Differential Responses of Nitrate Reducer Community Size,Structure, and Activity to Tillage Systems

The main objective of this study was to determine how the size, structure, and activity of the nitrate reducer community were affected by adoption of a conservative tillage system as an alternative to conventional tillage. The experimental field, established in Madagascar in 1991, consists of plots subjected to conventional tillage or direct-seeding mulch-based cropping systems (DM), both amended with three different fertilization regimes. Comparisons of size, structure, and activity of the nitrate reducer community in samples collected from the top layer in 2005 and 2006 revealed that all characteristics of this functional community were affected by the tillage system, with increased nitrate reduction activity and numbers of nitrate reducers under DM. Nitrate reduction activity was also stimulated by combined organic and mineral fertilization but not by organic fertilization alone. In contrast, both negative and positive effects of combined organic and mineral fertilization on the size of the nitrate reducer community were observed. The size of the nitrate reducer community was a significant predictor of the nitrate reduction rates except in one treatment, which highlighted the inherent complexities in understanding the relationships the between size, diversity, and structure of functional microbial communities along environmental gradients.The transition from intensive tillage to various forms of conservation tillage began more than 50 years ago with the development of herbicides which have replaced mechanical cultivation. Since then, the principles of no-till cropping have been extensively adopted by farmers worldwide. This cropping system, also known as direct seeding, mimics natural systems by leaving the soil mostly undisturbed and permanently covered with crop residues or living plants. The benefits of reducing tillage in sustainable agriculture are now well recognized for various environmental and economic reasons (14). Leaving all residues of the previous crop on the soil surface protects against evaporative water loss, wind erosion, and surface water runoff. Concomitant with reduced erosion, no-till cropping can also result in enhanced soil carbon storage in the topsoil layer, with estimated carbon sequestration rates of 30 to 60 g C m² year⁻¹ (27, 50). In turn, these changes in soil organic matter and soil structure under a no-till cropping system can affect microbial communities (20). Thus, the microbial biomass is most often higher in no-till systems than in conventional tillage systems (11, 26). Analysis of the structure or activity of soil microbial communities has also revealed significant differences between conventional tillage and minimal tillage or no-tillage systems (25, 29). However, although the effect of tillage practices on the total soil microbial community in relation to soil organic matter management has frequently been investigated, knowledge of the changes in N-cycling microbial communities induced by no-till management is limited and is mainly focused on N process rates (3, 11, 32).The aim of this work was to determine how conversion from conventional tillage to no-till affects microorganisms involved in the N cycle. For this purpose, we used the nitrate reducing community as a model functional guild (40). Prokaryote nitrate reducers constitute a wide taxonomic group with a shared ability to produce energy from the dissimilatory reduction of nitrate to nitrite, the first step of denitrification and of the dissimilatory processes of reduction of nitrate to ammonium (39). Nitrate reduction by denitrification is of great importance, since the resulting nitrite is then reduced to N₂O or N₂ gases, which can lead to considerable nitrogen losses in agriculture and emissions of the N₂O greenhouse gas (4, 13). We hypothesized that higher C and N contents in the no-till system will result in increased nitrate reduction rates and nitrate reducer abundance combined with shifts in the community composition. Relationships between the size, activity, and structure of the nitrate reducer community in the studied cropping systems were also investigated. The structure and size of the nitrate reducer community were assessed by fingerprinting and real-time PCR using the narG and napA genes, encoding the membrane-bound and periplasmic nitrate reductases, respectively, as molecular markers (40, 41). The potential activity of the nitrate reducing community was determined by colorimetric measurement of the nitrite produced during nitrate reduction.     

Mapping field-scale spatial patterns of size and activity of the denitrifier community

There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6–16 m) and mapped the distribution of this functional guild in the field. The spatial patterns of soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N₂O production and relative abundance of some denitrification genes but not on the size of the denitrifier community. Absolute abundance of most denitrification genes was not correlated with the distribution patterns of potential denitrification activity or potential N₂O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N₂O reductase in the total bacterial community was a strong predictor of the N₂O/(N₂ + N₂O) ratio, which provides evidence for a relationship between bacterial community composition based on the relative abundance of denitrifiers in the total bacterial community and ecosystem processes. More generally, the presented geostatistical approach allows integrated mapping of microbial communities, and hence can facilitate our understanding of relationships between the ecology of microbial communities and microbial processes along environmental gradients.     

Patterns of metal distribution in hypersaline microbialites during early diagenesis: Implications for the fossil record

The use of metals as biosignatures in the fossil stromatolite record requires understanding of the processes controlling the initial metal(loid) incorporation and diagenetic preservation in living microbialites. Here, we report the distribution of metals and the organic fraction within the lithifying microbialite of the hypersaline Big Pond Lake (Bahamas). Using synchrotron‐based X‐ray microfluorescence, confocal, and biphoton microscopies at different scales (cm–μm) in combination with traditional geochemical analyses, we show that the initial cation sorption at the surface of an active microbialite is governed by passive binding to the organic matrix, resulting in a homogeneous metal distribution. During early diagenesis, the metabolic activity in deeper microbialite layers slows down and the distribution of the metals becomes progressively heterogeneous, resulting from remobilization and concentration as metal(loid)‐enriched sulfides, which are aligned with the lamination of the microbialite. In addition, we were able to identify globules containing significant Mn, Cu, Zn, and As enrichments potentially produced through microbial activity. The similarity of the metal(loid) distributions observed in the Big Pond microbialite to those observed in the Archean stromatolites of Tumbiana provides the foundation for a conceptual model of the evolution of the metal distribution through initial growth, early diagenesis, and fossilization of a microbialite, with a potential application to the fossil record.     

Using click chemistry to access mono- and ditopic β-cyclodextrin hosts substituted by chiral amino acids

A wide range of chiral mono- and ditopic cyclodextrin-based receptors have been synthesized by CuI-catalyzed azide–alkyne cycloaddition starting from mono-6-azido-β-cyclodextrin and chiral amino acids. Of interest, microwaves proved very efficient to access a wide range of ditopic β-cyclodextrin receptors with quantitative yields.     

Increased Iron Sequestration in Alveolar Macrophages in Chronic Obtructive Pulmonary Disease

Free iron in lung can cause the generation of reactive oxygen species, an important factor in chronic obstructive pulmonary disease (COPD) pathogenesis. Iron accumulation has been implicated in oxidative stress in other diseases, such as Alzheimer’s and Parkinson’s diseases, but little is known about iron accumulation in COPD. We sought to determine if iron content and the expression of iron transport and/or storage genes in lung differ between controls and COPD subjects, and whether changes in these correlate with airway obstruction. Explanted lung tissue was obtained from transplant donors, GOLD 2–3 COPD subjects, and GOLD 4 lung transplant recipients, and bronchoalveolar lavage (BAL) cells were obtained from non-smokers, healthy smokers, and GOLD 1–3 COPD subjects. Iron-positive cells were quantified histologically, and the expression of iron uptake (transferrin and transferrin receptor), storage (ferritin) and export (ferroportin) genes was examined by real-time RT-PCR assay. Percentage of iron-positive cells and expression levels of iron metabolism genes were examined for correlations with airflow limitation indices (forced expiratory volume in the first second (FEV₁) and the ratio between FEV₁ and forced vital capacity (FEV₁/FVC)). The alveolar macrophage was identified as the predominant iron-positive cell type in lung tissues. Futhermore, the quantity of iron deposit and the percentage of iron positive macrophages were increased with COPD and emphysema severity. The mRNA expression of iron uptake and storage genes transferrin and ferritin were significantly increased in GOLD 4 COPD lungs compared to donors (6.9 and 3.22 fold increase, respectively). In BAL cells, the mRNA expression of transferrin, transferrin receptor and ferritin correlated with airway obstruction. These results support activation of an iron sequestration mechanism by alveolar macrophages in COPD, which we postulate is a protective mechanism against iron induced oxidative stress.     

CDKAL1-Related Single Nucleotide Polymorphisms Are Associated with Insulin Resistance in a Cross-Sectional Cohort of Greek Children

Five novel loci recently found to be associated with body mass in two GWAS of East Asian populations were evaluated in two cohorts of Swedish and Greek children and adolescents. These loci are located within, or in the proximity of: CDKAL1, PCSK1, GP2, PAX6 and KLF9. No association with body mass has previously been reported for these loci in GWAS performed on European populations. The single nucleotide polymorphisms (SNPs) with the strongest association at each loci in the East Asian GWAS were genotyped in two cohorts, one obesity case control cohort of Swedish children and adolescents consisting of 496 cases and 520 controls and one cross-sectional cohort of 2293 nine-to-thirteen year old Greek children and adolescents. SNPs were surveyed for association with body mass and other phenotypic traits commonly associated with obesity, including adipose tissue distribution, insulin resistance and daily caloric intake. No association with body mass was found in either cohort. However, among the Greek children, association with insulin resistance could be observed for the two CDKAL1-related SNPs: rs9356744 (β = 0.018, p = 0.014) and rs2206734 (β = 0.024, p = 0.001). CDKAL1-related variants have previously been associated with type 2 diabetes and insulin response. This study reports association of CDKAL1-related SNPs with insulin resistance, a clinical marker related to type 2 diabetes in a cross-sectional cohort of Greek children and adolescents of European descent.     

The influence of transferrin binding to L2C guinea pig leukemic lymphocytes on the endocytosis cycle kinetics of its receptor

The parameters regulating the internalization and recycling of transferrin-specific receptors were determined in guinea pig leukemic B lymphocytes, in the absence or presence of ligand. We show that after the cells were purified, 45-56% of the total receptors were on the cell surface. In the absence of transferrin, unoccupied receptors are quickly internalized (rate constant, 0.12 min-1) whereas their recycling is much slower (rate constant, 0.026 min-1). This difference between endocytosis and recycling rates leads to a balanced receptor distribution with only 22% of the total receptors outside after incubation of the cells for 20-30 min at 37 degrees C. The internalization rate of occupied receptors, measured in the presence of transferrin is faster (rate constant, 0.21 min-1) than that of unoccupied receptors calculated in the absence of transferrin (0.12 min-1; see above). On the other hand, mere binding of transferrin to its receptor, without internalization, arrested by cytoplasm acidification, is sufficient to induce a large increase (by a factor of seven) in the recycling rate of unoccupied internal receptors from 0.026 min-1 to 0.17 min-1. Thus, in these lymphocytes, transferrin mobilizes internal receptors by modifying the kinetic rates of internalization and recycling, leading to a new equilibrium between external and internal receptors.     

Uptake of irradiated human low density lipoprotein by cultured Chinese hamster V79 cells

Specific binding and degradation of native and gamma-rays irradiated (100-2000 rad; 100 rad/min; 137Cs) human low density lipoprotein by Chinese hamster V79 cells and mouse peritoneal macrophage line, J774G were studied. Low density lipoproteins were labeled with 125I for studying the specific binding and subsequent degradation. The specific binding and degradation of irradiated 125I-low density lipoproteins (mixed with irradiated native lipoprotein) by Chinese hamster V79 cells are considerably reduced. The uptake depends on the concentration of thiobarbutaric acid-reactive products generated in the irradiated lipoproteins which in turn depends on the concentration of carotenoids. In contrast the rate of uptake of oxidized low density lipoproteins is enhanced by Chinese hamster macrophages. The alteration in the surface amino groups of apo-B of low density lipoprotein either due to direct damage of peptide bonds by gamma-rays or via interaction with lipid peroxides (generated in the core upon irradiation) are invoked as possible mechanisms for the reduction in specific binding and subsequent degradation by V79 cells.     

Responses of Cajanus cajan and rhizospheric N-cycling communities to bioinoculants

Background and aims

Bioinoculants are commonly used for enhancing crop productivity but little information is available on their effect on key microbial communities such as those involved in the cycling of nitrogen, a major plant nutrient. Here we developed a formulation combining different bioinoculants (Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum) and examined their effects on both Cajanus cajan growth and N-cycling microorganisms.

Methods

Seven bioinoculant combinations were evaluated in pots under field conditions, and their effects on plant growth were measured using various biometric parameters. The abundances of the total bacterial and crenarchaeal communities along with those involved in N-cycling were monitored by qPCR at vegetative, pre-flowering, flowering and maturity stages of the crop.

Results

A significant increase in growth of C. cajan was observed when treated with mixture of three bioinoculants with dry biomass and grain yield increase by 330?% and 238?%, respectively. The combination of three bioinoculants also increased the abundance of nitrogen fixers and denitrifiers towards the flowering and maturity stages.

Conclusions

The consortium of three bioinoculants increased plant growth and grain yield of C. cajan. These bioinoculants also had a positive effect on the abundance of several N-cycling microbial communities stressing the importance of understanding non-target effects of bioinoculants together with their impact on plant growth.     

Standardisation of methods in soil microbiology: progress and challenges

A plethora of methods have been developed over the few last decades to enable a better understanding of the ecology of soil microbial communities and their roles in soil functioning. However, there is generally considerable variation (both subtle and more extensive) in the actual realisation of these methods, and limited efforts have been devoted to their standardisation, despite this being crucial to underpin data comparison and integration. Ensuring comparable data across studies through standardisation is arguably best-practice, as well as necessary to effectively meet the objectives of various schemas, which require assessment of the consequences of the global change and intensification of human activities on the functioning of the soil ecosystem and its biological diversity. This article presents an overview of the existing and forthcoming ISO standards in soil microbiology and highlights possible future research efforts to be undertaken for developing new standards. We also discuss some practical and theoretical bottlenecks and hurdles that have limited standardisation in soil microbiology up to now.