Fish track wastewater pollution to estuaries

Excess nitrogen is a forceful agent of ecological change in coastal waters, and wastewater is a prominent source of nitrogen. In catchments where multiple sources of nitrogen pollution co-exist, biological indicators are needed to gauge the degree to which wastewater-N can propagate through the receiving food webs. The purpose of this study was to test whether estuarine fish are suitable as indicators of sewage-N pollution. Fish were analysed from three estuaries within a 100-km strip on the Australian East Coast. The estuaries differ substantially in wastewater loading: (1) the Maroochy Estuary receives a large fraction of the local shire’s treated sewage, (2) the Mooloolah Estuary has no licensed treated wastewater outfalls but marinas/harbours and stormwater may contribute nitrogen, and (3) the Noosa Estuary which neither receives licensed discharges nor has suspected wastewater loads. Sampling for fish included both high rainfall (‘wet’ season) and low rainfall (‘dry’ season) periods. Muscle-δ¹⁵N was the variable predicted to respond to treated wastewater loading, reflecting the relative enrichment in ¹⁵N resulting from the treatment process and distinguishing it from alternative N sources such as fertiliser and natural nitrogen inputs (both ¹⁵N-depleted). Of the 19 fish species occurring in all three estuaries, those from the Maroochy Estuary had significantly elevated δ¹⁵N values (up to 9.9‰), and inter-estuarine differences in fish-δ¹⁵N were consistent across seasons. Furthermore, not only did all fish from the estuary receiving treated wastewater carry a very distinctive sewage-N tissue signal, but enriched muscle-δ¹⁵N was also evident in all species sampled from the one estuary in which sewage contamination was previously only suspected (i.e. the Mooloolah Estuary: 0.2–4.8‰ enrichment over fish from reference system). Thus, fish-δ¹⁵N is a suitable indicator of wastewater-N not only in systems that receive large loads, but also for the detection of more subtle nitrogen inputs. Arguably, fish may be preferred indicators of sewage-N contamination because they: (1) integrate nitrogen inputs over long time periods, (2) have an element of ‘ecological relevance’ because fish muscle-δ¹⁵N reflect movement of sewage-N through the food chain, and (3) pollution assessments can usually be based on evidence from multiple species.     

The species-area-energy relationship

Area and available energy are major determinants of species richness. Although scale dependency of the relationship between energy availability and species richness (the species-energy relationship) has been documented, the exact relationship between the species-area and the species-energy relationship has not been studied explicitly. Here we show, using two extensive data sets on avian distributions in different biogeographic regions, that there is a negative interaction between energy availability and area in their effect on species richness. The slope of the species-area relationship is lower in areas with higher levels of available energy, and the slope of the species-energy relationship is lower for larger areas. This three-dimensional species-area-energy relationship can be understood in terms of probabilistic processes affecting the proportions of sites occupied by individual species. According to this theory, high environmental energy elevates species' occupancies, which depress the slope of the species-area curve.     

Comparison of protein and peptide prefractionation methods for the shotgun proteomic analysis of Synechocystis sp. PCC 6803

Proteome analysis by gel-free "shotgun" proteomics relies on the simplification of a peptide mixture before it is analyzed in a mass spectrometer. While separation on a reverse-phase (RP) liquid chromatographic column is widely employed, a variety of other methods have been used to fractionate both proteins and peptides before this step. We compared six different protein and peptide fractionation workflows, using Synechocystis sp. PCC 6803, a useful model cyanobacterium for potential exploitation to improve its production of hydrogen and other secondary metabolites. Pre-digestion protein separation was performed by strip-based isoelectric focusing, one-dimensional polyacrylamide gel electrophoresis, or weak anion exchange chromatography, while pre-RP peptide separation was accomplished by isoelectric focusing (IEF) or strong cation exchange chromatography. Peptides were identified using electrospray ionization quadrupole time of flight-tandem mass spectrometry. Mass spectrometry (MS) and tandem mass spectra were analyzed using ProID software employing both a single organism database and the entire NCBI non-redundant database, and a total of 776 proteins were identified using a stringent set of selection criteria. Method comparisons were made on the basis of the results obtained (number and types of proteins identified), as well as ease of use and other practical aspects. IEF-IEF protein and peptide fractionation prior to RP gave the best overall performance.     

High pressure enhances hexacoordination in neuroglobin and other globins

The techniques of high applied pressure and flash photolysis have been combined to study ligand rebinding to neuroglobin (Ngb) and tomato Hb, globins that may display a His-Fe-His hexacoordination in the absence of external ligands. High pressure induces a moderate decrease in the His association rate and a large decrease in His dissociation rate, thus leading to an enhancement of the overall His affinity. The overall structural difference between penta- and hexacoordinated globins may be rather small and can be overcome by external modifications such as high pressure. Over the pressure range 0.1-700 MPa (7 kbar), the globins may show a loss of over a factor of 100 in the amplitude of the bimolecular rebinding phase after photodissociation. The kinetic data show that pressure induces a moderate increase of the rate for ligand binding from the correlated pair state (just after photodissociation) and a large (factor of 1000) decrease in rate for migration through the protein. The effect on the ligand migration phase was similar for both the external ligands (such as oxygen) as for the internal (histidine) ligand, suggesting the dominant role of protein fluctuations, rather than specific chemical barriers. Thus high pressure efficiently closes the protein migration channels; however, contrary to the effect of high viscosity, high pressure induces a greater decrease in rate for ligand migration toward the exterior (heme to the solvent) versus inward migration, as if the presence of the ligand itself induces an additional steric constraint.     

Constraint and competition in assemblages: a cross-continental and modeling approach for ants

The mechanisms leading to structure in local assemblages are controversial. On the one hand, assemblage structure is thought to be the outcome of local interactions determined by the properties of species and their responses to the local environment. Alternatively, this structure has been shown to be an emergent property of assemblages of identical individuals or of random sampling of a regional assemblage. In ants at baits, a combination of environmental stress and interspecific competition is widely held to lead to a unimodal relationship between the abundance of dominant ants and species richness. It is thought that in comparatively adverse environments, both abundance and richness are low. As habitats become more favorable, abundance increases until the abundance of dominant ants is so high that they exclude those that are subordinate and so depress richness. Here we demonstrate empirically that this relationship is remarkably similar across three continents. Using a null model approach, we then show that the ascending part of the relationship is largely constrained to take this form not simply as a consequence of stress but also as a result of the shape of abundance frequency distributions. While the form of the species-abundance frequency distribution can also produce the descending part of the relationship, interspecific competition might lead to it too. Scatter about the relationship, which is generally not discussed in the literature, may well be a consequence of resource availability and environmental patchiness. Our results draw attention to the significance of regional processes in structuring ant assemblages.     

Protected areas and regional avian species richness in South Africa

Protected areas are generally regarded as essential for the long-term maintenance of biodiversity. Evidence for their effectiveness in this regard is, however, somewhat equivocal. Here, we document the relationship between the proportion of protected land and species richness in a region, both with and without taking spatial variation in environmental energy availability into account. Using the South African avifauna as a case study, we find that total and threatened species richness exhibit modest increases with the proportion of protected land. While the protected area network should be expanded, it is essential that conservation efforts also focus on maintaining biodiversity in the wider unprotected landscape that supports high species richness.     

Isobaric tags for relative and absolute quantitation (iTRAQ) reproducibility: Implication of multiple injections

We analyzed 10 isobaric tags for relative and absolute quantitation (iTRAQ) experiments using three different model organisms across the domains of life: Saccharomyces cerevisiae KAY446, Sulfolobussolfataricus P2, and Synechocystis sp. PCC6803. A double database search strategy was employed to minimize the rate of false positives to less than 3% for all organisms. The reliability of proteins with single-peptide identification was also assessed using the search strategy, coupled with multiple analyses of samples into LC-MS/MS. The outcomes of the three LC-MS/MS analyses provided higher proteome coverage with an average increment in total proteins identified of 6%, 33%, and 50% found in S. cerevisiae, S. solfataricus, and Synechocystis sp., respectively. The iTRAQ quantification values were found to be highly reproducible across the injections, with an average coefficient of variation (CV) of 0.09 (scattering from 0.14 to 0.04) calculated based on log mean average ratio for all three organisms. Hence, we recommend multiple analyses of iTRAQ samples for greater proteome coverage and precise quantification.