Soil resilience and recovery: rapid community responses to management changes.

BACKGROUND AND AIMS: Soil degradation is a major global problem; to investigate the potential for recovery of soil biota and associated key functions, soils were monitored during the early years of conversion between permanent grassland, arable cropping and bare fallow (maintained by regular tilling). Distinct differences in soil properties had become apparent 50 years after a previous conversion. METHODS: Subplots on previously permanent grassland, arable and bare fallow soil were converted to the two alternatives, generating 9 treatments. Soil properties (soil organic carbon, mesofauna, microbial community structure and activity) were measured. RESULTS: After 2 years, mesofauna and microbial abundance increased where plants were grown on previously bare fallow soils and declined where grassland was converted to bare fallow treatment. Overall prokaryote community composition remained more similar to the previous treatments of the converted plots than to the new treatments but there were significant changes in the relative abundance of some groups and functional genes. Four years after conversion, SOC in arable and bare fallow soils converted to grassland had increased significantly. CONCLUSIONS: Conversion to permanent grassland effectively replenished C in previously degraded soil; the soil microbiome showed significant conversion-related changes; plant-driven recovery was quicker than C loss in the absence of plants.

Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment.

Bacterial denitrification results in the loss of fertilizer nitrogen and greenhouse gas emissions as nitrous oxides, but ecological factors in soil influencing denitrifier communities are not well understood, impeding the potential for mitigation by land management. Communities vary in the relative abundance of the alternative dissimilatory nitrite reductase genes nirK and nirS, and the nitrous oxide reductase gene nosZ; however, the significance for nitrous oxide emissions is unclear. We assessed the influence of different long-term fertilization and cultivation treatments in a 160-year-old field experiment, comparing the potential for denitrification by soil samples with the size and diversity of their denitrifier communities. Denitrification potential was much higher in soil from an area left to develop from arable into woodland than from a farmyard manure-fertilized arable treatment, which in turn was significantly higher than inorganic nitrogen-fertilized and unfertilized arable plots. This correlated with abundance of nirK but not nirS, the least abundant of the genes tested in all soils, showing an inverse relationship with nirK. Most genetic variation was seen in nirK, where sequences resolved into separate groups according to soil treatment. We conclude that bacteria containing nirK are most probably responsible for the increased denitrification potential associated with nitrogen and organic carbon in this soil.

Trehalose 6-phosphate is required for the onset of leaf senescence associated with high carbon availability.

Trehalose 6-phosphate (T6P) is an important regulator of plant metabolism and development. T6P content increases when carbon availability is high, and in young growing tissue, T6P inhibits the activity of Snf1-related protein kinase (SnRK1). Here, strong accumulation of T6P was found in senescing leaves of Arabidopsis (Arabidopsis thaliana), in parallel with a rise in sugar contents. To determine the role of T6P in senescence, T6P content was altered by expressing the bacterial T6P synthase gene, otsA (to increase T6P), or the T6P phosphatase gene, otsB (to decrease T6P). In otsB-expressing plants, T6P accumulated less strongly during senescence than in wild-type plants, while otsA-expressing plants contained more T6P throughout. Mature otsB-expressing plants showed a similar phenotype as described for plants overexpressing the SnRK1 gene, KIN10, including reduced anthocyanin accumulation and delayed senescence. This was confirmed by quantitative reverse transcription-polymerase chain reaction analysis of senescence-associated genes and genes involved in anthocyanin synthesis. To analyze if the senescence phenotype was due to decreased sugar sensitivity, the response to sugars was determined. In combination with low nitrogen supply, metabolizable sugars (glucose, fructose, or sucrose) induced senescence in wild-type and otsA-expressing plants but to a smaller extent in otsB-expressing plants. The sugar analog 3-O-methyl glucose, on the other hand, did not induce senescence in any of the lines. Transfer of plants to and from glucose-containing medium suggested that glucose determines senescence during late development but that the effects of T6P on senescence are established by the sugar response of young plants.

Upregulation of biosynthetic processes associated with growth by trehalose 6-phosphate.

Trehalose 6-phosphate (T6P), the precursor of trehalose, is a signaling molecule in plants with strong effects on metabolism, growth and development. We recently showed that in growing tissues T6P is an inhibitor of SnRK1 of the SNF1-related group of protein kinases. SnRK1 acts as transcriptional integrator in response to carbon and energy supply. In microarray experiments on seedlings of transgenic Arabidopsis with elevated T6P content we found that expression of SnRK1 marker genes was affected in a manner to be predicted by inhibition of SnRK1 by T6P in vivo. A large number of genes involved in reactions that utilize carbon, e.g., UDP-glucose dehydrogenase genes involved in cell wall synthesis, were upregulated. T6P was also found to affect developmental signaling pathways, probably in a SnRK1-independent manner. This includes upregulation of genes encoding UDP-glycosyltransferases that are involved in the glycosylation of hormones. In addition, genes involved in auxin response and light signaling were affected. Many of these genes belong to pathways that link the circadian clock to plant growth and development. The overall pattern of changes in gene expression supports a role for T6P in coordinating carbon supply with biosynthetic process involved in growth and development.

Inhibition of SNF1-related protein kinase1 activity and regulation of metabolic pathways by trehalose-6-phosphate.

Trehalose-6-phosphate (T6P) is a proposed signaling molecule in plants, yet how it signals was not clear. Here, we provide evidence that T6P functions as an inhibitor of SNF1-related protein kinase1 (SnRK1; AKIN10/AKIN11) of the SNF1-related group of protein kinases. T6P, but not other sugars and sugar phosphates, inhibited SnRK1 in Arabidopsis (Arabidopsis thaliana) seedling extracts strongly (50%) at low concentrations (1-20 microM). Inhibition was noncompetitive with respect to ATP. In immunoprecipitation studies using antibodies to AKIN10 and AKIN11, SnRK1 catalytic activity and T6P inhibition were physically separable, with T6P inhibition of SnRK1 dependent on an intermediary factor. In subsequent analysis, T6P inhibited SnRK1 in extracts of all tissues analyzed except those of mature leaves, which did not contain the intermediary factor. To assess the impact of T6P inhibition of SnRK1 in vivo, gene expression was determined in seedlings expressing Escherichia coli otsA encoding T6P synthase to elevate T6P or otsB encoding T6P phosphatase to decrease T6P. SnRK1 target genes showed opposite regulation, consistent with the regulation of SnRK1 by T6P in vivo. Analysis of microarray data showed up-regulation by T6P of genes involved in biosynthetic reactions, such as genes for amino acid, protein, and nucleotide synthesis, the tricarboxylic acid cycle, and mitochondrial electron transport, which are normally down-regulated by SnRK1. In contrast, genes involved in photosynthesis and degradation processes, which are normally up-regulated by SnRK1, were down-regulated by T6P. These experiments provide strong evidence that T6P inhibits SnRK1 to activate biosynthetic processes in growing tissues.

Trehalose metabolism and signaling.

Trehalose metabolism and signaling is an area of emerging significance. In less than a decade our views on the importance of trehalose metabolism and its role in plants have gone through something of a revolution. An obscure curiosity has become an indispensable regulatory system. Mutant and transgenic plants of trehalose synthesis display wide-ranging and unprecedented phenotypes for the perturbation of a metabolic pathway. Molecular physiology and genomics have provided a glimpse of trehalose biology that had not been possible with conventional techniques, largely because the products of the synthetic pathway, trehalose 6-phosphate (T6P) and trehalose, are in trace abundance and difficult to measure in most plants. A consensus is emerging that T6P plays a central role in the coordination of metabolism with development. The discovery of trehalose metabolism has been one of the most exciting developments in plant metabolism and plant science in recent years. The field is fast moving and this review highlights the most recent insights.

Highly conserved protein kinases involved in the regulation of carbon and amino acid metabolism.

It has been clear for over a decade and a half that ancient signalling pathways controlling fundamental cellular processes are highly conserved throughout the eukaryotes. Two plant protein kinases, sucrose non-fermenting 1 (SNF1)-related protein kinase (SnRK1) and general control non-derepressible 2 (GCN2)-related protein kinase are reviewed here. These protein kinases show an extraordinary level of conservation with their fungal and animal homologues given the span of time since they diverged from them. However, close examination of the signalling pathways in which they operate also reveals intriguing differences in activation and function.

Metabolic signalling and carbon partitioning: role of Snf1-related (SnRK1) protein kinase.

A protein kinase that plays a key role in the global control of plant carbon metabolism is SnRK1 (sucrose non-fermenting-1-related protein kinase 1), so-called because of its homology and functional similarity with sucrose non-fermenting 1 (SNF1) of yeast. This article reviews studies on the characterization of SnRK1 gene families, SnRK1 regulation and function, interacting proteins, and the effects of manipulating SnRK1 activity on carbon metabolism and development.