Linking recruitment to trophic factors: revisiting the Beverton--Holt recruitment model from a life history and multispecies perspective

The Beverton--Holt recruitment model can be derived from arguments about evolution of life history traits related to foraging and predation risk, along with spatially localized and temporarily competitive relationships in the habitats where juvenile fish forage and face predation risk while foraging. This derivation explicitly represents two key biotic factors, food supply (I) and predator abundance (R), which appear as a risk ratio (R/I) that facilitates modelling of changes in trophic circumstances and analysis of historical data. The same general recruitment relationship is expected whether the juvenile life history is simple or involves a complex sequence of stanzas; in the complex case, the Beverton--Holt parameters represent weighted averages or integrals of risk ratios over the stanzas. The relationship should also apply in settings where there is complex, mesoscale variation in habitat and predation risk, provided that animals sense this variation and move about so as to achieve similar survival at all mesoscale rearing sites. The model predicts that changes in food and predation risk can be amplified violently in settings where juvenile survival rate is low, producing large changes in recruitment rates over time.     

The Millennial model: in search of measurable pools and transformations for modeling soil carbon in the new century

Soil organic carbon (SOC) can be defined by measurable chemical and physical pools, such as mineral-associated carbon, carbon physically entrapped in aggregates, dissolved carbon, and fragments of plant detritus. Yet, most soil models use conceptual rather than measurable SOC pools. What would the traditional pool-based soil model look like if it were built today, reflecting the latest understanding of biological, chemical, and physical transformations in soils? We propose a conceptual model—the Millennial model—that defines pools as measurable entities. First, we discuss relevant pool definitions conceptually and in terms of the measurements that can be used to quantify pool size, formation, and destabilization. Then, we develop a numerical model following the Millennial model conceptual framework to evaluate against the Century model, a widely-used standard for estimating SOC stocks across space and through time. The Millennial model predicts qualitatively similar changes in total SOC in response to single factor perturbations when compared to Century, but different responses to multiple factor perturbations. We review important conceptual and behavioral differences between the Millennial and Century modeling approaches, and the field and lab measurements needed to constrain parameter values. We propose the Millennial model as a simple but comprehensive framework to model SOC pools and guide measurements for further model development.     

Introduced and native herbivores have different effects on plant composition in low productivity ecosystems

Questions

Understanding how livestock grazing alters plant composition in low productivity environments is critical to managing livestock sustainably alongside native and introduced wild herbivore populations. We asked four questions: (1) does recent livestock and rabbit grazing reduce some plant attributes more strongly than others; (2) does grazing by introduced herbivores (i.e. livestock and rabbits) affect plants more strongly than native herbivores (i.e. kangaroos); (3) do the effects of recent livestock grazing differ from the legacy effects of livestock grazing; and (4) does the probability of occurrence of exotic plants increase with increasing net primary productivity (NPP)?

Location

South‐eastern Australia.

Methods

We measured the recent grazing activity of co‐occurring livestock (cattle, sheep, goats), rabbits and kangaroos by counting faecal pellets; historic grazing activity by measuring livestock tracks; and derived NPP from satellite imagery. We used a hierarchical GLMM to simultaneously model the presence or absence (i.e. probability of occurrence) of all plant species as a function of their attributes (growth form, lifespan and origin) to assess their average response to recent grazing, historic grazing and productivity in a broad‐scale regional study.

Results

Recent and historic livestock grazing, rabbit grazing and increasing NPP reduced the average probability of occurrence of plant species, although responses varied among plant attributes. Both recent and historic livestock grazing strongly reduced the average probability of occurrence of native species, and forbs and geophytes, but differed in their relative effects on other growth forms. Recent livestock grazing, rabbit grazing and NPP had similar effects, strongly reducing native species and forbs, geophytes, shrubs and sub‐shrubs. The overall effects of recent kangaroo grazing were relatively weak, with no clear trends for any given plant attribute.

Conclusion

Our results highlight the complex nature of grazing by introduced herbivores compared with native herbivores on different plant attributes. Land managers need to be aware that domestic European livestock, rabbits and other free‐ranging introduced livestock such as goats have detrimental impacts on native plant communities. Our results also show that kangaroo grazing has a relatively benign effect on plant occurrence.     

Rounding precedes rupture and breakdown of vacuolar membranes minutes before malaria parasite egress from erythrocytes

Because Plasmodium falciparum replicates inside of a parasitophorous vacuole (PV) within a human erythrocyte, parasite egress requires the rupture of two limiting membranes. Parasite Ca²⁺, kinases, and proteases contribute to efficient egress; their coordination in space and time is not known. Here, the kinetics of parasite egress were linked to specific steps with specific compartment markers, using live‐cell microscopy of parasites expressing PV‐targeted fluorescent proteins, and specific egress inhibitors. Several minutes before egress, under control of parasite [Ca²⁺]_i, the PV began rounding. Then after ~1.5 min, under control of PfPKG and SUB1, there was abrupt rupture of the PV membrane and release of vacuolar contents. Over the next ~6 min, there was progressive vacuolar membrane deterioration simultaneous with erythrocyte membrane distortion, lasting until the final minute of the egress programme when newly formed parasites mobilised and erythrocyte membranes permeabilised and then ruptured—a dramatic finale to the parasite cycle of replication.     

Neutron crystallographic studies of T4 lysozyme at cryogenic temperature

Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics, and stability. Approximately 700 mutants of this protein and their respective complexes have been characterized by X‐ray crystallography; however, despite the high resolution diffraction limits attained in several studies, no hydrogen atoms were reported being visualized in the electron density maps. To address this, a 2.2 Å‐resolution neutron data set was collected at 80 K from a crystal of perdeuterated T4L pseudo‐wild type. We describe a near complete atomic structure of T4L, which includes the positions of 1737 hydrogen atoms determined by neutron crystallography. The cryogenic neutron model reveals explicit detail of the hydrogen bonding interactions in the protein, in addition to the protonation states of several important residues.     

The transcriptome of Toxoplasma gondii

Background  

Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown.     

Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands

Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.     

Bergmann glia and the recognition molecule CHL1 organize GABAergic axons and direct innervation of Purkinje cell dendrites

The geometric and subcellular organization of axon arbors distributes and regulates electrical signaling in neurons and networks, but the underlying mechanisms have remained elusive. In rodent cerebellar cortex, stellate interneurons elaborate characteristic axon arbors that selectively innervate Purkinje cell dendrites and likely regulate dendritic integration. We used GFP BAC transgenic reporter mice to examine the cellular processes and molecular mechanisms underlying the development of stellate cell axons and their innervation pattern. We show that stellate axons are organized and guided towards Purkinje cell dendrites by an intermediate scaffold of Bergmann glial (BG) fibers. The L1 family immunoglobulin protein Close Homologue of L1 (CHL1) is localized to apical BG fibers and stellate cells during the development of stellate axon arbors. In the absence of CHL1, stellate axons deviate from BG fibers and show aberrant branching and orientation. Furthermore, synapse formation between aberrant stellate axons and Purkinje dendrites is reduced and cannot be maintained, leading to progressive atrophy of axon terminals. These results establish BG fibers as a guiding scaffold and CHL1 a molecular signal in the organization of stellate axon arbors and in directing their dendritic innervation.