Using repeated winter surveys to estimate changes in abundance of seed‐eating passerines

Capsule Winter Atlas surveys of 16 species on lowland farmland revealed significant changes in count for four species.

Aims To estimate changes in abundance between the early 1980s and late 1990s, of wintering seed‐eating passerines, in ‘core’ areas of lowland Scotland.

Methods Ninety‐five Scottish 10‐km squares were selected that held high numbers of seed‐eating passerines in the 1981–84 Atlas of Wintering Birds in Britain and Ireland. The same survey methods were used to resurvey these in winters 1997/98 and 1998/99, and visits were matched as closely as possible for duration and date. Analyses compared counts between the two survey periods for 16 species of seed‐eating passerines and, for 12 of these, differences were also compared with national breeding population trend information for the same period.

Results Mean Corn Bunting Emberiza calandra count per visit declined by 62% between the early 1980s and late 1990s, a difference which was statistically significant (P = 0.026). Significant increases were recorded for Yellowhammer Emberiza citrinella (up 62%), Common Linnet Carduelis cannabina (up 3.4‐fold) and European Goldfinch Carduelis carduelis (up 13‐fold). For 12 species for which national breeding population trend data were available, trends were weakly positively correlated (r _s = 0.43, P = 0.08) with those from our results, but several species trends were more positive in our study. This difference was particularly marked for Eurasian Tree Sparrow Passer montanus, Goldfinch and Linnet.

Conclusion Repeating Winter Atlas surveys offers a useful additional method for assessing population trends. They are particularly useful in a region with low observer coverage and for species that are poorly covered by long‐term bird monitoring data sets. It would be valuable to validate this approach at a regional level, especially in a region for which detailed long‐term bird monitoring data are available.     

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.     

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

Background

The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia.

Results

We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C₁-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins.

Conclusion

The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria.

Reviewers

This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.     

Short-term studies of taurocholate uptake by ileal brush border membrane vesicles: Anion effects

Experiments allowing Na⁺-dependent short-term uptake measurements by ileal brush border vesicles were described. Glucose uptake was compared with taurocholate uptake in the presence of NaCl, NaSCN and Na₂SO₄. In contrast to the observation made with glucose, taurocholate transport was the same for the three electrolytes, indicating electroneutral taurocholate transport.     

Invasion facilitates hybridization with introgression in the Rattus rattus species complex

Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two nuclear gene sequences (Atp5a1 and DHFR) and nine microsatellite loci to examine the distribution of three invasive black rat lineages (Rattus tanezumi, Rattus rattus I and R. rattus IV) in the United States and Asia and to determine the extent of hybridization among these taxa. Our analyses revealed two mitochondrial lineages that have spread to multiple continents, including a previously undiscovered population of R. tanezumi in the south‐eastern United States, whereas the third lineage (R. rattus IV) appears to be confined to Southeast Asia. Analyses of nuclear DNA (both sequences and microsatellites) suggested significant hybridization is occurring among R. tanezumi and R. rattus I in the United States and also suggest hybridization between R. tanezumi and R. rattus IV in Asia, although further sampling of the latter species pair in Asia is required. Furthermore, microsatellite analyses suggest unidirectional introgression from both R. rattus I and R. rattus IV into R. tanezumi. Within the United States, introgression appears to be occurring to such a pronounced extent that we were unable to detect any nuclear genetic signal for R. tanezumi, and a similar pattern was detected in Asia.     

Plutonium(V/VI) Reduction by the Metal-Reducing Bacteria Geobacter metallireducens GS-15 and Shewanella oneidensis MR-1

We examined the ability of the metal-reducing bacteria Geobacter metallireducens GS-15 and Shewanella oneidensis MR-1 to reduce Pu(VI) and Pu(V). Cell suspensions of both bacteria reduced oxidized Pu [a mixture of Pu(VI) and Pu(V)] to Pu(IV). The rate of plutonium reduction was similar to the rate of U(VI) reduction obtained under similar conditions for each bacteria. The rates of Pu(VI) and U(VI) reduction by cell suspensions of S. oneidensis were slightly higher than the rates observed with G. metallireducens. The reduced form of Pu was characterized as aggregates of nanoparticulates of Pu(IV). Transmission electron microscopy images of the solids obtained from the cultures after the reduction of Pu(VI) and Pu(V) by S. oneidensis show that the Pu precipitates have a crystalline structure. The nanoparticulates of Pu(IV) were precipitated on the surface of or within the cell walls of the bacteria. The production of Pu(III) was not observed, which indicates that Pu(IV) was the stable form of reduced Pu under these experimental conditions. Experiments examining the ability of these bacteria to use Pu(VI) as a terminal electron acceptor for growth were inconclusive. A slight increase in cell density was observed for both G. metallireducens and S. oneidensis when Pu(VI) was provided as the sole electron acceptor; however, Pu(VI) concentrations decreased similarly in both the experimental and control cultures.Effective bioremediation and waste management strategies at nuclear sites require an understanding of the fundamental biogeochemical processes that control the mobility of actinides. Microorganisms can influence the chemical speciation, valence state, and distribution of actinides in subsurface environments (2, 8, 12, 14). Dissimilatory metal-reducing bacteria (DMRB), which derive energy by respiring oxidized metals (Fe and Mn in nature), may play a particularly important role in the mobility of actinides, since the oxidized forms of many radionuclides are more mobile than their reduced forms. Remedial strategies have been proposed to biomineralize radionuclides via direct reduction by DMRB or indirectly by DMRB by-products (9-11). Several DMRB have been shown to conserve energy for anaerobic growth via the reduction of U(VI) (9-11, 14).Plutonium redox chemistry is more complex than that of most other actinides. Under environmental conditions, plutonium can exist in the III, IV, V, and VI oxidation states, and multiple oxidation states can coexist simultaneously (4, 5). The oxidized species of plutonium [Pu(V) and Pu(VI)] generally are much more soluble than the reduced species (4). Predicting the influence DMRB have on plutonium biogeochemistry is complicated by the fact that both Pu(III) and Pu(IV) are possible products of biological reduction. Also, the presence of chelating ligands can greatly influence the oxidation state formed during reduction as well as the reduction rate. The reduction of oxidized Pu species to Pu(IV) is desired, because it is highly insoluble and not very mobile. However, in the presence of complexing ligands and under reducing conditions the production of Pu(III) is favored, and Pu(III) complexes can be quite soluble (2). The conditions leading to the reduction of Pu(V) and Pu(VI) need to be understood and controlled so that they do not lead to the production of Pu(III), if the biological reduction of Pu(V) or Pu(VI) is to be used as an effective remediation strategy.There is little information available concerning the influence DMRB have on plutonium biogeochemistry. Few previous studies have reported the biological reduction of Pu(IV) to Pu(III) (2, 7, 16). During the earlier experiments (16), the solubilization of PuO₂ increased approximately ∼40% in solutions with DMRB. In solutions with DMRB and nitrilotriacetic acid (NTA), approximately 90% of the available Pu was solubilized, but the production of Pu(III) was not observed in any of the cultures, either with or without NTA added (16). The enhanced solubility of Pu was attributed to Pu(IV) reduction, the solubilization of resultant Pu(III), and the reoxidation of Pu(III) to Pu(IV) with the NTA complexation of Pu(III). Since Pu(III) was not observed, the biological reduction of Pu(IV) was inferred from the data (16). The biological reduction of Pu(IV) to Pu(III) was first conclusively documented with the production of Pu(III) in monocultures of G. metallireducens GS-15 and S. oneidensis MR-1 both with and without the addition of a chelating agent (EDTA) (2). In experiments without EDTA, the aqueous concentration of Pu(III) in DMRB cultures was very low (<0.05 mM Pu) (2). The aqueous concentration of Pu(III) increased to approximately 60 to 80% (0.3 to 0.4 mM Pu) of the total Pu(IV) when EDTA was added to the cultures (2). To our knowledge, there are no published studies documenting the biological reduction of Pu(V) or Pu(VI) to either Pu(IV) or Pu(III). However, based on thermodynamics calculations, the reduction of Pu(V) and Pu(VI) by DMRB should be possible and yield greater energy for the bacteria than Pu(IV) reduction (2).The study presented here was designed first to assess the ability of G. metallireducens GS-15 and S. oneidensis MR-1 to reduce Pu(V) and Pu(VI) in monocultures under cell resting and growth conditions. Second, the aqueous and solid phases produced during the experiments were analyzed to determine the extent of biological reduction [i.e., to Pu(IV) or Pu(III)].     

A high yield optimized method for the production of acylated ACPs enabling the analysis of enzymes involved in P. falciparum fatty acid biosynthesis

The natural substrates of the enzymes involved in type-II fatty acid biosynthesis (FAS-II) are acylated acyl carrier proteins (acyl-ACPs). The state of the art method to produce acyl-ACPs involves the transfer of a phosphopantetheine moiety from CoA to apo-ACP by E. coli holo-ACP synthase (EcACPS), yielding holo-ACP which subsequently becomes thioesterified with free fatty acids by the E. coli acyl-ACP synthase (EcAAS). Alternatively, acyl-ACPs can be synthesized by direct transfer of acylated phosphopantetheine moieties from acyl-CoA to apo-ACP by means of EcACPS. The need for native substrates to characterize the FAS-II enzymes of P. falciparum prompted us to investigate the potential and limit of the two methods to efficiently acylate P. falciparum ACP (PfACP) with respect to chain length and β-modification and in preparative amounts. The EcAAS activity is found to be independent from the oxidation state at the β-position and accepts fatty acids as substrates with chain lengths starting from C8 to C20, whereas EcACPS accepts very efficiently acyl-CoAs with chain lengths up to C16, and with decreasing activity also longer chains (C18 to C20). Methods were developed to synthesize and purify preparative amounts of high quality natural substrates that are fully functional for the enzymes of the P. falciparum FAS-II system.