Thermal profiles and primer used for real-time PCR quantification of different functional genes and transcripts.

a<p>Touchdown: −1°C per cycle.</p><p>Thermal profiles and primer used for real-time PCR quantification of different functional genes and transcripts.</p

Time course analyses of the number of bacteria present in the three truckloads of bovine raw-milk samples (L1, L2, and L3), enumerated on PCA agar after 3 days incubation at 30°C under aerobic conditions: C (cold-stored milk at 6°C), N (milk flushed with N₂ gas while in cold storage at 6°C).

<p>Error bars indicate standard deviations. The blue line corresponds to the 3x10⁵ (5.5 log-units) threshold value for raw milk acceptance for dairy processing.</p

Gravimetric soil moisture related to water holding capacity (WHC), total N and C contents as well as extractable N and C pools of soil of soils at NW and SW, sampled in June (T1), after 39 days drought in August (T2), 24 and 72 hours after rewetting in August (T3, T4) and in September (T5) (n = 8, standard deviation of the mean in parentheses).

<p>Asterisks indicate significant differences between NW and SW at the respective sampling times (Student's T test), whereas lower case letters indicate differences among the sampling period for the respective site (multivariate ANOVA). Significant differences between the factors site and sampling time calculated by multivariate ANOVA are indicated by P values <0.05 (bold letters).</p><p>Gravimetric soil moisture related to water holding capacity (WHC), total N and C contents as well as extractable N and C pools of soil of soils at NW and SW, sampled in June (T1), after 39 days drought in August (T2), 24 and 72 hours after rewetting in August (T3, T4) and in September (T5) (n = 8, standard deviation of the mean in parentheses).</p

Transcript abundance of functional genes involved in the nitrogen cycle (<i>chiA</i>, <i>apr</i>, <i>amoA</i> AOA, <i>nirK</i>, <i>cnor</i> and <i>nosZ</i>) are shown for NW (black bar) and SW (grey bar) in June (T1), after 39 days drought in August (T2), 24 and 72 hours after rewetting in August (T3, T4) and in September (T5) (n = 8, error bars represent standard deviation of the mean).

<p>Asterisks indicate significant differences between NW and SW at the respective sampling times (Student's T test), whereas lower case letters indicate differences among the sampling period for the respective site (multivariate ANOVA). Significant differences between the factors site and sampling time calculated by multivariate ANOVA are indicated by P values <0.05 (bold letters).</p

Scheme of the microbial nitrogen cycle under different climate change conditions.

<p>(A) comparison between NW and SW at ambient climate change (T1), (B) comparison between NW and SW at ambient/roof-intensified summer drought (T2) and (C) comparison between NW and SW after rewetting (T3, T4). Decreased N turnover processes under climate change indicated by significantly lower transcripts at SW compared to NW are shown in grey (P <0.05).</p

Relative abundance of raw milk taxa that were significantly affected by cold storage at 6°C and by cold storage combined with N₂ gas flushing.

<p>Error bars represent the standard deviation of mean (n = 3) values. Average values sharing a common letter are not significantly different with a level of significance of 0.05 over all comparisons. (u_: unclassified).</p

Composition of the bacterial communities based on 16S rRNA transcripts in initial raw milk, in cold-stored milk, and in cold-stored while N₂-flushed for either 3 or 4 and 6 or 7 days, based on partial 16S rRNA gene sequences after RNA extraction, cDNA synthesis and PCR amplification.

<p>(a) Total phyla, (b) total classes, (c) families of Bacteroidetes, (d) genera of Bacteroidetes, (e) families of Bacilli, (f) genera of Bacilli, (g) families of Clostridia, (h) genera of Clostridia, (i) families of Gammaproteobacteria, (j) genera of Gammaproteobacteria.</p

Venn diagrams of Illumina sequence data comparing (A) initial and cold-stored raw-milk samples (B) initial and cold-stored N₂-flushed raw-milk samples.

<p>OTUs shared between the conditions are indicated in boldface.</p

Soil temperature differences (5 cm depth) between beech-soil-mesocosms incubated at SW exposure (warm-dry microclimate, climate change treatment) and at NW exposure (cool-moist microclimate, control treatment).

<p>Data represent mean values of five temperature probes per treatment directly installed horizontally in soil of transferred beech-soil-mesocosms. Arrows indicate the three sampling campaigns. The period between the sampling in June and August equals the roof period of 39 days.</p

Dynamics of volumetric soil moisture in 5 cm depth (mean values of n = 5 measurements) in intact beech-soil-mesocosms of the control treatment (NW exposure, cool-moist microclimate) and climate change treatment (SW exposure, warm-dry microclimate) in the growing season 2011, i.e., 1 year after implementation of treatments by transferring beech seedling-soil-mesocosms within NW exposure or to SW exposure in summer 2010.

<p>Arrows indicate sampling campaigns (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158823#pone.0158823.g001" target="_blank">Fig 1</a>).</p