Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil

Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N₂O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N₂O emissions increased when the size of inoculated C58 population in the soils was in the same range as the indigenous nosZ community. However, in two of the three soils, the increase in potential denitrification in inoculated microcosms compared with the noninoculated microcosms was higher than the increase in N₂O emissions. This suggests that the indigenous denitrifier community was capable of acting as a sink for the N₂O produced by A. tumefaciens. The relative amount of N₂O emitted also increased in two soils with the number of inoculated C58 cells, establishing a direct causal link between the denitrifier community composition and potential N₂O emissions by manipulating the proportion of denitrifiers having the nosZ gene. However, the number of denitrifiers which do not possess a nitrous oxide reductase might not be as important for N₂O emissions in soils having a high N₂O uptake capacity compared with those with lower. In conclusion, we provide a proof of principle that the inability of some denitrifiers to synthesize the nitrous oxide reductase can influence the nature of the denitrification end products, indicating that the extent of the reduction of N₂O to N₂ by the denitrifying community can have a genetic basis.     

Temperature effects on forest herbs assessed by warming and transplant experiments along a latitudinal gradient

Slow‐colonizing forest understorey plants are probably not able to rapidly adjust their distribution range following large‐scale climate change. Therefore, the acclimation potential to climate change within their actual occupied habitats will likely be key for their short‐ and long‐term persistence. We combined transplant experiments along a latitudinal gradient with open‐top chambers to assess the effects of temperature on phenology, growth and reproductive performance of multiple populations of slow‐colonizing understorey plants, using the spring flowering geophytic forb Anemone nemorosa and the early summer flowering grass Milium effusum as study species. In both species, emergence time and start of flowering clearly advanced with increasing temperatures. Vegetative growth (plant height, aboveground biomass) and reproductive success (seed mass, seed germination and germinable seed output) of A. nemorosa benefited from higher temperatures. Climate warming may thus increase future competitive ability and colonization rates of this species. Apart from the effects on phenology, growth and reproductive performance of M. effusum generally decreased when transplanted southwards (e.g., plant size and number of individuals decreased towards the south) and was probably more limited by light availability in the south. Specific leaf area of both species increased when transplanted southwards, but decreased with open‐top chamber installation in A. nemorosa. In general, individuals of both species transplanted at the home site performed best, suggesting local adaptation. We conclude that contrasting understorey plants may display divergent plasticity in response to changing temperatures which may alter future understorey community dynamics.     

Genetic and morphological divergence reveals local subdivision of perch (Perca fluviatilis L.)

The level of gene flow is an important factor influencing genetic differentiation between populations. Typically, geographic distance is considered to be the major factor limiting dispersal and should thus only influence the degree of genetic divergence at larger spatial scales. However, recent studies have revealed the possibility for small-scale genetic differentiation, suggesting that the spatial scale considered is pivotal for finding patterns of isolation by distance. To address this question, genetic and morphological differentiation were studied at two spatial scales (range 2–13 km and range 300 m to 2 km) in the perch ( Perca fluviatilis L.) from the east coast archipelago of Sweden, using seven microsatellite loci and geometric morphometrics. We found highly significant genetic differentiation between sampled locations at both scales. At the larger spatial scale, the distance per se was not affecting the level of divergence. At the small scale, however, we found subtle patterns of isolation by distance. In addition, we also found morphological divergence between locations, congruent with a spatial separation at a microgeographic scale, most likely due to phenotypic plasticity. The present study highlights the importance of geographical scale and indicates that there might be a disparity between the dispersal capacity of a species and the actual movement of genes. Thus, how we view the environment and possible barriers to dispersal might have great implications for our ability to fully understand the evolution of genetic differentiation, local adaptation, and, in the end, speciation.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 746–758.     

Effects of sample size,number of markers,and allelic richness on the detection of spatial genetic pattern

The influence of study design on the ability to detect the effects of landscape pattern on gene flow is one of the most pressing methodological gaps in landscape genetic research. To investigate the effect of study design on landscape genetics inference, we used a spatially‐explicit, individual‐based program to simulate gene flow in a spatially continuous population inhabiting a landscape with gradual spatial changes in resistance to movement. We simulated a wide range of combinations of number of loci, number of alleles per locus and number of individuals sampled from the population. We assessed how these three aspects of study design influenced the statistical power to successfully identify the generating process among competing hypotheses of isolation‐by‐distance, isolation‐by‐barrier, and isolation‐by‐landscape resistance using a causal modelling approach with partial Mantel tests. We modelled the statistical power to identify the generating process as a response surface for equilibrium and non‐equilibrium conditions after introduction of isolation‐by‐landscape resistance. All three variables (loci, alleles and sampled individuals) affect the power of causal modelling, but to different degrees. Stronger partial Mantel r correlations between landscape distances and genetic distances were found when more loci were used and when loci were more variable, which makes comparisons of effect size between studies difficult. Number of individuals did not affect the accuracy through mean equilibrium partial Mantel r, but larger samples decreased the uncertainty (increasing the precision) of equilibrium partial Mantel r estimates. We conclude that amplifying more (and more variable) loci is likely to increase the power of landscape genetic inferences more than increasing number of individuals.     

Evidence of a complex phylogeographic structure in the common dormouse,Muscardinus avellanarius (Rodentia: Gliridae)

This is the first mitochondrial phylogeography of the common dormouse, Muscardinus avellanarius (Linnaeus, 1758), a hibernating rodent strictly protected in Europe (Habitat Directive, annex IV; Bern Convention, annex III). The 84 individuals of M. avellanarius, sampled throughout the distributional range of the species, have been sequenced at the mitochondrial DNA gene (cytochrome b, 704 base pairs). The results revealed two highly divergent lineages, with an ancient separation around 7.7 Mya and a genetic divergence of 7.7%. Lineage 1 occurs in Western Europe (France, Belgium, and Switzerland) and Italy, and lineage 2 occurs in Central–Northern Europe (Poland, Germany, Latvia, and Lithuania), on the Balkan Peninsula, and in Turkey. Furthermore, these two lineages are subdivided into five sublineages genetically isolated with a strong geographical association. Therefore, lineage 1 branches into two further sublineages (Western European and Italian), whereas lineage 2 contained three sublineages (Central–Northern European, Turkish, and Balkan). We observed low genetic diversity within the sublineages, in contrast to the significant level of genetic differentiation between them. The understanding of genetic population structure is essential for identifying units to be conserved. Therefore, these results may have important implications for M. avellanarius conservation. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 648–664.     

Distribution and habitat of unionid mussels and invasive sea lamprey larvae in the Paw Paw River,a tributary of Lake Michigan

1. Lampricides are commonly used to control invasive sea lampreys (Petromyzon marinus) in tributaries around the Great Lakes (U.S.A.) by targeting their larvae (ammocoetes). As lampricides have sublethal effects on unionids, this study investigated unionid and ammocoete distribution and habitat use to aid in refining lampricide applications. 2. Habitat and unionid surveys were conducted in the Paw Paw River, in south‐west Michigan (U.S.A.). Unionids were predominately present in the upper main stem, while the probability of ammocoete presence was highest in the tributaries and lower main stem. 3. Generalised linear models revealed median particle size and gradient to be effective predictors of unionid distributions, while distance to sea lamprey spawning habitat and bank stability were effective predictors of ammocoete distributions. 4. Minimal overlap of unionid and ammocoete distributions suggests that refinement of lampricide treatment in the Paw Paw River is possible. We propose redefining the extent of the treatment unit so that only areas with a high probability of ammocoete presence and a low probability of unionid presence are treated with lampricide. This could result in reducing treatment costs and minimising threats to unionid conservation, while not jeopardising the success of lampricide treatment programmes.     

A rearrangement of the family Tethyidae (Porifera Hadromerida) with establishment of new genera and description of two new species

The discovery of new species, a study of the type material of already described species and an analysis of the literature data call for an extensive rearrangement of the Family Tethyidae, whose last revision dates from Burton (1924). The rearrangement proposed here attributes to the Family eight genera: Tethya Lam. (type genus), Burtonitethya gen nov. , Columnitis Schmidt, Halicomeies Topsent, Stellitethya gen. nov., Tectnitethya gen. nov., Tethycometes gen. nov . and Xenospongia Gray. The genus Aaptos is excluded from the Tethyidae. Three of the new genera have been established for species previously attributed to the genus Tethya and two are new: Burtonitethya gemmiformis (Burton & Rao) and Tethycometes sibogae sp. nov . Five species, previously attributed to Tethya , are considered 'incertae sedis'. An analytical key and discussion of the evolution of the family are included.     

Population Structure and Reproductive Biology of Saururus cernuus L. (Saururaceae)

Abstract The population structure and reproductive biology of Saururus cernuus (Lizard's Tail; Saururaceae; Piperales), is documented in five sites in southern Louisiana (Mississippi Delta). The species is common throughout the southeastern United States in marshes, along streams, edges of lakes, and in the understory of moist forests. The clonal species exhibits sexual and vegetative reproduction. Wind and insects both play important roles in pollination. Pollen may be borne by insects directly. Alternatively, the pollen may be borne by wind after its release is triggered from pendulous floral spikes (the “Lizard's Tail”) by either wind or insect landings (insect-mediated wind pollination). The plants are self-incompatible and seed set results from a combination of pollination modes with wind pollination being the primary mode (rare in the Magnoliidae). Inflorescence and floral structure exhibit adaptive features that facilitate the various modes of pollen transfer, viz., numerous, small scented, protogynous flowers with no perianth, ultraviolet patterns produced by stamen filaments, small pollen grains, curved inflorescences, and exerted stamens, etc. Fruit production and seed germination are documented and plant growth and densities are compared in sunny versus forest sites.     

Hypervariability in Gene Copy Number for the Glucose Transporter Genes in Trypanosomes

The copy number of the gene encoding the carrier protein responsible for the uptake of glucose in bloodstream form Trypanosoma brucei (THT1) was investigated in the genome of 55 different members of the subgenus Trypanozoon. The gene is present in multiple copies in tandem arrays on two homologous chromosomes in these organisms, and copy number varies both intra- and interspecifically. Variability is also apparent in the number of genes encoding a second hexose transporter (THT2) which is the only isoform expressed in procyclic organisms. Multiple copies of THT2 are conserved in representatives of the non-tsetse transmitted species, Trypanosoma evansi and Trypanosoma equiperdum.     

Factors Influencing the Growth and Division of Pea Mesophyll Protoplasts

High yields of viable protoplasts were produced from pea leaves provided that only leaves of the same age were used in each preparation. The conditions under which the pea plants were grown and the age of the plants were also important. The protoplasts were cultured in a medium supplemented with 1 mg/1 2iP and 1 mg/1 2,4-D. They were able to regenerate cell walls within two days. After 5 days cell divisions were apparent and sustained divisions led to callus formation. Special emphasis has been given in this paper to the choice of leaf material for protoplast isolation.