Temporal Succession Research Articles

Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome.

Tonsils, lympho-epithelial tissues located at the junction of the oropharynx and nasopharynx, play a key role in surveillance, colonization, and persistence of inhaled and ingested pathogens. In pigs, the tonsils are a reservoir for numerous bacteria and viruses, including host-specific pathogens and potential zoonotic pathogens as well as commensal organisms. However, there are no in depth studies of the development of the tonsillar microbiome in pigs, or any mammal, over time. The goal of this study was to follow the development of the tonsil microbiome in healthy pigs from birth to market weight. Samples were collected using tonsil brushes from 16 piglets (4 each from 4 sows) at newborn, 1, 2, 3, and 4 weeks of age, and from 8 of those piglets at 6, 8, 10, 12, 16, and 19 weeks of age. Bacterial DNA was isolated from each sample and 16S rDNA genes were amplified and sequenced. Sequence analysis showed that members of the Streptococcaceae, Pasteurellaceae, and Moraxellaceae were present at all time points and represent the three most abundant families identified. Other community members appeared transiently or increased or decreased significantly with disruption events or stress. We observed four significant shifts in the tonsil community that coincided with well-defined disruption events: weaning plus addition of Carbadox plus movement to the nursery at week 3, removal of Carbadox and addition of Tylan at week 5, removal of Tylan and habitat change at week 9, and habitat change at week 16. Weaning triggered a bloom of Streptococcaeae and decrease of Moraxellaceae. The shift from Carbadox to Tylan led to reduction in Proteobacteria and Streptococcaceae but an increase in other Firmicutes, accompanied by a dramatic increase in community richness. Cessation of Tylan coincided with a return to a less rich community, and a bloom in Clostridiales. The final shift in habitat was accompanied by a decrease in Clostridiales and increase in Proteobacteria. The tonsillar microbiome of older pigs resembled the previously described mature core tonsillar microbiome. This study demonstrates a temporal succession in the development of the pig tonsillar microbiome, and significant community shifts that correlate with disruption events.

Enrichment of Bacterioplankton Able to Utilize One-Carbon and Methylated Compounds in the Coastal Pacific Ocean

Understanding the temporal variations and succession of bacterial communities involved in the turnover of one-carbon and methylated compounds is necessary to better predict bacterial impacts on the marine carbon cycle and air-sea carbon fluxes. The ability of the local bacterioplankton community to exploit one-carbon and methylated compounds as main source of bioavailable carbon during a productive and less productive period was assessed through enrichment experiments. Surface seawater was amended with methanol and trimethylamine-N-oxide (TMAO), and bacterial abundance, production, oxygen consumption, as well as methanol turnover and growth rates of putative methylotrophs were followed. Bacterial community structure and functional diversity was examined through amplicon sequencing of 16S rRNA and methanol dehydrogenase (mxaF) marker genes. 2-fold increase in oxygen consumption and bacterial growth rates, and up to 4-fold higher methanol assimilation were observed in the amended seawater samples. Capacity to drawdown the substrates was similar between both experiments. In less productive conditions, methanol enriched obligate methylotrophs, especially Methylophaga spp., accounted for ~70% of bacterial cells analyzed by fluorescence in situ hybridization and 16S rRNA gene sequencing, while TMAO enriched taxa belonged to Oceanospirillales and putative β- and γ-Proteobacterial methylotrophs. In the experiment performed during the more productive period, bacterial communities were structurally resistant, suggesting that facultative organisms may have dominated the observed methylotrophic activity. Moreover, enrichment of distinct methylotrophic taxa but similar activity rates observed in response to different substrate additions suggests a functional redundancy of substrate specific marine methylotrophic populations. Marine bacterioplankton cycling of one-carbon and methylated compounds appears to depend on the system productivity, and hence may have predictable temporal impacts on air-sea fluxes of volatile organic compounds.

Antibiotic resistance genes and associated bacterial communities in agricultural soils amended with different sources of animal manures

Land application of animal manures is a major dissemination route for antibiotic resistance genes (ARGs) in agro-ecosystems, which are a potential risk to public health if they migrate into the food chain. Despite the fact that animal manure is a rich reservoir of ARGs our knowledge of the impacts of different types and amounts of animal manures on the temporal succession of a wide array of ARGs and potential ARG-hosts remains limited. Here, we constructed soil microcosms amended with two levels of swine, poultry or cattle manures to explore the time-course patterns of ARGs, mobile genetic elements (MGEs) including integrons and transposons, and bacterial communities. The high-throughput quantitative PCR detected 260 unique ARGs, and the application of all manure types, especially at the higher concentration (80 mg manure g−1 soil), significantly increased the diversity and abundances of ARGs and MGEs. The abundance of ARGs in manured soils declined over time, but was still higher than that in untreated soils after 120 days, indicating the persistence of ARGs in manured soils. The next-generation sequencing revealed a clear shift in the bacterial community compositions of manured soils during the incubation. Mantel test and network analysis revealed that the ARG profile was strongly correlated with the bacterial community compositions. Variation partitioning analysis, and structure equation models, further indicated that bacterial phylogeny played a primary role in shaping the ARG profiles in manured soils. However, the significant correlation between the abundances of MGEs and ARGs suggested that the potential effects of horizontal gene transfer on the persistence of ARGs should not be overlooked. In addition, soil properties, which were strongly affected by the added manures, could also affect the ARG patterns. These findings demonstrated the temporal patterns and dissemination risk of ARGs in manured soils, which might contribute to the development of effective strategies to minimise the spread of ARGs in agro-ecosystems.

Evolution of plesiadapid mammals (Eutheria, Euarchonta, Plesiadapiformes) in Europe across the Paleocene/Eocene boundary: implications for phylogeny, biochronology and scenarios of dispersal

Plesiadapid mammals (Eutheria, Euarchonta, Plesiadapiformes) are well represented in the late Paleocene to early Eocene of Europe (reference levels MP6, MP7 and MP8+9), but relationships among the described species and their links to North American plesiadapids remain disputed. To better understand the evolution of the group in Europe, to explore its potential for biochronological dating and to test hypotheses on plesiadapid phylogenies and dispersal patterns between Europe and North America, a morphometric analysis was performed for a succession of plesiadapid assemblages bracketing the Paleocene/Eocene boundary (PEB) in the Paris Basin, including recently made collections from Montchenot (MP6) and Le Quesnoy (MP7). Both dental size and shape were analysed for nearly all positions of the permanent plesiadapid dentition. Size variation at Cernay (MP6) is consistent with the presence of at least two species of Plesiadapis. A morphological succession is found in European large-sized Plesiadapis, continuing beyond the PEB but showing no clear continuity with Eocene Platychoerops. Large-sized Plesiadapis from Berru (MP6) is distinctly different from P. tricuspidens, justifying the definition of a new species, P. berruensis. Species of Plesiadapis confirm the temporal succession of the localities Cernay, Berru, Le Quesnoy and Meudon, allowing definition of a refined biochronology in the Paris Basin, with Montchenot correlated approximately to Cernay. Comparisons between plesiadapids from Europe and North America indicate a separation from at least the terminal Tiffanian, suggesting correlation of the European reference level MP6 with the North American biozones Ti-5b and Ti-6. Convergent evolution in those lineages and in Platychoerops seems to be linked mainly to trends towards folivory.

Lily Pollen Tubes Pulse According to a Simple Spatial Oscillator

Polar growth is a fundamental mode of cell morphogenesis observed in nearly all major groups of organisms. Among polarly growing cells, the angiosperm pollen tubes have emerged as powerful experimental systems in large part because of their oscillatory growth, which provides a window into the network of interactions regulating morphogenesis. Empirical studies of oscillatory pollen tubes have sought to uncover the temporal sequence of cellular and molecular events that constitutes an oscillatory cycle. Here we show that in lily pollen tubes the distance or wavelength (λ = 6.3 ± 1.7 μm) over which an oscillatory cycle unfolds is more robust than the period of oscillation (τ = 39.1 ± 17.6 s) (n = 159 cells). Moreover, the oscillatory cycle is divided into slow and fast phases, with each phase unfolding over precisely one half of the wavelength. Using these observations, we show that a simple spatial bi-oscillator predicts the most common modes of oscillation observed in pollen tubes. These results call into question the traditional view of pollen tube morphogenesis as a temporal succession of cellular events. Space, not time, may be the most natural metric to inteprete the morphogenetic dynamics of these cells.

Climate warming leads to divergent succession of grassland microbial communities

Accurate climate projections require an understanding of the effects of warming on ecological communities and the underlying mechanisms that drive them1–3. However, little is known about the effects of climate warming on the succession of microbial communities4,5. Here we examined the temporal succession of soil microbes in a long-term climate change experiment at a tall-grass prairie ecosystem. Experimental warming was found to significantly alter the community structure of bacteria and fungi. By determining the time-decay relationships and the paired differences of microbial communities under warming and ambient conditions, experimental warming was shown to lead to increasingly divergent succession of the soil microbial communities, with possibly higher impacts on fungi than bacteria. Variation partition- and null model-based analyses indicate that stochastic processes played larger roles than deterministic ones in explaining microbial community taxonomic and phylogenetic compositions. However, in warmed soils, the relative importance of stochastic processes decreased over time, indicating a potential deterministic environmental filtering elicited by warming. Although successional trajectories of microbial communities are difficult to predict under future climate change scenarios, their composition and structure are projected to be less variable due to warming-driven selection. Experimental warming at a tall-grass prairie significantly altered bacteria and fungi community structure. Under climate change microbial community composition and structure are projected to be less variable due to warming-driven selection.

Training-Induced Changes in Rapid Auditory Processing in Children With Specific Language Impairment: Electrophysiological Indicators.

The brain’s ability to recognize acoustic changes occurring in rapid temporal succession is important for speech and successful language development. Children with specific language impairment (SLI) are characterized by deficient dynamics of temporal information processing (TIP) in the millisecond time range accompanied by disordered language development. Furthermore, previous studies have found that intervention based on amelioration of TIP resulted in improvement of both language and other cognitive functions. This study aimed to explain the changes associated with TIP training from the perspective of event-related potentials (ERPs). Thirty-six children aged 5–8 years (26 boys, 10 girls) diagnosed with SLI underwent two types of intense audio-visual computer intervention: experimental TIP training targeted at the millisecond time range (n = 18) or control non-TIP training (n = 18). Paired 50 ms tones of 1000 Hz and 1200 Hz were presented with inter-stimulus intervals (ISIs) of either 50 ms (Short ISI Condition) or 200 ms (Long ISI Condition). Auditory ERPs were measured in a passive oddball paradigm before and after each type of training. The mismatch negativity (MMN) paradigm was applied as an electrophysiological indicator of the brain’s ability to automatically detect violations of regularity in paired tones presented in rapid succession. Moreover, the P3a component was also analyzed. After 24 sessions of temporal training (in the experimental group) MMN amplitude enhancement was observed in both ISI conditions, reflecting increased efficiency in perceiving changes in rapid auditory sequences. In both experimental and control groups, P3a amplitude was enhanced in both ISIs. This may be due to the improvement of involuntary attention shifting to the auditory events involved in each training type. To conclude, temporal training, compared to non-temporal control training, improved the ability to detect changes in a rapid auditory stream in children with SLI.

Decreased occurrence of carbon cycle functions in microbial communities along with long-term secondary succession

The succession of microbial community structure and function is a central ecological topic; however, the mechanisms that underlie community assembly and promote temporal succession remain unclear. We studied microbial community-associated functional dynamics in a well-established secondary successional chronosequence that spans approximately 160 years of ecosystem development on the Loess Plateau of China, by sequencing both 16S and ITS rRNA genes and soil metagenomes, resulting in a total of 132.5 Gb of data. Notably, both bacterial and fungal communities shifted with succession, but the microbial community changed little from the pioneer forest stage (approximately 110 years) to the latter successional forest stage. Fungi showed higher variability with succession than bacteria, and the shift of both the bacterial and fungal communities was related more to the soil characteristics than to the litter characteristics. Shifts in soil microbial functions were associated with microbial phylogenetic changes, but microbial gene function also showed changes in the absence of phylogenetic changes at the late successional stages. The reduction in microbial C cycle genes was related to a decrease in litter decomposition ability, thus resulting in a steady state of nutrient cycle in the ecosystem. In addition, high microbial respiration in nutrient-rich soil does not necessarily indicate high microbial decomposition functions; the latter also depend on the abundance of related genes, on enzyme activity and on the physicochemical properties of the litter. Our study provides a metagenome profile of a successional chronosequence and provides insight into the mechanisms underlying the soil microbe-driven functional changes in nutrient cycles during succession.

Development of the tonsillar microbiome in pigs from newborn through weaning

BackgroundPorcine tonsils are lympho-epithelial tissues, colonized by numerous bacteria and viruses, that act as a reservoir for both host-specific pathogens and zoonotic pathogens with a high potential of transmission to humans. There are no existing studies describing the development of the tonsillar microbiome. We sequenced 16S rRNA genes from tonsillar samples of pigs to follow the development of the microbial communities from birth through weaning. Samples derived from sows were also analyzed to determine potential sources for the tonsil microbiome in piglets.ResultsThe composition of the newborn piglet tonsil microbiome could be differentiated by litter and had strong similarity to the sow teat skin as well as sow vaginal microbiome. The tonsil microbiome in these young piglets was mainly dominated by members of the Pasteurellaceae, Moraxellaceae, and Streptococcaceae families, while there were some transient members of the microbiome that were abundant at specific times, such as Staphylococcaceae in newborns and Fusobacteriaceae and Leptotrichiaceae in weeks 2 and 3. The microbiome initially differed between litters but over the following 3 weeks the communities of different litters converged in composition and then diverged in week 4 due to a combination of changes and stresses associated with weaning, including a shift from milk to a solid diet, in-feed Carbadox® and room change.ConclusionsA significant portion of the tonsil microbiome was acquired either at birth from the sow vaginal tract or within a few hours post-birth from the sow teat skin. Our data demonstrate a temporal succession in the development of the pig tonsillar microbiome through the first weeks of life, with a convergence in the composition of the microbiome in all piglets by 3 weeks of age. The combination of management practices associated with weaning coincided with dramatic shifts in the tonsillar microbiome.

Riva Fire v Commission: Infringement of Essential Procedural Requirements and Temporal Succession of Procedural Rules in EU Competition Law

Riva Fire v Commission: Infringement of Essential Procedural Requirements and Temporal Succession of Procedural Rules in EU Competition Law

Increased Amazon freshwater discharge during late Heinrich Stadial 1

The temporal succession of changes in Amazonian hydroclimate during Heinrich Stadial 1 (HS1) (ca. 18–14.7 cal ka BP) is currently poorly resolved. Here we present HS1 records based on isotope, inorganic and organic geochemistry from a marine sediment core influenced by the Amazon River discharge. Our records offer a detailed reconstruction of the changes in Amazonian hydroclimate during HS1, integrated over the basin. We reconstructed surface water hydrography using stable oxygen isotopes (δ18O) and Mg/Ca-derived paleotemperatures from the planktonic foraminifera Globigerinoides ruber, as well as salinity changes based on stable hydrogen isotope (δD) of palmitic acid. We also analyzed branched and isoprenoid tetraether concentrations, and compared them to existing bulk sediment ln(Fe/Ca) data and vegetation reconstruction based on stable carbon isotopes from n-alkanes, in order to understand the relationship between continental precipitation, vegetation and sediment production. Our results indicate a two-phased HS1 (HS1a and HS1b). During HS1a (18–16.9 cal ka BP), a first sudden increase of sea surface temperatures (SST) in the western equatorial Atlantic correlated with the slowdown of the Atlantic Meridional Overturning Circulation (AMOC) and the associated southern hemisphere warming phase of the bipolar seesaw. This phase was also characterized by an increased delivery of terrestrial material. During HS1b (16.9–14.8 cal ka BP), a decrease in terrestrial input was, however, associated with a marked decline of seawater δ18O and palmitic acid δD. Both isotopic proxies independently indicate a drop in sea surface salinity (SSS). A number of records under the influence of the North Brazil Current, in contrast, indicate increases in SST and SSS resulting from a weakened AMOC during HS1. Our records thus suggest that the expected increase in SSS due to the AMOC slowdown was overridden by a two-phased positive precipitation anomaly in Amazonian hydroclimate.

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

The Lateglacial/early Holocene sediments from the ancient lake at Hässeldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hässeldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerød and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog.

Supplementation of gamma-aminobutyric acid (GABA) affects temporal, but not spatial visual attention

In a randomized, double-blind, and placebo-controlled experiment, the acute effects of gamma-aminobutyric acid (GABA) supplementation on temporal and spatial attention in young healthy adults were investigated. A hybrid two-target rapid serial visual presentation task was used to measure temporal attention and integration. Additionally, a visual search task was used to measure the speed and accuracy of spatial attention. While temporal attention depends primarily on the distribution of limited attentional resources across time, spatial attention represents the engagement and disengagement by relevant and irrelevant stimuli across the visual field. Although spatial attention was unaffected by GABA supplementation altogether, we found evidence supporting improved performance in the temporal attention task. The attentional blink was numerically, albeit not significantly, attenuated at Lag 3, and significantly fewer order errors were committed at Lag 1, compared to the placebo condition. No effect was found on temporal integration rates. Although there is controversy about whether oral GABA can cross the blood-brain barrier, our results offer preliminary evidence that GABA intake might help to distribute limited attentional resources more efficiently, and can specifically improve the identification and ordering of visual events that occur in close temporal succession.

Akinetes May Be Representative of Past Nostocalean Blooms: a Case Study of Their Benthic Spatiotemporal Distribution and Potential for Germination in a Eutrophic Lake.

Monitoring of water and surface sediment in a French eutrophic lake (Lake Aydat) was carried out over a 2-year period in order to determine whether akinetes in sediment could be representative of the most recent bloom and to estimate their germination potential. Sediment analysis revealed two akinete species, Dolichospermum macrosporum and Dolichospermumflos-aquae, present in the same proportions as observed for the pelagic populations. Moreover, similar spatial patterns observed for vegetative cells in the water column and akinete distributions in the sediment suggest that akinetes in the sediment may be representative of the previous bloom. However, the relationship between akinetes in the sediment and vegetative cells in the water column was not linear, and other factors may interfere. For example, our results highlighted horizontal transport of akinetes during the winter. The benthic overwinter phase did not seem to influence the percentages of intact akinetes, which remained stable at approximately 7% and 60% for D. macrosporum and D. flos-aquae, respectively. These percentages may thus be the result of processes that occurred in the water column. The intact overwintering akinetes showed germination rates of up to 90% after 72 h for D. flos-aquae or 144 h for D. macrosporum The difference in akinete germination rates between these two species demonstrates different ecological strategies, which serve to expand the window for germination in time and space and thus optimize colonization of the water column by nostocalean cyanobacteria.IMPORTANCE Cyanobacteria have the ability to proliferate and to form blooms. These blooms can then affect the local ecology, health, and economy. The akinete, a resistant cell type that persists in sediment, is an important intermediate phase between previous and future blooms. We monitored the water column and the surface sediment of a French eutrophic lake (Lake Aydat) to investigate the relationship between vegetative cells in the water column and akinetes in the sediment. This study focused on the characterization of spatiotemporal akinete distributions, cellular integrity, and germination potential. Species-specific ecological strategies were highlighted and may partly explain the temporal succession of species in the water column. Akinetes may also be used to understand past nostocalean blooms and to predict future ones.

Bio-Heat Is a Key Environmental Driver Shaping the Microbial Community of Medium-Temperature Daqu.

"Daqu" is a saccharifying and fermenting agent commonly used in the traditional solid-state fermentation industry (e.g., baijiu and vinegar). The patterns of microbial community succession and flavor formation are highly similar among batches, yet the mechanisms promoting temporal succession in the Daqu microbial ecology remain unclear. Here, we first correlated temporal profiles of microbial community succession with environmental variables (temperature, moisture, and titratable acidity) in medium temperature Daqu (MT-Daqu) throughout fermentation. Temperature dynamics significantly correlated (P < 0.05) with the quick succession of MT-Daqu microbiota in the first 12 d of fermentation, while the community structure was relatively stable after 12 d. Then, we explored the effect of temperature on the MT-Daqu community assembly. In the first 4 d of fermentation, the rapid propagation of most bacterial taxa and several fungal taxa, including Candida, Wickerhamomyces, and unclassified Dipodascaceae and Saccharomycetales species, significantly increased MT-Daqu temperature to 55°C. Subsequently, sustained bio-heat generated by microbial metabolism (53 to 56°C) within MT-Daqu inhibited the growth of most microbes from day 4 to day 12, while thermotolerant taxa, including Bacillus, unclassified Streptophyta, Weissella, Thermoactinomyces, Thermoascus, and Thermomyces survived or kept on growing. Furthermore, temperature as a major driving force on the shaping of MT-Daqu microbiota was validated. Lowering the fermentation temperature by placing the MT-Daqu in a 37°C incubator resulted in decreased relative abundances of thermotolerant taxa, including Bacillus, Thermoactinomyces, and Thermoascus, in the MT-Daqu microbiota. This study revealed that bio-heat functioned as a primary endogenous driver promoting the formation of functional MT-Daqu microbiota.IMPORTANCE Humans have mastered the Daqu preparation technique of cultivating functional microbiota on starchy grains over thousands of years, and it is well known that the metabolic activity of these microbes is key to the flavor production of Chinese baijiu. The pattern of microbial community succession and flavor formation remains highly similar between batches, yet mechanistic insight into these patterns and into microbial population fidelity to specific environmental conditions remains unclear. Our study revealed that bio-heat was generated within Daqu bricks in the first 4 d of fermentation, concomitant with rapid microbial propagation and metabolism. The sustained bio-heat may then function as a major endogenous driving force promoting the formation of the MT-Daqu microbiota from day 4 to day 12. The bio-heat-driven growth of thermotolerant microorganisms might contribute to the formation of flavor metabolites. This study provides useful information for the temperature-based modulation of microbiota function during the fermentation of Daqu.

Massive Mn carbonate formation in the Landsort Deep (Baltic Sea): Hydrographic conditions, temporal succession, and Mn budget calculations

The sediments of the Landsort Deep and Gotland Basin in the central Baltic Sea are strongly enriched in Mn carbonate. However, conceptual models attempting to explain the intense Mn carbonate precipitation in both basins are in part conflicting. In the Gotland Basin model, deposited Mn oxides are converted to Mn carbonate after the oxygenation of euxinic bottom waters enriched in dissolved Mn by major Baltic inflows (Huckriede and Meischner, 1996). By contrast, according to the Landsort Deep model, Mn carbonate precipitation occurs independent of oxygenation events below a euxinic water column (Lepland and Stevens, 1998; Lenz et al., 2015). In this study, we investigated Mn solid-phase signatures in recent/sub-recent well-dated sediments from the Landsort Deep and compared them to long-term observations to identify the hydrographic conditions favoring Mn carbonate formation. The comparisons of water column O2 and sulfide time series with sedimentary Mn carbonate enrichments identified long-lasting bottom water oxygenation as an important environmental factor in the enhancement of Mn carbonate precipitation (up to 32wt% Mn) in the Landsort Deep. Thus, by preventing the escape of dissolved Mn from still reducing sediments into the open water column, these conditions allow the accumulation of large amounts of Mn-oxide particles at the sediment/water interface, with their subsequent conversion to Mn carbonate. The euxinic conditions that have prevailed almost continuously in the Landsort Deep since roughly AD 2000 do not favor Mn enrichment (maximum 0.9wt% Mn), highlighting the importance of the recurring oxygenation of bottom water, most likely via medium-intensity inflows. The Mn abundances in seven sediment cores from water depths of 190–437m together with Mn balance calculations indicated that the Mn inventory in the water column in response to porewater Mn reflux and detrital Mn input is sufficient for Mn carbonate enrichment only in the deepest part of the basin.

Can fine-scale post-pollination variation of fig volatile compounds explain some steps of the temporal succession of fig wasps associated with Ficus racemosa?

Volatile organic compounds (VOCs) emitted by flowers play an essential role in mediating the attraction of pollinators. However, they also attract other species exploiting resources associated with flowers. For instance, VOCs emitted by figs play a major role in encounters between Ficus spp., their mutualistic pollinating wasps, and all the members of the community of non-pollinating fig wasps (NPFWs) that exploit the mutualistic interaction. Because pollinators might be in limited supply for a tree bearing many inflorescences, the plant might maximize its individual reproductive success by reducing the attractiveness of inflorescences once they are pollinated, so that pollinators orient only towards the tree's unpollinated figs. Changes in VOCs emission that bring this about could represent an important cue for NPFWs that exploit particular stages of fig development. In this study, by monitoring precisely the presence of fig-associated wasps on figs of F. racemosa, a common widespread fig species, we demonstrated that 4–5 days and 15 days following pollination represent two critical transitional steps in the succession of different wasp species. Then, focusing on the first one of these transitional steps, by investigating the composition of fig VOCs at receptivity and from 1 to 5 days following pollination, we detected progressive quantitative and qualitative variation of floral scent following pollination. These changes are significant at 5 days following pollination. The qualitative changes are mainly due to an increase in the relative proportions of two monoterpenes (α-pinene and limonene). These variations of the floral VOCs following pollination could explain why pollinating wasps stop visiting figs very shortly after the first pollinators enter receptive figs. They also possibly explain the succession of non-pollinating wasps on the figs following pollination.

Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics

Land application of animal manure is a common agricultural practice potentially leading to dispersal and propagation of antibiotic resistance genes (ARGs) in environmental settings. However, the fate of resistome in agro-ecosystems over time following application of different manure sources has never been compared systematically. Here, soil microcosm incubation was conducted to compare effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs. The high-throughput quantitative PCR detected a total of 185 unique ARGs, with Macrolide-Lincosamide-Streptogramin B resistance as the most frequently encountered ARG type. The diversity and abundance of ARGs significantly increased following application of manure and manure spiked with tylosin, with more pronounced effects observed in the swine and poultry manure treatments than in the cattle manure treatment. The level of antibiotic resistance gradually decreased over time in all manured soils but was still significantly higher in the soils treated with swine and poultry manures than in the untreated soils after 130 days’ incubation. Tylosin-amended soils consistently showed higher abundances of ARGs than soils treated with manure only, suggesting a strong selection pressure of antibiotic-spiked manure on soil ARGs. The relative abundance of ARGs had significantly positive correlations with integrase and transposase genes, indicative of horizontal transfer potential of ARGs in manure and tylosin treated soils. Our findings provide evidence that application of swine and poultry manures might enrich more soil ARGs than cattle manure, which necessitates the appropriate treatment of raw animal manures prior to land application to minimise the spread of environmental ARGs.

Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils

Composting has been suggested as a potential strategy to eliminate antibiotic residues and pathogens in livestock manure before its application as an organic fertilizer in agro-ecosystems. However, the impacts of composting on antibiotic resistance genes (ARGs) in livestock manure and their temporal succession following the application of compost to land are not well understood. We examined how aerobic composting affected the resistome profiles of cattle manure, and by constructing laboratory microcosms we compared the effects of manure and compost application to agricultural soils on the temporal succession of a wide spectrum of ARGs. The high-throughput quantitative PCR array detected a total of 144 ARGs across all the soil, manure and compost samples, with Macrolide-Lincosamide-Streptogramin B, aminoglycoside, multidrug, tetracycline, and β-lactam resistance as the most dominant types. Composting significantly reduced the diversity and relative abundance of ARGs and mobile genetic elements (MGEs) in the cattle manure. In the 120-day microcosm incubation, the diversity and abundance of ARGs in manure-treated soils were significantly higher than those in compost-treated soils at the beginning of the experiment. The level of antibiotic resistance rapidly declined over time in all manure- and compost-treated soils, coupled with similar temporal patterns of manure- and compost-derived bacterial communities as revealed by SourceTracker analysis. The network analysis revealed more intensive interactions/associations among ARGs and MGEs in manure-treated soils than in compost-treated soils, suggesting that mobility potential of ARGs was lower in soils amended with compost. Our results provide evidence that aerobic composting of cattle manure may be an effective approach to mitigate the risk of antibiotic resistance propagation associated with land application of organic wastes.

Reply to the comment on “First records of syn-diagenetic non-tectonic folding in Quaternary thermogene travertines caused by hydrothermal incremental veining” by Billi et alii

In our previous paper (Billi et al., 2017), using field geological observations, U-Th dating, and stable isotope analyses, we studied two deposits of Pleistocene thermogene travertines from Tuscany in central Italy. We concluded our study (1) warning that the common stratigraphic concept of travertine being a sedimentary succession with age younging from bottom to top is not always correct, (2) demonstrating that CaCO3 mineralization and veins can develop within the travertines after their formation with this syn-diagenetic process being able to modify the continuous bottom-up age evolution, and (3) showing that this post-depositional mineralization-veining process can not only modify the temporal succession but also deform and change the initial depositional travertine structure and its petrophysical properties. These conclusions could potentially make the interpretation of a travertine series more difficult than commonly thought. Alcicek et alii questioned our conclusions claiming that the travertine structures that we observed in Tuscany and interpreted as post-depositional features should have been interpreted, in analogy to similar structures from travertines elsewhere, as primary structures. Although we recognize, as already thoroughly stated in Billi et al. (2017), that the travertine depositional/post-depositional processes generally require further studies, we reaffirm the validity of our original interpretation at least for the structures analyzed in our previous paper. We, therefore, counter all criticisms by Alcicek et alii and conclude by indicating the way forward to further explore the depositional and post-depositional processes of thermogene travertines.