The relationship between species richness and evenness: a meta-analysis of studies across aquatic ecosystems

Biological diversity comprises both species richness, i.e., the number of species in a community, and evenness, measuring how similar species are in their abundances. The relationship between species richness and evenness (RRE) across communities remains, however, a controversial issue in ecology because no consistent pattern has been reported. We conducted a systematic meta-review of RRE in aquatic ecosystems along regional to continental gradients and across trophic groups, differing in body size by 13 orders of magnitude. Hypotheses that RRE responded to latitudinal and scale variability across trophic groups were tested by regression analyses. Significant correlations of species richness and evenness only existed in 71 out of 229 datasets. Among the RRE, 89 were negative and 140 were positive. RRE did not vary with latitude but showed a positive response to scale. In a meta-analysis with ecosystem type as a single explaining variable, RRE did not vary among ecosystem types, i.e. between marine and freshwater. Finally, autotrophs had more positive RRE than heterotrophs. The weak RRE in many aquatic datasets suggests that richness and evenness often reflect independent components of biodiversity, highlighting that richness alone may be an incomplete surrogate for biodiversity. Our results further elucidate that RRE is driven by organismal and environmental properties, both of which must be considered to gain a deeper understanding of large-scale patterns of biodiversity.     

Mitochondrial 2,4-dienoyl-CoA Reductase Deficiency in Mice Results in Severe Hypoglycemia with Stress Intolerance and Unimpaired Ketogenesis

The mitochondrial β-oxidation system is one of the central metabolic pathways of energy metabolism in mammals. Enzyme defects in this pathway cause fatty acid oxidation disorders. To elucidate the role of 2,4-dienoyl-CoA reductase (DECR) as an auxiliary enzyme in the mitochondrial β-oxidation of unsaturated fatty acids, we created a DECR–deficient mouse line. In Decr^−/− mice, the mitochondrial β-oxidation of unsaturated fatty acids with double bonds is expected to halt at the level of trans-2, cis/trans-4-dienoyl-CoA intermediates. In line with this expectation, fasted Decr^−/− mice displayed increased serum acylcarnitines, especially decadienoylcarnitine, a product of the incomplete oxidation of linoleic acid (C_18:2), urinary excretion of unsaturated dicarboxylic acids, and hepatic steatosis, wherein unsaturated fatty acids accumulate in liver triacylglycerols. Metabolically challenged Decr^−/− mice turned on ketogenesis, but unexpectedly developed hypoglycemia. Induced expression of peroxisomal β-oxidation and microsomal ω-oxidation enzymes reflect the increased lipid load, whereas reduced mRNA levels of PGC-1α and CREB, as well as enzymes in the gluconeogenetic pathway, can contribute to stress-induced hypoglycemia. Furthermore, the thermogenic response was perturbed, as demonstrated by intolerance to acute cold exposure. This study highlights the necessity of DECR and the breakdown of unsaturated fatty acids in the transition of intermediary metabolism from the fed to the fasted state.     

Residual Factor VIII-like cofactor activity of thioredoxin and related oxidoreductases

Background

Factor VIII is the cofactor for Factor X activation by Factor IXa. Activated Factor X, Factor Xa, in turn activates prothrombin in a sequence that leads to fibrin clot formation at the site of vascular injury. Although the biochemistry of the cascade has been well studied, the molecular mechanism underlying the cofactor role of Factor VIII is not understood.

Methods

We screened a bacterial peptide display library with Factor IXa and Factor X co-immobilized on tosylactivated Dynabeads which were then used as platelet surrogates. Validation of peptide selection procedure and comparison of Factor VIII-like cofactor activity of oxidoreductases was performed using COATEST assays. Determination of Factor VIII as a folding catalyst with potential disulphide isomerase activity was determined using the RNase A renaturation assay.

Results

We set out to identify the cofactor requirements of the Factor IXa/Factor X procoagulant complex by random peptide display, and isolated a peptide with the active-site sequence, CGPC, of thioredoxin. This peptide was able to activate Factor X in a Factor IXa-dependent manner. Redox catalysts or oxidoreductases with homologous active-site vicinal cysteines such as PDI and DsbA also mimicked Factor VIII in their requirement of Factor IXa in Factor X activation. However, the cofactor activity of these peptides was up to a 1000-fold lower than that of Factor VIII and they were therefore unable to catalyse blood coagulation. Factor X activation by PDI and by Factor VIII was abolished by oxidation in an isolated system, which implies a possible role for thiol–disulphide exchange in the activity of the tenase complex. Using scrambled RNase A as a surrogate substrate, we also found that Factor VIII could renature this enzyme.

Conclusion

Our findings suggest that Factor VIII may be a specialized folding catalyst with disulphide isomerase activity. We suggest that it is this activity that may underlie its cofactor function in Factor X activation, and that this function is interchangeable with classical oxidoreductases.

General significance

The possible involvement of thiol–disulphide interchange as a mechanism underlying Factor VIII cofactor activity may provide some insight into the biochemistry of the intrinsic tenase complex.     

An ericoid shrub plays a dual role in recruiting both pines and their fungal symbionts along primary succession gradients

Relative importance of positive and negative interactions between plant species may change along disturbance and resource gradients. Positive interactions are suggested to prevail in low resource, low productivity (high stress) conditions and negative interactions in high resource availability. A dwarf shrub, mountain crowberry Empetrum nigrum ssp. hermaphroditum, is known to have allelopathic impacts on both Scots pine Pinus sylvestris and its ectomycorrhizal symbionts. We aimed to study if the outcome of Empetrum impacts on Scots pine changes along primary succession gradients on the dune shores of Bothnian Bay, in Finland, where abiotic stress gradually changes to biotic stress along the succession. We found that Empetrum may act as a facilitator despite its allelopathic effects, since the proportion of Scots pine seedlings established in Empetrum patches was higher than in patches without the shrub in early and mid succession stages, whereas patches without Empetrum were preferred in late succession. The amount of mycelial fungal biomass (ergosterol) in the soil in the vicinity of the seedling roots was higher in Empetrum patches than in patches without Empetrum and it increased along the succession gradient. Proportion of pine root tips colonised by suilloid morphotypes with abundant external mycelia and the diversity of ectomycorrhizal morphotypes were higher in mid successional stage in Empetrum patches compared to patches without Empetrum. Our results suggest that in the harsh physical conditions of the dune shore Empetrum facilitates pine seedling establishment in the early and mid stages of succession by providing mechanical and physical shelter whereas in late succession negative interactions (competition and allelopathy) between the shrub and the pine are dominating. To our knowledge we present the first finding that an ericoid mycorrhizal shrub could enhance both the performance of the ectomycorrhizal host tree and the tree's fungal symbionts.     

Geographical patterns of micro‐organismal community structure: are diatoms ubiquitously distributed across boreal streams?

A topic under intensive study in community ecology and biogeography is the degree to which microscopic, as well as macroscopic organisms, show spatially-structured variation in community characteristics. In general, unicellular microscopic organisms are regarded as ubiquitously distributed and, therefore, without a clear biogeographic signal. This view was summarized 75  years ago by Baas-Becking, who stated "everything is everywhere, but, the environment selects". Within the context of metacommunity theory, this hypothesis is congruent with the species sorting model. By using a broad-scale dataset on stream diatom communities and environmental predictor variables across most of Finland, our main aim was to test this hypothesis. Patterns of spatial autocorrelation were evaluated by Moran's I based correlograms, whereas partial regression analysis and partial redundancy analysis were used to quantify the relative importance of environmental and spatial factors on total species richness and on community composition, respectively. Significant patterns of spatial autocorrelation were found for all environmental variables, which also varied widely. Our main results were clear-cut. In general, pure spatial effects clearly overcame those of environmental effects, with the former explaining much more variation in species richness and community composition. Most likely, missing environmental variables cannot explain the higher predictive power of spatial variables, because we measured key factors that have previously been found to be the most important variables (e.g. pH, conductivity, colour, phosphorus, nitrogen) shaping the structure of diatom communities. Therefore, our results provided only limited support for the Baas-Becking hypothesis and the species sorting perspective of metacommunity theory.     

Bacterial diversity at different stages of the composting process

Background  

Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA.     

Three-dimensional reconstruction of hibiscus chlorotic ringspot virus

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense, single-stranded RNA virus, which belongs to the Tombusviridae family and infects plants of the Hibiscus genus, including kenaf, a woody plant of agricultural importance. These icosahedral viruses have a capsid consisting of 180 copies of coat protein (CP) arranged with T=3 symmetry. The CP consists of an internal RNA-binding domain, a shell-forming domain and a protruding domain. The HCRSV virion was reconstructed to about 12A resolution from cryo-EM images using the program EMAN. The structure had the arrangement of 90 dimers of protruding domains characteristic of the Tombusviridae. Reconstructions were also made from negatively stained samples, and showed essentially the same features. In addition, a particle of a different, "smooth" appearance was also identified in the negatively stained samples. These particles were slightly smaller and lacked protruding domains. Biochemical analysis confirmed the presence of two protein products: a 37 kDa protein identified as HCRSV CP and a 54 kDa protein that appeared to be of non-HCRSV origin.     

Projection structure at 8 A resolution of the melibiose permease,an Na-sugar co-transporter from Escherichia coli

The ion-coupled sugar membrane symporter or co-transporter melibiose permease (MelB), responsible for alpha-galactoside accumulation in Escherichia coli, is a representative member of the glycoside-pentoside- hexuronide family of the vast class of electrochemical potential-driven porters. Pure solubilized preparations of a MelB recombinant protein were subjected to two-dimensional crystallization trials and several crystal forms were observed. Two of these appeared as large wide tubes suitable for analysis by electron crystallography. Flattened tubes on carbon support film, embedded in amorphous ice prior to electron cryomicroscopy, showed two-sided plane group symmetries P12(1) or P222(1), with unit cell dimensions a = 89.9 A, b = 51.6 A, gamma = 91.9 degrees and a = 188.9 A, b = 48.8 A, gamma = 90 degrees, respectively. The projection map from the P222(1 )crystals at 8 A resolution displayed an asymmetric protein unit consisting of two domains lining a central and curve-shaped cleft. Together, the MelB monomer could host the 12 predicted transmembrane alpha-helices. Overall, the MelB helix packing arrangement compared more favorably with that of the Na(+)/H(+) antiporter NhaA than that of the oxalate antiporter.