Senna siamea trees recycle Ca from a Ca-rich subsoil and increase the topsoil pH in agroforestry systems in the West African derived savanna zone

The functioning of trees as a safety-net for capturing nutrients leached beyond the reach of crop roots was evaluated by investigating changes in exchangeable cations (Ca, Mg, and K) and pH in a wide range of medium to long term alley cropping trials in the derived savanna of West Africa, compared to no-tree control plots. Topsoil Ca content, effective cation exchange capacity, and pH were substantially higher under Senna siamea than under Leucaena leucocephala, Gliricidia sepium, or the no-tree control plots in sites with a Bt horizon rich in exchangeable Ca. This was shown to be largely related to the recovery of Ca from the subsoil under Senna trees. The increase of the Ca content of the topsoil under Senna relative to the no-tree control treatment was related to the total amount of dry matter applied since trial establishment. The lack of increase in Ca accumulation under the other species was related to potential recovery of Ca from the topsoil itself and/or substantial Ca leaching. The accumulation of Ca in the topsoil under Senna had a marked effect on the topsoil pH, the latter increasing significantly compared with the Leucaena, Gliridia, and no-tree control treatments. In conclusion, the current work shows that the functioning of the often hypothesized ‘safety-net’ of trees in a cropping system depends on (i) the tree species and on (ii) the presence of a subsoil of suitable quality, i.e., clay enriched and with high Ca saturation.     

Effect of conventional versus mechanized sugarcane cropping systems on soil organic carbon stocks and labile carbon pools in Mauritius as revealed by 13C natural abundance

Aims

Maintenance of adequate levels of soil organic carbon (SOC) is crucial for the biological, chemical and physical functioning of soils. This study was conducted (i) to determine the impact of long-term sugarcane monoculture on total SOC stocks and on its labile fractions and (ii) to quantify the loss of original SOC and the accretion of sugarcane-derived C following the adoption of new management practices namely de-rocking/land grading and mechanized harvesting.

Methods

Five study sites representing the five major soil groups under sugarcane in Mauritius were selected with a classical “paired-plot” design adopted. In this design, two sites with similar initial conditions were developed in different ways over time. One represents the reference soil (virgin land with predominantly C₃ type vegetation) and the other represents one of the following cropping treatments: (i) fields continuously cultivated with sugarcane for more than 25 or 50 years without de-rocking or land grading, (ii) fields under long-term sugarcane but having undergone de-rocking and land grading for mechanized harvesting in the last 3 years. Soil samples were taken to a depth of 50 cm and analysed for total organic C, labile C, ¹³C natural abundance, bulk density and stone content.

Results

Changes in SOC stock in the 0–50 cm profile following >50 years of cane cropping were not significant (P?>?0.05) compared to virgin land at any site. Soil δ¹³C values revealed that long-term sugarcane cultivation resulted in a depletion of original SOC by 34 to 70 %. However, this loss was fully compensated by C input from sugarcane residues at all sites studied resulting in no net change in SOC stock. Adoption of mechanized harvest did not have any detrimental effect on SOC stocks due to C inputs from crop residues. However, long-term sugarcane cultivation resulted in significant decline in a labile C (KMnO₄-oxidizable) fraction.

Conclusion

Despite the large losses of original C following conversion from forest to sugarcane, long-term sugarcane cultivation resulted in sequestration of sugarcane-derived C which adequately compensated these losses. Moreover, intensive de-rocking and land grading preceding mechanized harvesting did not have any detrimental effect on SOC stocks. However, the quality of sugarcane soils, as indicated by a decline in labile C, could be degraded.     

Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth

Blood vessels form either when dispersed endothelial cells (the cells lining the inner walls of fully formed blood vessels) organize into a vessel network (vasculogenesis), or by sprouting or splitting of existing blood vessels (angiogenesis). Although they are closely related biologically, no current model explains both phenomena with a single biophysical mechanism. Most computational models describe sprouting at the level of the blood vessel, ignoring how cell behavior drives branch splitting during sprouting. We present a cell-based, Glazier-Graner-Hogeweg model (also called Cellular Potts Model) simulation of the initial patterning before the vascular cords form lumens, based on plausible behaviors of endothelial cells. The endothelial cells secrete a chemoattractant, which attracts other endothelial cells. As in the classic Keller-Segel model, chemotaxis by itself causes cells to aggregate into isolated clusters. However, including experimentally observed VE-cadherin-mediated contact inhibition of chemotaxis in the simulation causes randomly distributed cells to organize into networks and cell aggregates to sprout, reproducing aspects of both de novo and sprouting blood-vessel growth. We discuss two branching instabilities responsible for our results. Cells at the surfaces of cell clusters attempting to migrate to the centers of the clusters produce a buckling instability. In a model variant that eliminates the surface-normal force, a dissipative mechanism drives sprouting, with the secreted chemical acting both as a chemoattractant and as an inhibitor of pseudopod extension. Both mechanisms would also apply if force transmission through the extracellular matrix rather than chemical signaling mediated cell-cell interactions. The branching instabilities responsible for our results, which result from contact inhibition of chemotaxis, are both generic developmental mechanisms and interesting examples of unusual patterning instabilities.     

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.     

Differential responses of soil bacteria,fungi, archaea and protists to plant species richness and plant functional group identity

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454‐pyrosequencing to analyse the soil microbial community composition in a long‐term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.