Using a multimethod approach, including polarized light microscopy (PLM), scanning electron microscopy (SEM) with X-ray energy dispersive spectroscopy (EDS), SEM with mineral liberation analyzer (MLA), X-ray diffraction (XRD), and Raman spectroscopy, we examined sub-recent ferruginous crusts in the Xingu River in the Amazon Basin that have formed since the Early Pleistocene (<1.2 Ma), as indicated by (U-Th)/He dating of goethite. Although now preserved as goethite, the size and form of the smallest components of the ironstone (nanorods) and the nature of isomorphic substitution in the goethite point to very early transformation of the original precipitate, an unstable hydrous ferrous oxide (HFO) mineral, into goethite. The fine, multiply undulating laminae of the ironstone contain abundant filamentous microbial molds and casts that together support identification of the crusts as ferruginous microbialites and suggest a role of bioinduction/bioinfluence in ironstone precipitation, although inorganic precipitation is also evident. The Xingu Quaternary ironstones are the first evidence of ferruginous microbialite in a modern freshwater system in South America and may hold clues to the recent history of the Xingu River.

We used two sunflower genotypes displaying pericarp-imposed dormancy at high incubation temperatures (i.e. 30°C) to investigate the role of the pericarp as a limitation to oxygen availability to the embryo (hypoxia), and its impact on embryo abscisic acid (ABA) content and sensitivity to ABA. Results showed that both genotypes displayed very different oxygen threshold values for inhibition of embryo germination when incubation was performed at 30°C. Expression of dormancy in one genotype was therefore related to exacerbated embryo sensitivity to hypoxia, whereas in the other genotype, the pericarp appeared to act as a more severe restraint to oxygen entry. Increased sensitivity to hypoxia was, in part, related to increased sensitivity to ABA, but not to alterations in ABA metabolism. The activity of pericarp-microbial communities (bacteria and fungi) at high temperatures was also assessed as a potential determinant of hypoxia to the embryo. Oxygen consumption in pericarps incubated at 30°C was attenuated with antibiotics, which concomitantly promoted achene germination. In agreement with the observed more severe oxygen deprivation to the embryo exerted by the pericarp, the bacterial load in the pericarp was significantly higher in the commercial hybrid than in the inbred line; however, the application of antibiotics strongly reduced the bacterial colony counts for each genotype. Different bacterial and fungal communities, assessed through their profiles of carbon-source utilization, were determined between genotypes and after treatment with antibiotics. This work highlights the relationship between enhancement of sensitivity to hypoxia with incubation temperature and seed dormancy expression, and suggests that microbial activity might be part of the mechanism through which hypoxia is imposed.

The triazines are one of the most widely used herbicide classes ever developed and are critical for managing weed populations that have developed herbicide resistance. These herbicides are traditionally valued for their residual weed control in more than 50 crops. Scientific literature suggests that atrazine, and perhaps other s-triazines, may no longer remain persistent in soils due to enhanced microbial degradation. Experiments examined the rate of degradation of atrazine and two other triazine herbicides, simazine and metribuzin, in both atrazine-adapted and non-history Corn Belt soils, with similar soils being used from each state as a comparison of potential triazine degradation. In three soils with no history of atrazine use, the t1/2 of atrazine was at least four times greater than in three soils with a history of atrazine use. Simazine degradation in the same three sets of soils was 2.4 to 15 times more rapid in history soils than non-history soils. Metribuzin in history soils degraded at 0.6, 0.9, and 1.9 times the rate seen in the same three non-history soils. These results indicate enhanced degradation of the symmetrical triazine simazine, but not of the asymmetrical triazine metribuzin.

The significance of the potential impacts of microbial activity on the transport properties of host rocks for geological repositories is an area of active research. Most recent work has focused on granitic environments. This paper describes pilot studies investigating changes in transport properties that are produced by microbial activity in sedimentary rock environments in northern Japan. For the first time, these short experiments (39 days maximum) have shown that the denitrifying bacteria, Pseudomonas denitrificans, can survive and thrive when injected into flow-through column experiments containing fractured diatomaceous mudstone and synthetic groundwater under pressurized conditions. Although there were few significant changes in the fluid chemistry, changes in the permeability of the biotic column, which can be explained by the observed biofilm formation, were quantitatively monitored. These same methodologies could also be adapted to obtain information from cores originating from a variety of geological environments including oil reservoirs, aquifers and toxic waste disposal sites to provide an understanding of the impact of microbial activity on the transport of a range of solutes, such as groundwater contaminants and gases (e.g. injected carbon dioxide).

In bioassays, rice (Oryza sativa L.) recovery from metolachlor [2-chloro-N-(2-ethyl-6-methylphenyl)-N-(2-methoxy-1-methylethyl)acetamide] injury tended to be slower in flooded rice, but was not significantly different from the recovery rate in a nonflooded rice. In soils treated with 1 ppm (w/w) metolachlor and incubated in constant-temperature chambers, the half-life of metolachlor was shorter at 40 C than at 30 C. The degradation rate of metolachlor was not significantly correlated with declining moisture potentials in the range of −30 to −80 kPa. The CO2 evolution from metolachlor-treated soil was negatively correlated with incubation time and positively correlated to declining moisture levels. In a field study, metolachlor, as determined by bioassay, was mobile in a Taloka silt loam soil profile. After being incorporated to 7.5 cm, it became evenly distributed in the top 15 cm of the soil profile within 18 days. Metolachlor adsorption was positively correlated with clay and organic carbon content.

Although the effectiveness of vegetative filter strips (VFS) for reducing herbicide runoff is well documented, a comprehensive review of the literature does not exist. The objectives of this article are to denote the methods developed for evaluating herbicide retention in VFS; ascertain the efficacy of VFS regarding abating herbicide runoff; identify parameters that affect herbicide retention in VFS; review the environmental fate of herbicides retained by VFS; and identify future research needs. The retention of herbicide runoff by VFS has been evaluated in natural rainfall, simulated rainfall, and simulated run-on experiments. Parameters affecting herbicide retention in VFS include width of VFS, area ratio, species established in the VFS, time after establishment of the VFS, antecedent moisture content, nominal herbicide inflow concentration, and herbicide properties. Generally, subsequent transport of herbicides retained by VFS is reduced relative to adjacent cultivated soil because of enhanced sorption and degradation in the former.

Coeliac disease (CD) is an immune-mediated enteropathy resulting from exposure to gluten in genetically predisposed individuals. Gluten proteins are partially digested by human proteases generating immunogenic peptides that cause inflammation in patients carrying HLA-DQ2 and DQ8 genes. Although intestinal dysbiosis has been associated with patients with CD, bacterial metabolism of gluten has not been studied in depth thus far. The aim of this study was to analyse the metabolic activity of intestinal bacteria associated with gluten intake in healthy individuals, CD patients and first-degree relatives of CD patients. Faecal samples belonging to twenty-two untreated CD patients, twenty treated CD patients, sixteen healthy volunteers on normal diet, eleven healthy volunteers on gluten-free diet (GFD), seventy-one relatives of CD patients on normal diet and sixty-nine relatives on GFD were tested for several proteolytic activities, cultivable bacteria involved in gluten metabolism, SCFA and the amount of gluten in faeces. We detected faecal peptidasic activity against the gluten-derived peptide 33-mer. CD patients showed differences in faecal glutenasic activity (FGA), faecal tryptic activity (FTA), SCFA and faecal gluten content with respect to healthy volunteers. Alterations in specific bacterial groups metabolising gluten such as Clostridium or Lactobacillus were reported in CD patients. Relatives showed similar parameters to CD patients (SCFA) and healthy volunteers (FTA and FGA). Our data support the fact that commensal microbial activity is an important factor in the metabolism of gluten proteins and that this activity is altered in CD patients.

The aim of this study was to assess the effects of hop cones (Humulus lupulus L.) from two varieties Aurora and Dana, differing in their α- and β-acid contents, on rumen microbial activity measured with in vitro gas production kinetics and short-chain fatty acids (SCFA) production. Hop cones were added to the total mixed dairy cow ration (CONT) in concentrations simulating a cow’s daily intake of 50, 100 and 200 g of hop cones – the concentrations of hop cones expressed on a substrate basis were 43, 82 and 153 mg/g of substrate. Substrates were anaerobically incubated in glass syringes, and gas production kinetic parameters were determined by fitting data with the Gompertz model. Gas produced after 24 h (Gas24), maximum fermentation rate (MFR) and time of maximum fermentation rate (TMFR) were calculated from the estimated gas production kinetic parameters. After 24 h of incubation, the fermentation liquids of each substrate were taken for the determination of SCFA. Increasing the hop cone concentration decreased the total potential gas production, Gas24, MFR and shortened TMFR. The highest hop cone concentration significantly decreased acetic and butyric acid productions and total SCFA production after 24 h of incubation, but not propionic acid production, resulting in a decreased ratio between acetic acid and propionic acid.

Ecologically based farming conserves and improves the soil resource and protects environmental quality by using organic or natural resources without the application of synthetic chemicals. Soil quality assessment indicates the ability of management systems to optimize soil productivity and to maintain its structural and biological integrity. Our objective was to evaluate the effect of ecologically based management on biochemical characteristics of soil [soil quality indicators (SQI)] as an assessment of soil quality. The study was conducted on an ecologically based farming enterprise established on gently sloping soils of Sharpsburg silt loam (fine montmorillonitic, mesic Typic Argiudolls) in Clay County, Missouri, which was previously under conventional corn and soybean production. The transition to organic farming began in 1995, which included a primary management strategy to restore soil organic matter consisting of the establishment of native prairie plants and the application of composted vegetative residues and litter from horse and laying hen operations. Soils were collected at 0–10cm depths from sites under organic production (orchard and vegetable), managed prairie/pasture and from adjacent unmanaged fields during 2003–2008 for soil quality assessment. Soil organic carbon (SOC) and water-stable soil aggregates were considerably increased by up to 60 and 72%, respectively, in organic production sites compared with tilled cropland by the fifth year of assessment. Organically managed systems and restored prairie sites significantly increased (P<0.05) soil enzyme activities compared with unmanaged grass and tilled cropland. For example, dehydrogenase and glucosaminidase activities increased by 60 and 73%, respectively, under organic vegetables compared with tilled cropland. Soil enzyme activities were significantly correlated with SOC content (r values up to 0.90, P<0.001). The results of the soil quality assessment suggest that ecologically based management successfully restored biological activity of silt loam soils previously under intensive conventional agriculture. The system practiced at the study sites illustrates how resources internal to the farm (i.e., composts) can be used to manage soil productivity.

The contribution of a population of mound building, detritivorous termites (Amitermes laurensis (Mjöberg)) to nett carbon mineralization in an Australian tropical semi-arid woodland has been examined. Carbon mineralization rates were estimated by measuring daily CO2 flux from five termite mounds at monthly intervals for 12 months. Carbon flux from the mounds was found to be due to microbial activity as well as termite activity. It is conservatively estimated that the association of A. laurensis and the microbial population present in their mounds is responsible for between 4%–10% of carbon mineralized in this ecosystem, and the contribution of all termites together (mound builders and subterranean) may account for up to 20% of carbon mineralized. Regression analysis showed that rates of carbon mineralization in termite mounds were significantly related to mound moisture and mound temperature. Soil moisture was the most important factor in soil carbon mineralization, with temperature and a moisture X temperature interaction term also exerting significant affects.

The functional adaptability of the digestive system to the level of feed intake was investigated in the young rabbits by comparing two groups of 12 litters each, weaned at 21 (W21) or 35 (W35) days of age. From 14 days onwards, rabbits were fed a pelleted feed (NDF: 332 g/kg, CP: 177 g/kg, starch: 98 g/kg, as-fed basis). Until 49 days of age, the profile of digestive enzymes was weekly determined in the small intestinal content and mucosa, as well as caecal fermentation traits and fibrolytic activities. In the W21 group, the solid feed intake was increased by 57% between 21 and 35 days (P < 0.01), while the daily body growth was lower from 21 till 42 days (−17%, P < 0.05) when compared with the W35 group. Activities of enzymes of pancreatic origin were only scarcely influenced by the weaning age. In the W21 group, amylase activity tended to be lower at 28 days of age (−36%, P = 0.064), and trypsin activity was decreased by 31% at 49 days of age (P < 0.01). Lipase activity was similar in both weaning groups. Duodenal and jejunal activities of maltase and aminopeptidase N (APN) were higher on day 28 in the W21 group as compared with the W35 group (×1.4 to ×2.4, respectively, P < 0.05). On day 35, duodenal APN activity was twice as higher in the W21 group than in the W35 group (P < 0.01). In caecum, major differences between both weaning groups were observed at 28 days of age with a decrease in ammonia concentration (−43%, P < 0.01) in W21 compared with W35 rabbits. Conversely, the acetate proportion was 5% higher in the W21 group (P < 0.01) on day 28. In conclusion, the digestive tract of early-weaned rabbits showed some adaptative properties in response to nutritional environment changes, but they were insufficient to maintain their growth rate.

The effect of a dietary supplementation with mannan-oligosaccharide (MOS, Bio-Mos, Alltech Inc.) and inulin (Frutafit® IQ) on growth, health, and caecal traits was studied on 348 rabbits (Hyplus®), weaned at 25 days of age. Three hundred and thirty rabbits (110 per group) were used for the health status and growth performance trial, while 18 rabbits (six per group) were used for caecal metabolism evaluation at the age of 42 days of age. Three diets were formulated: C (control), M (0.3% MOS) and I diet (4% inulin). Digestibility of the diets was measured in 10 rabbits per group between 36 and 40 days of age. The control diet was fed to rabbits of the C group from weaning to 74 days of age (slaughter). Diets M and I were fed to rabbits of the respective group from weaning to 46 days of age, then were fed with control diet till slaughter. From 25 to 46 days of age, the weight gain was slightly higher in control rabbits ( P = 0.11), while no differences were recorded for the whole period. No differences among groups in the mortality, which was high due to an enteropathy-infected environment, were significant. The lowest morbidity ( P = 0.05) as well as the health risk index were recorded in rabbits fed the diet with inulin ( P = 0.03). After change of diet, the health risk index increased in the rabbits previously fed the diet with additives, thereby no significant differences in the health status were recorded for the whole period. Total caecal volatile fatty acids concentration was higher ( P < 0.01) and the pH ( P < 0.01) and ammonia concentration ( P = 0.01) lower in rabbits fed the inulin diet than in other rabbits. In these animals, acetate molar proportion was higher ( P = 0.01) and that of propionate as well as the propionate/butyrate ratio significantly lower than in other rabbits. Butyrate molar proportion was higher in rabbits fed the diet with MOS ( P < 0.01). In rabbits fed the inulin diet a higher activity of inulinase was recorded ( P < 0.001) than in other rabbits. A significantly lower digestibility of cellulose was observed in rabbits fed the diet with MOS. The results of our study suggest the importance of using inulin-type fructans in the nutrition of young rabbits. The higher health risk index of rabbits after change of diets indicates that prebiotics should be given for a longer time during the fattening period.

Kefir is an acidic, mildly alcoholic dairy beverage produced by the fermentation of milk with a grain-like starter culture (Koroleva, 1988). These grains usually contain a relatively stable and specific balance of microbes that exist in a complex symbiotic relationship (Obermann & Libudzisz, 1998; Witthuhn et al. 2004). The different groups of microbes present in the grains are active at different stages of the fermentation (Koroleva, 1982). The lactococci, including Lactococcus lactis subsp. lactis, Lc. lactis subsp. cremoris and Lc. lactis subsp. diacetilactis provide rapid acid development during the first hours of the fermentation (Litopoulou-Tzanetaki & Tzanetakis, 2000). As the acidity of the milk increases it provides favourable conditions for the growth of the lactobacilli (Rea et al. 1996). The yeasts, acetic acid bacteria and the aroma-producing microbes, mainly leuconostocs, have a much slower growth rate than the lactic acid producers, resulting in the slow production of the aroma compounds and the gradual increase in the concentration of these substances in the later stages of the fermentation (Koroleva, 1982).

There is considerable uncertainty about how rates of soil carbon (C) and nitrogen (N) cycling will change as CO2 accumulates in the Earth's atmosphere. We summarized data from 47 published reports on soil C and N cycling under elevated CO2 in an attempt to generalize whether rates will increase, decrease, or not change. Our synthesis centres on changes in soil respiration, microbial respiration, microbial biomass, gross N mineralization, microbial immobilization and net N mineralization, because these pools and processes represent important control points for the below-ground flow of C and N. To determine whether differences in C allocation between plant life forms influence soil C and N cycling in a predictable manner, we summarized responses beneath graminoid, herbaceous and woody plants grown under ambient and elevated atmospheric CO2. The below-ground pools and processes that we summarized are characterized by a high degree of variability (coefficient of variation 80–800%), making generalizations within and between plant life forms difficult. With few exceptions, rates of soil and microbial respiration were more rapid under elevated CO2, indicating that (1) greater plant growth under elevated CO2 enhanced the amount of C entering the soil, and (2) additional substrate was being metabolized by soil microorganisms. However, microbial biomass, gross N mineralization, microbial immobilization and net N mineralization are characterized by large increases and declines under elevated CO2, contributing to a high degree of variability within and between plant life forms. From this analysis we conclude that there are insufficient data to predict how microbial activity and rates of soil C and N cycling will change as the atmospheric CO2 concentration continues to rise. We argue that current gaps in our understanding of fine-root biology limit our ability to predict the response of soil microorganisms to rising atmospheric CO2, and that understanding differences in fine-root longevity and biochemistry between plant species are necessary for developing a predictive model of soil C and N cycling under elevated CO2.

While crop rotations improve soil quality indicators and crop yields in humid temperate regions, much less information is available under harsher arid tropical and subtropical conditions. A field experiment conducted from 1990 to 1993 compared the effect of continuous pearl millet and pearl millet-fallow systems with six rotations of pearl millet that included one, two, or three years of a legume (cluster bean or mung bean). Data were collected on several soil quality indicators and pearl millet yield. Continuous pearl millet monoculture for three y ears did not affect soil organic C, NaHCO3-soluble P, DTPA extractable Fe, Cu, Mn, or Zn, or several soil organic N fractions, but slightly increased activity of dehydrogenase and acid and alkaline phosphatase enzymes. Similar trends were observed for fallow-based cropping systems, except that enzyme activities were lower. Cropping systems containing mung bean or cluster bean improved availability of soil N and other nutrients and increased enzyme activity. These effects increased with number of years of legume. Improvements from cluster bean generally were greater than from mung bean. The lowest pearl milkt yield was obtained with continuous pearl millet and no N, and yields f or fallow-based cropping systems were 13% greater than with continuous pearl millet. Grain yields of pearl millet with two or three years of mung bean in the cropping system were, respectively, 37 and 65% greater than for continuous pearl millet; with cluster bean the corresponding increases were 68 and 101%. Pearl millet yield increased with N applications up to 40 kg/ha under all cropping systems, and up to 60 kg/ha for some cluster bean-based systems. Yield of pearl millet following cluster bean was nearly double that of continuous pearl millet. These results indicate that in hot, dry climates cropping systems that include a legume, especially cluster bean, are more productive, use the limited water supply and fertilizer N more effectively, and improve several soil quality indicators more than do cropping systems without legumes.

The relationship between in vitro gas production, concomitant in vitro apparent and true DM degradability has been examined in forty-two roughages. The partitioning of truly-degraded substrate between gas volume and microbial biomass yield and 15N incorporation into cells was also investigated. The relevance of this partitioning for the regulation of DM intake (DMI) was examined for fifty-four roughages. The results can be summarized as follows. In vitro gas production and in vitro apparent and true degradability are highly correlated (P<0.0001), r being 0.96 and 0.95 respectively. There is an inverse relationship between in vitro gas production and microbial biomass yield (r—0.67, (P<0.0001) and also 15N enrichment (P<0.001)when the variables were related to a given unit of substrate truly degraded. Selecting roughages by in vitro gas production may well be a selection against maximum microbial yield and a combination of in vitro gas volume measurements with a complementary determination of the substrate truly degraded is proposed, to calculate a partitioning factor (PF) reflecting the variation of short-chain fatty acid production per unit substrate degraded. PF is calculated as the ratio, substrate truly degraded: gas produced by it. PF was highly significant (P<0.0001) in DMI prediction when included in stepwise multiple correlations together with in vitro gas volume variables reflecting the extent and rate of gas production; 11 % of the variation in DMI was accounted for by the PF. The total model, including extent and rate of gas production and the PF, accounted for 84 % of the variation in DMI. Roughages producing proportionally less gas per unit substrate truly degraded had higher feed intakes.

Using a first-order model to describe ruminal in situ digestion implies that the rate of digestion is affected only by the quantity of potentially digestible substrate remaining. Other factors, like the microbial efficacy for digesting substrate, are assumed to be constant. However, microbes are not only the cause but also the result of digestion, being one of the digestion end-products. Two sigmoidal models (a logistic and a Gompertz-like model) were derived from a general digestion function in which the rate of digestion equals the product of the quantity of potentially digestible substrate remaining and a non-constant fractional rate of digestion (microbial efficacy function). The models were compared with a first-order model with a discrete lag time. The logistic model specifically accounted for the conversion of substrate mass to microbial mass, but did not describe microbial migration between the substrate and the ruminal fluid. In contrast, the Gompertz-like model assumed that the change in microbial efficacy was only time-dependent. There was little difference between models in estimates of scale parameters, but the asymptotic microbial efficacy was consistently higher for the logistic model than for the other models. Estimates of discrete lag time in the first-order model were biased towards obtaining values identical to the independent variable. Scale estimators appeared to be more robust than kinetic estimators. Lack-of-fit was present for most model-data set combinations. The similar patterns of residuals between models suggested that a four-parameter model may be insufficient to describe the data. It was concluded that if a four-parameter model is to be used, the model with a discrete lag time would be the least biologically appropriate.

The present work was undertaken to study the microbial activity in various segments of the gastrointestinal (GI) tract of pigs as influenced by the source and level of wheat and oat dietary fibre (DF). Eight experimental diets were prepared from wheat and oat fractions and studied in a series of two experiments using wheat flour as the DF-depleted control. The diets in Expt 1 were based on wheat flour and three iso-DF enriched diets comprising fractions rich in wheat aleurone, pericarp/testa or bran. In Expt 2, oat bran was added to wheat flour to achieve the same DF intake level as in Expt 1. This series included further diets based on rolled oats and rolled oats plus oat bran. The eight diets were given to thirty-two ileal-cannulated pigs, with sixteen pigs in each experiment. After a total period of 34 d (Expt 1) and 42 d (Expt 2), the pigs were slaughtered 4 h post-feeding and samples taken for adenine nucleotides (adenosine 5'-triphosphate (ATP); adenylate energy charge (AEC)), organic acids (lactic acid (LA); short chain fatty acids (SCFA)) and pH at twelve sites of the GI tract. The microbial activity as measured by the ATP concentration was low in the stomach and the cranial two-thirds of the small intestine, but tended to increase in the distal third. In the caecum a sharp rise in microbial activity was observed; the highest level was found for the diet providing most fermentable substrates. In all the diets but the rolled oats+oat bran diets, microbial activity showed a descending pattern as the digesta moved through the colon. In the large intestine source and level of residues had a marked influence on microbial activity. LA was the chief organic acid in the stomach and small intestine (10–40 mmol/l) while LA relative to SCFA was a minor component in the caecum and colon (10–20 mmol/l). The contribution of SCFA to total organic acids was reciprocal to LA, i. e. low in the stomach and small intestine (<20 mmol/l) and high in the caecum and colon. In the large intestine the concentration of SCFA decreased from 100–140 mmol/l in the caecum and proximal colon to 40–80 mmol/l in the distal colon. The acetic: propionic acid ratio increased from the caecum to the distal colon. With the diets based on oat alone (rolled oats; rolled oats+oat bran) the increase was less significant. DF addition and oats in particular increased the butyric acid molar ratio, from 0.06–0.08 for the wheat flour diet to 0.10–0.12 for the diet based on rolled oats+oat bran. For the same two diets the proportion of isobutyric and isovaleric acids increased more rapidly with the wheat-flour diet compared with the rolled oats+oat bran diet.