Effects of Amendment with Ferrihydrite and Gypsum on the Structure and Activity of Methanogenic Populations in Rice Field Soil

Methane emission from paddy fields may be reduced by the addition of electron acceptors to stimulate microbial populations competitive to methanogens. We have studied the effects of ferrihydrite and gypsum (CaSO₄·2H₂O) amendment on methanogenesis and population dynamics of methanogens after flooding of Italian rice field soil slurries. Changes in methanogen community structure were followed by archaeal small subunit (SSU) ribosomal DNA (rDNA)- and rRNA-based terminal restriction fragment length polymorphism analysis and by quantitative SSU rRNA hybridization probing. Under ferrihydrite amendment, acetate was consumed efficiently (<60 μM) and a rapid but incomplete inhibition of methanogenesis occurred after 3 days. In contrast to unamended controls, the dynamics of Methanosarcina populations were largely suppressed as indicated by rDNA and rRNA analysis. However, the low acetate availability was still sufficient for activation of Methanosaeta spp., as indicated by a strong increase of SSU rRNA but not of relative rDNA frequencies. Unexpectedly, rRNA amounts of the novel rice cluster I (RC-I) methanogens increased significantly, while methanogenesis was low, which may be indicative of transient energy conservation coupled to Fe(III) reduction by these methanogens. Under gypsum addition, hydrogen was rapidly consumed to low levels (~0.4 Pa), indicating the presence of a competitive population of hydrogenotrophic sulfate-reducing bacteria (SRB). This was paralleled by a suppressed activity of the hydrogenotrophic RC-I methanogens as indicated by the lowest SSU rRNA quantities detected in all experiments. Full inhibition of methanogenesis only became apparent when acetate was depleted to nonpermissive thresholds (<5 μM) after 10 days. Apparently, a competitive, acetotrophic population of SRB was not present initially, and hence, acetotrophic methanosarcinal populations were less suppressed than under ferrihydrite amendment. In conclusion, although methane production was inhibited effectively under both mitigation regimens, different methanogenic populations were either suppressed or stimulated, which demonstrates that functionally similar disturbances of an ecosystem may result in distinct responses of the populations involved.     

Planktonic primary production in the German Wadden Sea

By combining weekly data of irradiance, attenuation and chlorophylla concentrations with photosynthesis (P) versus light intensity(E) curve characteristics, the annual cycle of planktonic primaryproduction in the estuarine part of the Northfrisian WaddenSea was computed for a 2 year period. Daily water column particulategross production ranged from 5 to 2200 mg C m^–2 day^–1and showed a seasonal pattern similar to chlorophyll a. Budgetcalculation yielded annual gross particulate primary productionsof 124 and 176 g C m^–2 year^–1 in 1995 and 1996,respectively. Annual amounts of phytoplankton respiration, calculatedaccording to a two-compartment model of Langdon [in Li,W.K.W.and Maestrini,S.Y. (eds), Measurement of Primary Productionfrom the Molecular to the Global Scale. International Councilfor the Exploration of the Sea, Copenhagen, 1993, pp. 20–36],and dissolved production in 1996, were both in the range of24–39 g C m^–2 year^–1. Annual total net productionwas thus very similar to particulate gross production (127 and177 g C m^–2 year^–1 in 1995 and 1996, respectively).Phytoplankton growth was low or even negative in winter. Inspring and summer, production/biomass (Pr/B) ratios varied from0.2 up to 1.7. Phytoplankton growth during the growth seasonalways surpassed average flushing time in the area, thus underliningthe potential of local phytoplankton bloom development in thispart of the Wadden Sea. The chlorophyll-specific maximum photosyntheticrate (P^B_max) ranged from 0.8 to 9.9 mg C mg^–1 Chl h^–1and was strongly correlated with water temperature (r² = 0.67).By contrast, there was no clear seasonal cycle in ^B, which rangedfrom 0.007 to 0.039 mg C mg^–1 Chl h^–1 (µmolphotons m^–2 s^–1)^–1. Its variability was muchless than P^B_max and independent of temperature. The magnitudeand part of the variability of P^B_max and ^B are presumably causedby changes in species composition, as evidenced from the rangeof these parameters found among 10 predominant diatom speciesisolated from the Wadden Sea. The ratio of average light conditionsin the water column (E_av) to the light saturation parameterE_k indicates that primary production in the Wadden Sea regionunder study is predominantly controlled by light limitationand that nutrient limitation was likely to occur for a few hoursper day only during 5 (dissolved inorganic nitrogen) to 10 (PO₄,Si) weeks in the 2 year period investigated.     

Sibling Growth Patterns in Great tits: Does Increased Selection on Last-hatched Chicks Favour an Asynchronous Hatching Strategy?

In birds, competitive abilities of siblings in relation to their sex and the magnitude of hatching delay are still poorly understood. We compared the sex-specific growth of the last-hatched, competitively disadvantaged chicks with that of synchronously hatched chicks in two successive years. Sons exhibited higher growth rates than daughters in a year with delayed onset of breeding, and this sex-related difference was more pronounced among the asynchronously hatched chicks. Females apparently do not selectively allocate more resources to the last-laid eggs because neonatal body mass and the growth rate of asynchronously hatched chicks did not differ between years, despite the fact that in one of the years, asynchronous chicks hatched from replaced eggs taken randomly from other nests and not from eggs laid last by the incubating female. Among chicks that survived, moderately asynchronous siblings grew at a lower rate than synchronous ones, whereas no difference in mass gain was revealed between synchronous and strongly asynchronous siblings irrespective of their contrasting competitive abilities. We suggest that selection of the fittest asynchronous chicks may improve the overall quality of asynchronous broods, thus favouring the maintenance of asynchronous hatching strategies in variable environments.     

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ~4% read abundance across biological, and ~2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific 'in vivo' fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.     

Economic importance ofRhagoletis cerasi L., the feasibility of genetic control and resulting research problems

The authors — all members of the recently established O.I.L.B. working group — give in this first report a brief introduction into the pest problem and the biological, economic and environmental aspects which are favourable for the application of genetic control methods againstR. cerasi.

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Résumé En vue du développement des recherches sur la Mouche des cerises en Europe, un groupe de travail de l'O.I.L.B. pour la lutte génétique contreRhagoletis cerasi a été formé par les 4 auteurs. Des contributions du groupe seront désormais publiées sur le problème de la lutte autocide sous ce titre. Les hautes exigences imposées par le marché à la qualité intérieure et extérieure des cerises de table et de conserves d'une part, les pertes financières importantes causées par la disqualification des fruits infestés pour la distillation d'autre part, exigent des moyens de lutte efficaces. L'influence des mesures de lutte sur la biocénose doit cependant être minime. Les possibilités et avantages ainsi que les limites de l'application de la lutte génétique sont discutés en fonction de la situation favorable des points de vue topographique, écologique et biologique. En conclusion, la situation pour l'application de la lutte génétique peut être jugée favorable dans des cas choisis. Les taches de recherche qui en résultent sont commentées et complétées par un exposé sur la situation actuelle des travaux en cours.

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First Report of the O.I.L.B. working group on genetic control of the European cherry fruit fly,Rhagoletis cerasi L.     

Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil-contaminated aquifer by Pyro-SIP

The diversity of archaeal communities growing in four hot springs (65-90 °C, pH 6.5) was assessed with 16S rRNA gene primers specific for the domain Archaea. Overall, mainly uncultured members of the Desulfurococcales, the Thermoproteales and the Korarchaeota, were identified. Based on this diversity, a set of chaperonin heat-shock protein (Hsp60) gene sequences from different archaeal species were aligned to design two degenerate primer sets for the amplification of the chaperonin gene: Ths and Kor (which can also detect the korarchaeotal chaperonin gene from one of the samples). A phylogenetic tree was constructed using the chaperonin sequences retrieved and other sequences from cultured representatives. The Alpha and Beta paralogs of the chaperonin gene were observed within the main clades and orthologs among them. Cultivated representatives from these clades were assigned to either paralog in the chaperonin tree. Uncultured representatives observed in the 16S rRNA gene analysis were found to be related to the Desulfurococcales. The topologies of the 16S rRNA gene and chaperonin phylogenetic trees were compared, and similar phylogenetic relationships were observed. Our results suggest that the chaperonin Hsp60 gene may be used as a phylogenetic marker for the clades found in this extreme environment.     

Inducible gene manipulations in brain serotonergic neurons of transgenic rats

The serotonergic (5-HT) system has been implicated in various physiological processes and neuropsychiatric disorders, but in many aspects its role in normal and pathologic brain function is still unclear. One reason for this might be the lack of appropriate animal models which can address the complexity of physiological and pathophysiological 5-HT functioning. In this respect, rats offer many advantages over mice as they have been the animal of choice for sophisticated neurophysiological and behavioral studies. However, only recently technologies for the targeted and tissue specific modification of rat genes - a prerequisite for a detailed study of the 5-HT system - have been successfully developed. Here, we describe a rat transgenic system for inducible gene manipulations in 5-HT neurons. We generated a Cre driver line consisting of a tamoxifen-inducible CreERT2 recombinase under the control of mouse Tph2 regulatory sequences. Tissue-specific serotonergic Cre recombinase expression was detected in four transgenic TPH2-CreERT2 rat founder lines. For functional analysis of Cre-mediated recombination, we used a rat Cre reporter line (CAG-loxP.EGFP), in which EGFP is expressed after Cre-mediated removal of a loxP-flanked lacZ STOP cassette. We show an in-depth characterisation of this rat Cre reporter line and demonstrate its applicability for monitoring Cre-mediated recombination in all major neuronal subpopulations of the rat brain. Upon tamoxifen induction, double transgenic TPH2-CreERT2/CAG-loxP.EGFP rats show selective and efficient EGFP expression in 5-HT neurons. Without tamoxifen administration, EGFP is only expressed in few 5-HT neurons which confirms minimal background recombination. This 5-HT neuron specific CreERT2 line allows Cre-mediated, inducible gene deletion or gene overexpression in transgenic rats which provides new opportunities to decipher the complex functions of the mammalian serotonergic system.