Breaking up and making up: The secret life of the vacuolar H+‐ATPase

The vacuolar ATPase (V‐ATPase; V₁V_o‐ATPase) is a large multisubunit proton pump found in the endomembrane system of all eukaryotic cells where it acidifies the lumen of subcellular organelles including lysosomes, endosomes, the Golgi apparatus, and clathrin‐coated vesicles. V‐ATPase function is essential for pH and ion homeostasis, protein trafficking, endocytosis, mechanistic target of rapamycin (mTOR), and Notch signaling, as well as hormone secretion and neurotransmitter release. V‐ATPase can also be found in the plasma membrane of polarized animal cells where its proton pumping function is involved in bone remodeling, urine acidification, and sperm maturation. Aberrant (hypo or hyper) activity has been associated with numerous human diseases and the V‐ATPase has therefore been recognized as a potential drug target. Recent progress with moderate to high‐resolution structure determination by cryo electron microscopy and X‐ray crystallography together with sophisticated single‐molecule and biochemical experiments have provided a detailed picture of the structure and unique mode of regulation of the V‐ATPase. This review summarizes the recent advances, focusing on the structural and biophysical aspects of the field.     

Factors Controlling the Year-Round Variability in Carbon Flux Through Bacteria in a Coastal Marine System

Data from several years of monthly samplings are combined with a 1-year detailed study of carbon flux through bacteria at a NW Mediterranean coastal site to delineate the bacterial role in carbon use and to assess whether environmental factors or bacterial assemblage composition affected the in situ rates of bacterial carbon processing. Leucine (Leu) uptake rates [as an estimate of bacterial heterotrophic production (BHP)] showed high interannual variability but, on average, lower values were found in winter (around 50 pM Leu⁻¹ h⁻¹) as compared to summer (around 150 pM Leu⁻¹ h⁻¹). Leu-to-carbon conversion factors ranged from 0.9 to 3.6 kgC mol Leu⁻¹, with generally higher values in winter. Leu uptake was only weakly correlated to temperature, and over a full-year cycle (in 2003), Leu uptake peaked concomitantly with winter chlorophyll a (Chl a) maxima, and in periods of high ectoenzyme activities in spring and summer. This suggests that both low molecular weight dissolved organic matter (DOM) released by phytoplankton, and high molecular weight DOM in periods of low Chl a, can enhance BHP. Bacterial respiration (BR, range 7–48 μg C l⁻¹ d⁻¹) was not correlated to BHP or temperature, but was significantly correlated to DOC concentration. Total bacterial carbon demand (BHP plus BR) was only met by dissolved organic carbon produced by phytoplankton during the winter period. We measured bacterial growth efficiencies by the short-term and the long-term methods and they ranged from 3 to 42%, increasing during the phytoplankton blooms in winter (during the Chl a peaks), and in spring. Changes in bacterioplankton assemblage structure (as depicted by denaturing gradient gel electrophoresis fingerprinting) were not coupled to changes in ecosystem functioning, at least in bacterial carbon use.     

The influence of tree species on canopy soil nutrient status in a tropical lowland wet forest in Costa Rica

The canopy is host to a large percentage of the flora and fauna in tropical wet forests and is distinct from the forest floor in plant richness, soil type and microclimate. In this study, we examined the influence of tree species and season on soil nutrient cycling processes in canopy soils of four tree species common to Costa Rican wet forests. We also compared the canopy soils to the associated forest floor mineral soils. Both tree species and season had strong effects on canopy soil nutrients and processes. Canopy soils from trees with high litter lignin concentrations had higher net N-mineralization rates and higher dissolved inorganic N concentrations than those with low lignin concentrations. During the dry season, net N-immobilization occurred and dissolved organic and inorganic N and available P concentrations were significantly higher than during the wet season. Overall, canopy soils had higher N levels and higher fungi + bacteria richness than forest floor mineral soils. The differences in canopy soil properties observed among tree species indicates that these species have distinct N cycles that reflect differences in both soil origin and biological controls.     

The nutrient status of epiphytes and their host trees along an elevational gradient in Costa Rica

Vascular epiphytes are a conspicuous and highly diverse group in tropical wet forests; yet, we understand little about their mineral nutrition across sites. In this study, we examined the mineral nutrition of three dominant vascular epiphyte groups: ferns, orchids, and bromeliads, and their host trees from samples collected along a 2600 m elevational gradient in the tropical wet forests of Costa Rica. We predicted that the mineral nutrition of ferns, orchids, and bromeliads would differ because of their putative differences in nutrient acquisition mechanisms and nutrient sources—atmospherically dependent, foliar feeding bromeliads would have lower nitrogen (N) and phosphorous (P) concentrations and more depleted δ¹⁵N values than those in canopy soil-rooted ferns because canopy soil is higher in available N, and more enriched in δ¹⁵N than the atmospheric sources of precipitation and throughfall. We also predicted that epiphyte foliar chemistry would mirror that of host trees because of the likely contribution of host trees to the nutrient cycle of epiphytes via foliar leaching and litter contributions to canopy soil. In the same vein, we predicted that epiphyte and host tree foliar chemistry would vary with elevation reflecting ecosystem-level nutrients—soil N availability increases and P availability decreases with increasing elevation. Our results confirmed that canopy soil-rooted epiphytes had higher N concentrations than atmospheric epiphytes; however, our predictions were not confirmed with respect to P which did not vary among groups indicating fixed P availability within sites. In addition, foliar δ¹⁵N values did not match our prediction in that canopy soil-rooted as well as atmospheric epiphytes had variable signatures. Discriminant function analysis (DFA) on foliar measurements determined that ferns, orchids, and bromeliads are statistically distinct in mineral nutrition. We also found that P concentrations of ferns and orchids, but not bromeliads, were significantly correlated with those of host trees indicating a possible link in their mineral nutrition’s via canopy soil. Interestingly, we did not find any patterns of epiphyte foliar chemistry with elevation. These data indicate that the mineral nutrition of the studied epiphyte groups are distinct and highly variable within sites and the diverse uptake mechanisms of these epiphyte groups enhance resource partitioning which may be a mechanism for species richness maintenance in tropical forest canopies.     

Stone walls and sacred forest conservation in Ethiopia

Many tropical forests worldwide are protected due to their sacredness to religious communities. In the south Gondar region of Ethiopia, most of the remaining native forests are tiny fragments (5.42 ha ± 0.34) surrounded by pasture and agriculture that are protected because they encompass churches of the Ethiopian Orthodox Tewahido Church (EOTC). A small number of communities have erected stone walls around the perimeter of the forests to demarcate the boundary, and/or protect the interior of the forest. We evaluated the effectiveness of these walls at protecting ecological conditions by examining tree and seedling communities among sacred forests with and without walls in Montane and Upper Montane sites. We found the wall to be an effective conservation tool as regeneration potential was higher in forests with a wall. The density and species richness of seedlings were significantly higher in forests with a wall and these effects were more pronounced in Upper Montane forests. Forests with a wall also had seedlings of many native tree species that were not found in forests without walls. As expected, there were few differences in tree communities in forests with and without a wall. Although rare on the landscape, the presence of a stone wall around these forests was effective at protecting the seedling community because it likely reduced access to the forests by grazers and directed human visitors to trails. The use of a stone wall may protect seedling communities in other sacred forest fragments, particularly for those that are small, isolated, surrounded by agriculture, and have a depleted seed bank.