Ecophysiology and the energetic benefit of mixotrophic Fe(II) oxidation by various strains of nitrate-reducing bacteria

In order to assess the importance of nitrate-dependent Fe(II) oxidation and its impact on the growth physiology of dominant Fe oxidizers, we counted these bacteria in freshwater lake sediments and studied their growth physiology. Most probable number counts of nitrate-reducing Fe(II)-oxidizing bacteria in the sediment of Lake Constance, a freshwater lake in Southern Germany, yielded about 10⁵ cells mL⁻¹ of the total heterotrophic nitrate-reducing bacteria, with about 1% (10³ cells mL⁻¹) of nitrate-reducing Fe(II) oxidizers. We investigated the growth physiology of Acidovorax sp. strain BoFeN1, a dominant nitrate-reducing mixotrophic Fe(II) oxidizer isolated from this sediment. Strain BoFeN1 uses several organic compounds (but no sugars) as substrates for nitrate reduction. It also reduces nitrite, dinitrogen monoxide, and O₂, but cannot reduce Fe(III). Growth experiments with cultures amended either with acetate plus Fe(II) or with acetate alone demonstrated that the simultaneous oxidation of Fe(II) and acetate enhanced growth yields with acetate alone (12.5 g dry mass mol⁻¹ acetate) by about 1.4 g dry mass mol⁻¹ Fe(II). Also, pure cultures of Pseudomonas stutzeri and Paracoccus denitrificans strains can oxidize Fe(II) with nitrate, whereas Pseudomonas fluorescens and Thiobacillus denitrificans strains did not. Our study demonstrates that nitrate-dependent Fe(II) oxidation contributes to the energy metabolism of these bacteria, and that nitrate-dependent Fe(II) oxidation can essentially contribute to anaerobic iron cycling.     

Imaging Transient Blood Vessel Fusion Events in Zebrafish by Correlative Volume Electron Microscopy

The study of biological processes has become increasingly reliant on obtaining high-resolution spatial and temporal data through imaging techniques. As researchers demand molecular resolution of cellular events in the context of whole organisms, correlation of non-invasive live-organism imaging with electron microscopy in complex three-dimensional samples becomes critical. The developing blood vessels of vertebrates form a highly complex network which cannot be imaged at high resolution using traditional methods. Here we show that the point of fusion between growing blood vessels of transgenic zebrafish, identified in live confocal microscopy, can subsequently be traced through the structure of the organism using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) and Serial Block Face/Scanning Electron Microscopy (SBF/SEM). The resulting data give unprecedented microanatomical detail of the zebrafish and, for the first time, allow visualization of the ultrastructure of a time-limited biological event within the context of a whole organism.     

Shellfish Face Uncertain Future in High CO2 World: Influence of Acidification on Oyster Larvae Calcification and Growth in Estuaries

Background

Human activities have increased atmospheric concentrations of carbon dioxide by 36% during the past 200 years. One third of all anthropogenic CO₂ has been absorbed by the oceans, reducing pH by about 0.1 of a unit and significantly altering their carbonate chemistry. There is widespread concern that these changes are altering marine habitats severely, but little or no attention has been given to the biota of estuarine and coastal settings, ecosystems that are less pH buffered because of naturally reduced alkalinity.

Methodology/Principal Findings

To address CO₂-induced changes to estuarine calcification, veliger larvae of two oyster species, the Eastern oyster (Crassostrea virginica), and the Suminoe oyster (Crassostrea ariakensis) were grown in estuarine water under four pCO₂ regimes, 280, 380, 560 and 800 µatm, to simulate atmospheric conditions in the pre-industrial era, present, and projected future concentrations in 50 and 100 years respectively. CO₂ manipulations were made using an automated negative feedback control system that allowed continuous and precise control over the pCO₂ in experimental aquaria. Larval growth was measured using image analysis, and calcification was measured by chemical analysis of calcium in their shells. C. virginica experienced a 16% decrease in shell area and a 42% reduction in calcium content when pre-industrial and end of 21^st century pCO₂ treatments were compared. C. ariakensis showed no change to either growth or calcification. Both species demonstrated net calcification and growth, even when aragonite was undersaturated, a result that runs counter to previous expectations for invertebrate larvae that produce aragonite shells.

Conclusions and Significance

Our results suggest that temperate estuarine and coastal ecosystems are vulnerable to the expected changes in water chemistry due to elevated atmospheric CO₂ and that biological responses to acidification, especially calcifying biota, will be species-specific and therefore much more variable and complex than reported previously.     

Repeat subtraction‐mediated sequence capture from a complex genome

Sequence capture technologies, pioneered in mammalian genomes, enable the resequencing of targeted genomic regions. Most capture protocols require blocking DNA, the production of which in large quantities can prove challenging. A blocker‐free, two‐stage capture protocol was developed using NimbleGen arrays. The first capture depletes the library of repetitive sequences, while the second enriches for target loci. This strategy was used to resequence non‐repetitive portions of an approximately 2.2 Mb chromosomal interval and a set of 43 genes dispersed in the 2.3 Gb maize genome. This approach achieved approximately 1800–3000‐fold enrichment and 80–98% coverage of targeted bases. More than 2500 SNPs were identified in target genes. Low rates of false‐positive SNP predictions were obtained, even in the presence of captured paralogous sequences. Importantly, it was possible to recover novel sequences from non‐reference alleles. The ability to design novel repeat‐subtraction and target capture arrays makes this technology accessible in any species.     

Light intensity limits foraging activity in nocturnal and crepuscular bees

A crepuscular or nocturnal lifestyle has evolved in bees severaltimes independently, probably to explore rewarding pollen sourceswithout competition and to minimize predation and nest parasites.Despite these obvious advantages, only few bee species are nocturnal.Here we show that the sensitivity of the bee apposition eyeis a major factor limiting the ability to forage in dim light.We present data on eye size, foraging times, and light levelsfor Megalopta genalis (Augochlorini, Halictidae) in Panama,and Lasioglossum (Sphecodogastra) sp. (Halictini, Halictidae)in Utah, USA. M. genalis females forage exclusively during twilight,but as a result of dim light levels in the rain forest, theyare adapted to extremely low intensities. The likely factorlimiting their foraging activity is finding their nest entranceon return from a foraging trip. The lowest light intensity atwhich they can do this, both in the morning and the evening,is 0.0001 cd m^–2. Therefore, they leave the nest at dimmerlight levels in the morning than in the evening. Lasioglossum(Sphecodogastra) foraging is limited by light intensity in theevening, but probably by temperature in the morning in the temperateclimate of Utah. We propose that the evolution of nocturnalityin bees was favored by the large variance in the size of females.     

A novel method for the determination of electrical potentials across cellular membranes. II. Membrane potentials of acholeplasmas, mycoplasmas, streptococci and erythrocytes

The membrane potentials of Acholeplasma laidlawii, Mycoplasma mycoides subsp. capri, Mycoplasma gallisepticum, Streptococcus faecalis and human erythrocytes have been determined by applying a novel technique. The membrane potentials were calculated simply from potassium concentrations determined by atomic absorption spectroscopy, and gravimetry. The versatility of the new technique is demonstrated by comparing our results with data obtained by different techniques.     

Crystal structure of the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase from Bacillus subtilis

Two types of isopentenyl diphosphate:dimethylallyl diphosphate isomerases (IDI) have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. Here, we report the first structure of an IDI-2 from Bacillus subtilis at 1.9A resolution in the ligand-free form and of the FMN-bound form at 2.8A resolution. The enzyme is an octamer that forms a D4 symmetrical open, cage-like structure. The monomers of 45 kDa display a classical TIM barrel fold. FMN is bound only with very moderate affinity and is therefore completely lost during purification. However, the enzyme can be reconstituted in the crystals by soaking with FMN. Three glycine-rich sequence stretches that are characteristic for IDI-2 participate in FMN binding within the interior of the cage. Regions harboring strictly conserved residues that are implicated in substrate binding or catalysis remain largely disordered even in the presence of FMN.     

Purification and characterization of a small (7.3 kDa) putative lipid transfer protein from maize seeds

The present study reports, for the first time in literature, the purification and biochemical characterization of a small basic protein from maize seeds similar to plant lipid transfer proteins-2, named mLTP2. The mLTP2 consists of 70 amino acid residues and has an M(r) of 7303.83, determined by electrospray ionization mass spectrometry. The primary structure of mLTP2 was determined by automated Edman degradation of the intact protein and peptides obtained from digestions with trypsin and by C-terminal sequencing using carboxypeptidase Y. The mLTP2 exhibits high sequence similarity (51-44% identical positions) with other plant LTP2s previously described.     

Individual voice recognition in a territorial frog (Rana catesbeiana)

Some territorial animals display low levels of aggression towards a familiar territorial neighbour in its usual territory, but exhibit high levels of aggression towards neighbours in novel locations and unfamiliar individuals. Here, we report results from a field playback study that investigated whether territorial males of the North American bullfrog (Rana catesbeiana) could discriminate between the acoustic signals of simulated neighbours and strangers in the absence of contextual cues associated with a specific location. Following repeated exposures to synthetic bullfrog calls from a particular location, subjects responded significantly less aggressively to a familiar call, compared with an unfamiliar one, when both calls were broadcast from familiar and novel locations, indicating that bullfrogs could recognize a neighbour's calls independently of the contextual cues provided by the direction of the neighbour's territory. Subjects responded equally aggressively to unfamiliar calls broadcast from either a familiar or a novel location, which indicates that they could perceive unfamiliar calls as those of a stranger, regardless of where the stranger was encountered. Together, these two results provide evidence that a frog possesses a capacity for individual voice recognition.