Microbial growth response to substrate complexity under different temperature regimes

Soil microbial communities mediate soil feedbacks to climate change and a thorough understanding of their response to increasing temperatures is central for predicting climate-induced changes in carbon fluxes. However, it is still unclear how microbial communities will change their structure and functions in response to temperature change and availability of organic carbon of varying complexity. Here, we present results from a lab-based study where soil microbial communities were exposed to different temperatures and organic C of different stability. Soil samples were collected from vegetated and bare fallow plots located in two regions in southwest Germany varying in climatic and edaphic conditions. Soils amended with cellobiose (CB), xylan or coniferyl alcohol (CA, lignin precursor) were incubated at 5, 15 and 25 °C. We generally found highest cumulative respiration (CO2-C) at 25 °C in all substrate treatments even though total microbial growth (measured as total extracted DNA) was higher at 15 °C. Fungal biomass (measured from ergosterol content and fungal PLFAs) responded significantly to added substrate and incubation temperature, with higher fungal biomass at 5 or 15 °C than 25 °C in all substrate amendments. Xylan addition resulted in significantly higher ergosterol contents than for CB and CA. Within region, land-use significantly affected fungal biomass response to added substrate; however, the temperature response was similar between fallow and vegetated plots. Bacterial community response was also significantly affected by substrate quality. In contrast to fungi, the growth response of Gram+ and Gram- bacteria declined in the order CB > xylan > CA. Currently, we are analyzing the qPCR data understand the response of different bacterial taxa to temperature and substrate complexity. Our results demonstrate the importance of the interaction between soil temperature and substrate quality for soil microbial community functions and growth strategies

Auto- und Heterotrophic Respiration in the Hohenheim Climate Change Experiment - The Importance of Temperature Change and Vegetation Period

Current Climate change (CC) research in soil science mainly focusses on natural ecosystems, without considering the potential of agro-ecosystems for feedback mechanisms to CC and CC mitigation through Carbon(C)-sequestration. We expect that CC induces increasing water limitation under elevated temperature, lowers the intensity of soil respiration and changes the ratio between the amount of root-dependent and basal soil respiration. Such changes might be due to differences in the intrinsic temperature and moisture sensitivity of microbial and root respiration and due to altered root exudation. In this project, we focus on CC-induced effects on plant-dependent and basal soil respiration to improve the estimation of long-term soil organic matter stabilization. Within the Hohenheim Climate Change (HoCC) experiment (established in 2008), barley plants were pulse-labelled with 20-atom% 13CO2 for 4 h using ventilated transparent chambers on warmed and control plots in an agricultural field. The labeling was done during three different stages (advanced tillering, booting and grain-filling) of the vegetation period, at which C-sink strength of shoot and root differs according to plant development. CO2-fluxes and isotopic composition were measured in real time in the field for the first 50h (post labeling) using a 13CO2 isotope analyzer. Results from tracing 13C-fluxes will clarify how soil moisture and long-term elevated temperature affect the overall C-balance in agricultural soils in dependence of the vegetation period. This will allow estimations of direction and strength of feedback mechanisms of terrestrial C-cycling under CC. Overall, insights obtained in this project will provide better understanding of the CC impact on and of temperate agricultural production systems

Effects of warming and drought on potential N2O emissions and denitrifying bacteria abundance in grasslands with different land-use

Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensit

Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects

A three year field study (2007-2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted at the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. The result demonstrated that there was no consistent effect of either organic or conventional soil management across the three years on the diversity or quantity of either diazotrophic or total bacterial communities. However, ordination analyses carried out on data from each individual year showed that factors associated with the different fertility management measures including availability of nitrogen species, organic carbon and pH, did exert significant effects on the structure of both diazotrophic and total bacterial communities. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions. The diazotrophic community showed no significant change in diversity across the three years, however, the total bacterial community significantly increased in diversity year on year. Diversity was always greatest during March for both diazotrophic and total bacterial communities. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. Seasonal effects were less consistent in this quantitative study

Test System Stability and Natural Variability of a Lemna Gibba L. Bioassay

BACKGROUND: In ecotoxicological and environmental studies Lemna spp. are used as test organisms due to their small size, rapid predominantly vegetative reproduction, easy handling and high sensitivity to various chemicals. However, there is not much information available concerning spatial and temporal stability of experimental set-ups used for Lemna bioassays, though this is essential for interpretation and reliability of results. We therefore investigated stability and natural variability of a Lemna gibba bioassay assessing area-related and frond number-related growth rates under controlled laboratory conditions over about one year. METHODOLOGY/PRINCIPAL FINDINGS: Lemna gibba L. was grown in beakers with Steinberg medium for one week. Area-related and frond number-related growth rates (r(area) and r(num)) were determined with a non-destructive image processing system. To assess inter-experimental stability, 35 independent experiments were performed with 10 beakers each in the course of one year. We observed changes in growth rates by a factor of two over time. These did not correlate well with temperature or relative humidity in the growth chamber. In order to assess intra-experimental stability, we analysed six systematic negative control experiments (nontoxicant tests) with 96 replicate beakers each. Evaluation showed that the chosen experimental set-up was stable and did not produce false positive results. The coefficient of variation was lower for r(area) (2.99%) than for r(num) (4.27%). CONCLUSIONS/SIGNIFICANCE: It is hypothesised that the variations in growth rates over time under controlled conditions are partly due to endogenic periodicities in Lemna gibba. The relevance of these variations for toxicity investigations should be investigated more closely. Area-related growth rate seems to be more precise as non-destructive calculation parameter than number-related growth rate. Furthermore, we propose two new validity criteria for Lemna gibba bioassays: variability of average specific and section-by-section segmented growth rate, complementary to average specific growth rate as the only validity criterion existing in guidelines for duckweed bioassays

Veränderungen der mikrobiellen Gemeinschaft in Grünlandböden als Reaktion auf kurz- und langfristiges Flächenmanagement

Im Rahmen des DFG Schwerpunktprogramms Biodiversitäts-Exploratorien (www.biodiversity-exploratories.de) wurden in 150 Grünlandböden die Veränderungen der mikrobiellen Gemeinschaftsstruktur und Enzymaktivität über einen Zeitraum von drei Jahren untersucht. Je 50 der Untersuchungsflächen liegen in der Schwäbischen Alb, dem Hainich-Dün und der Schorfheide-Chorin. Im Mai 2011 und 2014 wurden zeitgleich Oberbodenproben in allen Regionen genommen und die mikrobielle Biomasse (C, N, P), Gemeinschaftsstruktur (Phospholipidfettsäuren) sowie Enzymaktivitäten des C-, N- und P-Kreislaufs bestimmt. Zwischen 2011 und 2014 hat sich die Landnutzungsintensität (LUI) einiger Flächen stark verändert, während die LUI anderer fast identisch blieb. Unsere zentrale Hypothese ist, dass die Veränderung der LUI, durch die direkte Nährstoffzufuhr über Dünger, zu Veränderungen in den mikrobiellen Bodeneigenschaften zwischen den Jahren geführt hat. Tatsächlich konnten Veränderungen der mikrobiellen Bodeneigenschaften im untersuchten Zeitraum detektiert werden. Ob diese direkt durch Veränderungen (V) der LUI, oder durch Variationen in Temperatur, Wasserhaltekapazität, pH-Wert und Pflanzenbestand erklärt werden können oder ob die Änderungen der Mikroorganismen (MO) durch die historischen Bedingungen (H) auf den Flächen beeinflusst wurden, wurde mittels hierarchischer Regressionsanalysen untersucht. Dabei gingen folgende Variablen in fünf Stufen in die Modelle ein: Umwelt: Temperatur (V), Wasserhaltekapazität (V), pH (H); Landmanagement: LUI (V, H); pH-Wertänderung: pH (V); Pflanzenfunktionen: Mykorrhizierungsintensität (V, H), spezifische Blattfläche (V, H), Blatt-P (V, H), Blatt-N (V, H) und Pflanzenbiomasse: Biomasse (V), Cellulose (V), Hemicellulosen (V), Lignin (V), Biomasse P (V), Biomasse N (V), Lignin:N (V). Dabei zeigte sich, dass die funktionellen Pflanzeneigenschaften, insbesondere der Blatt-P-Gehalt, einen erheblichen Einfluss auf die Veränderung der MO im Boden hatten. Am häufigsten signifikant war ihr Einfluss auf die MO der Schwäbischen Alb und des Hainich-Dün, während in der Schorfheide-Chorin die Änderung des pH-Wertes dominierte. Direkt wirkte sich die Änderung der LUI nur auf Pilze aus, nicht auf Bakterien und Enzymaktivitäten. Ob sich die LUI indirekt über die Pflanzen auf Enzyme und Bakterien auswirkte, ist Gegenstand weiterer Analysen

How many is enough? Determining optimal count totals for ecological and palaeoecological studies of testate amoebae

Testate amoebae are increasingly used in ecological and palaeoecological studies of wetlands. To characterise the amoeba community a certain number of individuals need to be counted under the microscope. To date, most studies have aimed for 150 individuals, but that sample size is not based on adequate evidence. When testate amoeba concentrations are low, it can be difficult or impossible to reach this total. The impacts of lower count totals have never been seriously scrutinised. We investigated the impact of count size on number of taxa identified, quantitative inferences of environmental variables and the strength of the links between amoebae and environmental data in the context of predicting depth to water table. Low counts were simulated by random selection of individuals from four existing datasets. Results show progressively diminishing returns by all criteria as count size increases from low numbers to counts of 150. A higher count is required to identify all taxa than to adequately characterise the community for transfer function inference. We suggest that in most cases, it will be a more efficient use of time to count a greater number of samples to a lower count. While a count of 50 individuals may be sufficient for some samples from some sites we recommend that counts of 100 individuals should be sufficient for most samples. Counts need only be increased to 150 or more where the aim is to identify relatively minor, but still potentially ecologically relevant community changes. This approach will help reduce lack of replication and low resolution, which are common limitations in testate amoeba-based palaeoecological and ecological studies

Multitrophic Interaction in the Rhizosphere of Maize: Root Feeding of Western Corn Rootworm Larvae Alters the Microbial Community Composition

BACKGROUND: Larvae of the Western Corn Rootworm (WCR) feeding on maize roots cause heavy economical losses in the US and in Europe. New or adapted pest management strategies urgently require a better understanding of the multitrophic interaction in the rhizosphere. This study aimed to investigate the effect of WCR root feeding on the microbial communities colonizing the maize rhizosphere. METHODOLOGY/PRINCIPAL FINDINGS: In a greenhouse experiment, maize lines KWS13, KWS14, KWS15 and MON88017 were grown in three different soil types in presence and in absence of WCR larvae. Bacterial and fungal community structures were analyzed by denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene and ITS fragments, PCR amplified from the total rhizosphere community DNA. DGGE bands with increased intensity were excised from the gel, cloned and sequenced in order to identify specific bacteria responding to WCR larval feeding. DGGE fingerprints showed that the soil type and the maize line influenced the fungal and bacterial communities inhabiting the maize rhizosphere. WCR larval feeding affected the rhiyosphere microbial populations in a soil type and maize line dependent manner. DGGE band sequencing revealed an increased abundance of Acinetobacter calcoaceticus in the rhizosphere of several maize lines in all soil types upon WCR larval feeding. CONCLUSION/SIGNIFICANCE: The effects of both rhizosphere and WCR larval feeding seemed to be stronger on bacterial communities than on fungi. Bacterial and fungal community shifts in response to larval feeding were most likely due to changes of root exudation patterns. The increased abundance of A. calcoaceticus suggested that phenolic compounds were released upon WCR wounding

The effect of nutrients on pyrrolizidine alkaloids in Senecio plants and their interactions with herbivores and pathogens

The aim of this review is to combine the knowledge of studies on effects of nutrients on pyrrolizidine alkaloids (PAs) in Senecio with those studies of effects of PAs on herbivores and pathogens in order to predict the effects that nutrients may have on herbivores and pathogens via changes in PAs. We discuss whether these predictions match with the outcome of studies where the effect of nutrients on herbivores and insects were measured. PA concentrations in S. jacobaea, S. vulgaris and S. aquaticus were mostly reduced by NPK fertilization, with genotype-specific effects occurring. Plant organs varied in their response to increased fertilization; PA concentrations in flowers remained constant, while shoot and roots were mostly negatively affected. Biomass change is probably largely responsible for the change in concentrations. Nutrients affect both the variety and the levels of PAs in the plant. The reduced PA concentrations after NPK fertilization was expected to benefit herbivores, but no or negative responses from insect herbivores were observed. Apparently other changes in the plant after fertilization are overriding the effect of PAs. Pathogens do seem to benefit from the lower PA concentrations after fertilization; they were more detrimental to fertilized plants than to unfertilized control plants. Future studies should include the effect of each element of nutrients separately and in combinations in order to gain more insight in the effect of specific nutrients on PA content in Senecio plants