) and a finer eroded sediment with 72% of particles <106 μm. Our findings suggested that (i) bacteria carried in the coarser sediment and fine dust were effective fingerprints of the source soil, although their distribution may vary depending on the soil characteristics because certain bacteria may be more protected in soil surfaces than others; (ii) coarser wind-eroded sediment showed higher bacterial diversity than fine dust in two of the three soils evaluated; and (iii) certain bacteria were more predominant in fine dust (, , and ) than coarse sediment ( and ), revealing different locations and niches of bacteria in soil, which, depending on wind erosion processes, can have important implications on the soil sustainability and functioning. Infrared spectroscopy showed that wind erosion preferentially removes particular kinds of C from the soil that are lost via fine dust. Our study shows that eroded sediments remove the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functioning of the source soil.

An integrated spectroscopic and wet chemical approach to investigate grass litter decomposition chemistry

The chemical transformations that occur during litter decomposition are key processes for soil organic matter formation and terrestrial biogeochemistry; yet we still lack complete understanding of these chemical processes. Thus, we monitored the chemical composition of Andropogon gerardii (big bluestem grass) litter residue over a 36 month decomposition experiment in a prairie ecosystem using: traditional wet chemical fractionation based upon digestibility, solid state 13C nuclear magnetic resonance (NMR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy. The goals of this study were to (1) determine the chemical changes occurring during A. gerardii litter decomposition, and (2) compare the information obtained from each method to assess agreement. Overall, we observed a 97 % mass loss of the original litter, through a two-stage decomposition process. In the first stage, within 12 months, non-structural, cellulose and hemicellulose fractions not encrusted in lignin were preferentially and rapidly lost, while the acid unhydrolyzable residue (AUR) and microbial components increased. During the second stage, 12–36 months, all wet chemical fraction masses decreased equivalently and slowly with time, and the AUR and the lignin-encrusted cellulose fractions decomposition rates were comparable to each other. Method comparisons revealed that wet chemical fractionation did not accurately follow the initial litter structures, particularly lignin, likely because of chemical transformations and accumulation of microbial biomass. FTIR and NMR were able to determine bulk structural characteristics, and aid in elucidating chemical transformations but lacked the ability to measure absolute quantities of structural groups. As a result, we warn from the sole use of wet chemical methods, and strongly encourage coupling them with spectroscopic methods. Our results overall support the traditional chemical model of selective preservation of lignin, but shows that this is limited to the early stages of decomposition, while lignin is not selectively preserved at subsequent stages. Our study also provides important evidence regarding the impact of chemically different litter structures on decomposition rates and pathways.

A comparison of corn (Zea mays L.) residue and its biochar on soil C and plant growth.

In order to properly determine the value of charring crop residues, the C use efficiency and effects on crop performance of biochar needs to be compared to the un-charred crop residues. In this study we compared the addition of corn stalks to soil, with equivalent additions of charred (300 °C and 500 °C) corn residues. Two experiments were conducted: a long term laboratory mineralization, and a growth chamber trial with proso millet plants. In the laboratory, we measured soil mineral N dynamics, C use efficiency, and soil organic matter (SOM) chemical changes via infrared spectroscopy. The 300 °C biochar decreased plant biomass relative to a nothing added control. The 500°C biochar had little to no effect on plant biomass. With incubation we measured lower soil NO3 content in the corn stalk treatment than in the biochar-amended soils, suggesting that the millet growth reduction in the stalk treatment was mainly driven by N limitation, whereas other factors contributed to the biomass yield reductions in the biochar treatments. Corn stalks had a C sequestration use efficiency of up to 0.26, but charring enhanced C sequestration to values that ranged from 0.64 to 1.0. Infrared spectroscopy of the soils as they mineralized showed that absorbance at 3400, 2925-2850, 1737 cm-1, and 1656 cm-1 decreased during the incubation and can be regarded as labile SOM, corn residue, or biochar bands. Absorbances near 1600, 1500-1420, and 1345 cm-1 represented the more refractory SOM moieties. Our results show that adding crop residue biochar to soil is a sound C sequestration technology compared to letting the crop residues decompose in the field. This is because the resistance to decomposition of the chars after soil amendment offsets any C losses during charring of the crop residues.

Nitrapyrin delays denitrification on manured soils

Excessive application of manure may lead to NO3− leaching to groundwater and fluxes of nitrogen oxides to the atmosphere. Nitrification inhibitors such as nitrapyrin (N-serve; 2-chloro-6-(trichloromethyl)pyridine) may help to conserve manure N in the root zone by limiting NO3− supply to denitrifiers. The objective of this study was to test the effect of nitrapyrin on the timing and amounts of denitrification and N2O fluxes in manured soils under conditions favorable to denitrification. The study consisted of a laboratory incubation of soils under aerobic conditions. Three agricultural soils and a sand were included in the study, all with high moisture and initial NO3−-N content. Each soil received three treatments: 1) manure plus nitrapyrin (190 mg nitrapyrin kg−1 soil), 2) manure alone (0.15 mg manure N g−1), and 3) soil alone controls. Nitrapyrin was mixed with the manure before addition to soil. Destructive samplings were carried out weekly for 10 weeks. At each sampling, soil-extractable mineral N, microbial biomass N, denitrified N, and N2O fluxes were measured. Nitrapyrin was effective in reducing nitrification, thus enhancing soil NH4+-N accumulation and possibly reducing the potential for nitrate leaching. Although nitrapyrin was effective in reducing nitrification in manured soils, the effect on soil mineral N and potential N supply to plants varied across soils because of the interaction between nitrification, denitrification, and N immobilization. Neither manure nor nitrapyrin consistently affected net N mineralization in the five different soil types. Microbial N immobilization and/or denitrification were strong sinks of N that reduced net N mineralization. Nitrapyrin did not affect cumulative denitrification, but some soils had delayed denitrification when nitrapyrin was added. Manure had a strong effect on N2O fluxes and denitrified N in some soils, but the effects of nitrapyrin were inconsistent. Nitrapyrin significantly reduced microbial N immobilization in two agricultural soils. The observed reductions in microbial biomass may affect N availability beyond the time frame of the experiment because less N will be available for remineralization.