Application of organic amendments to restore degraded soil: effects on soil microbial properties.

Topsoil removal, compaction, and other practices in urban and industrial landscapes can degrade soil and soil ecosystem services. There is growing interest to remediate these for recreational and residential purposes, and urban waste materials offers potential to improve degraded soils. Therefore, the objective of this study was to compare the effects of urban waste products on microbial properties of a degraded industrial soil. The soil amendments were vegetative yard waste compost (VC), biosolids (BioS), and a designer mix (DM) containing BioS, biochar (BC), and drinking water treatment residual (WTR). The experiment had a completely randomized design with following treatments initiated in 2009: control soil, VC, BioS-1 (202 Mg ha(-1)), BioS-2 (403 Mg ha(-1)), and DM (202 Mg BioS ha(-1) plus BC and WTR). Soils (0-15-cm depth) were sampled in 2009, 2010, and 2011 and analyzed for enzyme activities (arylsulfatase, ß-glucosaminidase, ß-glucosidase, acid phosphatase, fluorescein diacetate, and urease) and soil microbial community structure using phospholipid fatty acid analysis (PLFA). In general, all organic amendments increased enzyme activities in 2009 with BioS treatments having the highest activity. However, this was followed by a decline in enzyme activities by 2011 that were still significantly higher than control. The fungal PLFA biomarkers were highest in the BioS treatments, whereas the control soil had the highest levels of the PLFA stress markers (P < 0.10). In conclusion, one-time addition of VC or BioS was most effective on enzyme activities; the BioS treatment significantly increased fungal biomass over the other treatments; addition of BioS to soils decreased microbial stress levels; and microbial measures showed no statistical differences between BioS and VC treatments after 3 years of treatment.

Comparison of whole-cell fatty acid (MIDI) or phospholipid fatty acid (PLFA) extractants as biomarkers to profile soil microbial communities.

The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (RespPOM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.

Optimization of a corn steep medium for production of ethanol from synthesis gas fermentation by Clostridium ragsdalei.

Fermentation of biomass derived synthesis gas to ethanol is a sustainable approach that can provide more usable energy and environmental benefits than food-based biofuels. The effects of various medium components on ethanol production by Clostridium ragsdalei utilizing syngas components (CO:CO(2)) were investigated, and corn steep liquor (CSL) was used as an inexpensive nutrient source for ethanol production by C. ragsdalei. Elimination of Mg(2+), NH(4) (+) and PO(4) (3-) decreased ethanol production from 38 to 3.7, 23 and 5.93 mM, respectively. Eliminating Na(+), Ca(2+), and K(+) or increasing Ca(2+), Mg(2+), K(+), NH(4) (+) and PO(4) (3-) concentrations had no effect on ethanol production. However, increased Na(+) concentration (171 mM) inhibited growth and ethanol production. Yeast extract (0.5 g l(-1)) and trace metals were necessary for growth of C. ragsdalei. CSL alone did not support growth and ethanol production. Nutrients limiting in CSL were trace metals, NH(4) (+) and reducing agent (Cys: cysteine sulfide). Supplementation of trace metals, NH(4) (+) and CyS to CSL (20 g l(-1), wet weight basis) yielded better growth and similar ethanol production as compared to control medium. Using 10 g l(-1), the nutritional limitation led to reduced ethanol production. Higher concentrations of CSL (50 and 100 g l(-1)) were inhibitory for cell growth and ethanol production. The CSL could replace yeast extract, vitamins and minerals (excluding NH(4) (+)). The optimized CSL medium produced 120 and 50 mM of ethanol and acetate, respectively. The CSL could provide as an inexpensive source of most of the nutrients required for the syngas fermentation, and thus could improve the economics of ethanol production from biomass derived synthesis gas by C. ragsdalei.

Effect of trace metals on ethanol production from synthesis gas by the ethanologenic acetogen, Clostridium ragsdalei.

The effect of trace metal ions (Co²+, Cu²+, Fe²+, Mn²+, Mo6+, Ni²+, Zn²+, SeO4⁻ and WO4⁻) on growth and ethanol production by an ethanologenic acetogen, Clostridium ragsdalei was investigated in CO:CO2-grown cells. A standard acetogen medium (ATCC medium no. 1754) was manipulated by varying the concentrations of trace metals in the media. Increasing the individual concentrations of Ni²+, Zn²+, SeO4⁻ and WO4⁻ from 0.84, 6.96, 1.06, and 0.68 µM in the standard trace metals solution to 8.4, 34.8, 5.3, and 6.8 µM, respectively, increased ethanol production from 35.73 mM under standard metals concentration to 176.5, 187.8, 54.4, and 72.3 mM, respectively. Nickel was necessary for growth of C. ragsdalei. Growth rate (µ) of C. ragsdalei improved from 0.34 to 0.49 (day⁻¹), and carbon monoxide dehydrogenase (CODH) and hydrogenase (H2ase)-specific activities improved from 38.45 and 0.35 to 48.5 and 1.66 U/mg protein, respectively, at optimum concentration of Ni²+. At optimum concentrations of WO4⁻ and SeO4⁻, formate dehydrogenase (FDH) activity improved from 32.3 to 42.6 and 45.4 U/mg protein, respectively. Ethanol production and the activity of FDH reduced from 35 mM and 32.3 U/mg protein to 1.14 mM and 8.79 U/mg protein, respectively, upon elimination of WO4⁻ from the medium. Although increased concentration of Zn²+ enhanced growth and ethanol production, the activities of CODH, FDH, H2ase and alcohol dehydrogenase (ADH) were not affected by varying the Zn²+ concentration. Omitting Fe²+ from the medium decreased ethanol production from 35.7 to 6.30 mM and decreased activities of CODH, FDH, H2ase and ADH from 38.5, 32.3, 0.35, and 0.68 U/mg protein to 9.07, 7.01, 0.10, and 0.24 U/mg protein, respectively. Ethanol production improved from 35 to 54 mM when Cu²+ was removed from the medium. The optimization of trace metals concentration in the fermentation medium improved enzyme activities (CODH, FDH, and H2ase), growth and ethanol production by C. ragsdalei.

Exploitation of dietary tannins to improve rumen metabolism and ruminant nutrition.

Tannins (hydrolysable and condensed tannin) are polyphenolic polymers of relatively high molecular weight with the capacity to form complexes mainly with proteins due to the presence of a large number of phenolic hydroxyl groups. They are widely distributed in nutritionally important forage trees, shrubs and legumes, cereals and grains, which are considered as anti-nutritional compounds due to their adverse effects on intake and animal performance. However, tannins have been recognised to modulate rumen fermentation favourably such as reducing protein degradation in the rumen, prevention of bloat, inhibition of methanogenesis and increasing conjugated linoleic acid concentrations in ruminant-derived foods. The inclusion of tannins in diets has been shown to improve body weight and wool growth, milk yields and reproductive performance. However, the beneficial effects on rumen modulation and animal performance have not been consistently observed. This review discusses the effects of tannins on nitrogen metabolism in the rumen and intestine, and microbial populations (bacteria, protozoa, fungi and archaea), metabolism of tannins, microbial tolerance mechanisms to tannins, inhibition of methanogenesis, ruminal biohydrogenation processes and performance of animals. The discrepancies of responses of tannins among different studies are attributed to the different chemical structures (degree of polymerisation, procyanidins to propdelphinidins, stereochemistry and C-C bonding) and concentrations of tannins, and type of diets. An establishment of structure-activity relationship would be required to explain differences among studies and obtain consistent beneficial tannin effects.

Dietary phytochemicals as rumen modifiers: a review of the effects on microbial populations.

In the recent years, the exploration of bioactive phytochemicals as natural feed additives has been of great interest among nutritionists and rumen microbiologists to modify the rumen fermentation favorably such as defaunation, inhibition of methanogenesis, improvement in protein metabolism, and increasing conjugated linoleic acid content in ruminant derived foods. Many phytochemicals such as saponins, essential oils, tannins and flavonoids from a wide range of plants have been identified, which have potential values for rumen manipulation and enhancing animal productivity as alternatives to chemical feed additives. However, their effectiveness in ruminant production has not been proved to be consistent and conclusive. This review discusses the effects of phytochemicals such as saponins, tannins and essential oils on the rumen microbial populations, i.e., bacteria, protozoa, fungi and archaea with highlighting molecular diversity of microbial community in the rumen. There are contrasting reports of the effects of these phytoadditives on the rumen fermentation and rumen microbes probably depending upon the interactions among the chemical structures and levels of phytochemicals used, nutrient composition of diets and microbial components in the rumen. The study of chemical structure-activity relationships is required to exploit the phytochemicals for obtaining target responses without adversely affecting beneficial microbial populations. A greater understanding of the modulatory effects of phytochemicals on the rumen microbial populations together with fermentation will allow a better management of the rumen ecosystem and a practical application of this feed additive technology in livestock production.

Butanol and hexanol production in Clostridium carboxidivorans syngas fermentation: Medium development and culture techniques.

Clostridium carboxidivorans was grown on model syngas (CO:H2:CO2 [70:20:10]) in a defined nutrient medium with concentrations of nitrogen, phosphate and trace metals formulated to enhance production of higher alcohols. C. carboxidivorans was successfully grown in a limited defined medium (no yeast extract, no MES buffer and minimal complex chemical inputs) using an improved fermentation protocol. Low partial pressure of CO in the headspace, coupled with restricted mass transfer for CO and H2, was required for successful fermentation. In the absence of substrate inhibition (particularly from CO), growth limitation increased production of alcohols, especially butanol and hexanol. Concentrations of butanol (over 1.0g/L), hexanol (up to 1.0g/L) and ethanol (over 3.0g/L) were achieved in bottle fermentations. Minimal medium and controlled supply of CO and H2 should be used in characterizing candidate butanol and hexanol producing strains to select for commercial potential.

A new perspective on the use of plant secondary metabolites to inhibit methanogenesis in the rumen.

Recently, greenhouse gas emissions have been of great concern globally. Ruminant livestock due to production of methane during normal fermentation in the rumen contributes substantially to the greenhouse effects. During the recent decade, a paradigm shift has been initiated whether plant secondary metabolites (PSM) could be exploited as natural safe feed additives alternative to chemical additives to inhibit enteric methanogenesis. More than 200,000 defined structures of PSM have been known. Some plants or their extracts with high concentrations of bioactive PSM such as saponins, tannins, essential oils, organosulphur compounds, flavonoids and many other metabolites appear to have potential to inhibit methane production in the rumen. The possible mechanisms and effects of many PSM on rumen methanogenesis are not clearly understood. Saponins may decrease methanogenesis through the inhibition of rumen protozoa and in turn may suppress the numbers and activity of methanogens. Although the direct effect of saponins on methanogens has not been demonstrated, saponins might inhibit methanogens at high doses. Tannins may inhibit the methanogenesis directly and also via inhibition of protozoal growth. Essential oils, organosulphur compounds and flavonoids appear to have direct effects against methanogens, and a reduction of protozoa associated methanogenesis probably plays a minor role for these metabolites. The chemical structure and molecular weight of the PSM and chemical composition of diets dependent upon the different feeding regimes may influence the effects of PSM on methane production. Although PSM may negatively affect nutrient utilization, there is evidence that methanogenesis could be suppressed without adversely affecting rumen fermentation, which could be exploited to mitigate methane emission in ruminants.