The influence of aggregate size fraction and horizon position on microbial community composition

peer-reviewedThe influence of horizon position and aggregate size on bacterial and fungal community composition was determined. From nine sites, soils were collected from the top three horizon positions (H1, H2 and H3). Physical fractionation separated samples into large macroaggregate (LM, >2000 μm), macroaggregate (MAC, >250 μm), microaggregate (MIC, <250 μm), and silt and clay (SC, 53 μm) fractions. In all samples, the structure of the bacterial and fungal community composition was assessed via restriction fragment length polymorphism (T-RFLP), and for the four aggregate sizes from the top two horizons positions an in-depth analysis of the bacterial community was conducted using next generation sequencing (NGS). Bacterial and fungal communities both differed between aggregate-sizes. Changes in the composition of the bacterial and fungal communities also occurred among horizon positions, with a significant interaction between aggregate size and horizon position evident for the bacterial community. Using NGS, it was shown that aggregate-size had a significant effect on the bacterial community in both horizon positions at both the phyla and family taxonomic levels. MAC and MIC significantly differed in the % relative abundance of bacterial groups, potentially indicating differing predation pressures. These results indicate that both horizon position and aggregate size support distinct microbial communities. Understanding these parameters is critical in our comprehension of the patterns of microbial diversity in soil

Exploring Climate‐Smart Land Management for Atlantic Europe

peer-reviewedCore Ideas Managing soil organic carbon is an essential aspect of climate‐smart agriculture. Combining component research, we derive a soil carbon management concept for Ireland. Optimized soil carbon management is differentiated in accordance with soil type. Existing policy tools can be tailored to incentivize climate‐smart land management. Soils can be a sink or source of carbon, and managing soil carbon has significant potential to partially offset agricultural greenhouse gas emissions. While European Union (EU) member states have not been permitted to account for this offsetting potential in their efforts to meet the EU 2020 reduction targets, this policy is now changing for the period 2020 to 2030, creating a demand for land management plans aimed at maximizing the offsetting potential of land. In this letter, we derive a framework for climate‐smart land management in the Atlantic climate zone of the EU by combining the results from five component research studies on various aspects of the carbon cycle. We show that the options for proactive management of soil organic carbon differ according to soil type and that a spatially tailored approach to land management will be more effective than blanket policies.Research Stimulus Fun

C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays

Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, the conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggest that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells

Soils and Carbon Storage

Soils act as both sources and sinks of atmospheric C and as such there is great interest in investigating the impact of land use and land use change on C stocks in soils. Peatlands occupy ~20% of the irish landscape and store 75% of all C stocks. While pristine peatlands are long term C sinks, drainage and land use may change these systems to sources of soil C. Forests are generally recognised to be C sinks although the role of soil differs between soil types. Studies to date suggest that afforested Gley soils are C sinks while afforested Brown Earths may lose C. Grassland is the dominant land use and site based studies suggest that it could be a C sink of 0.5 t C ha−1 year−1. Cropland is a net C source with cultivation being the principal driver of this loss. Options to maintain or enhance C stocks in tillage systems include the use of cover crops, straw and manure incorporation and a move to minimum tillage. Despite the progress that has been made in quantifying C stocks in Irish soils and in understanding the impact of land use on soil C stocks many information gaps remain

Microbial community structure and function respond more strongly to temporal progression than to the application of slurry in an Irish grassland

The application of slurry to grassland for fertilization purposes is common practice, but its effect on the soil microbiota is mostly overlooked. This study investigated the short term response of the functionality and composition of the soil microbiome to slurry application. A 180 m2 field was divided into 36 plots. Slurry was splash-plate applied at a rate of 30 t ha−1. Sampling was conducted 5, 30 and 65 days after application. The functionality of the soil microbial community was examined using assays on 8 carbon cycling enzymes as well as basal respiration analysis. Microbial community structure was analysed via bacterial 16S rRNA gene and fungal internal transcribed spacer region terminal restriction fragment length polymorphism. Bacterial and fungal abundance was determined via quantitative PCR aiming at the same genetic targets. Furthermore, microbial biomass carbon and nitrogen were quantified. A significant increase in enzymatic activity with slurry treatment was reported on days 5 and 65, indicating a sequential response of the microbiota to slurry-derived carbon with the utilization of labile carbon on day 5 and the more stable carbon on day 65. This activity seemingly resulted from the microbial demand for N. In contrast, T-RFLP revealed that only bacterial community structures on day 5 were significantly affected by slurry application, all other bacterial and all fungal communities were not significantly altered by slurry. However, bacterial and fungal community structures, microbial biomass carbon and basal respiration significantly responded to temporal progression (day 5, 30 and 65). These findings suggest that soil microbial communities are responding to slurry applications via enhanced microbial activity but their structure remains largely unchanged with temporal progression having a greater impact.</p

Direct Synthesis of Amides from Carboxylic Acids and Amines Using B(OCH₂CF₃)₃

B­(OCH₂CF₃)₃, prepared from readily available B₂O₃ and 2,2,2-trifluoroethanol, is as an effective reagent for the direct amidation of a variety of carboxylic acids with a broad range of amines. In most cases, the amide products can be purified by a simple filtration procedure using commercially available resins, with no need for aqueous workup or chromatography. The amidation of <i>N</i>-protected amino acids with both primary and secondary amines proceeds effectively, with very low levels of racemization. B­(OCH₂CF₃)₃ can also be used for the formylation of a range of amines in good to excellent yield, via transamidation of dimethylformamide

Organic &amp; Biomolecular Chemistry B(OCH 2 CF 3 ) 3 -mediated direct amidation of pharmaceutically relevant building blocks in cyclopentyl methyl ether †

The use of B(OCH 2 CF 3 ) 3 for mediating direct amidation reactions of a wide range of pharmaceutically relevant carboxylic acids and amines is described, including numerous heterocycle-containing examples. An initial screen of solvents for the direct amidation reaction suggested that cyclopentyl methyl ether, a solvent with a very good safety profile suitable for use over a wide temperature range, was an excellent replacement for the previously used solvent acetonitrile. Under these conditions amides could be prepared from 18 of the 21 carboxylic acids and 18 of the 21 amines examined. Further optimisation of one of the low yielding amidation reactions (36% yield) via a design of experiments approach enabled an 84% yield of the amide to be obtained

Effects of soil type and depth on carbon distribution within soil macroaggregates from temperate grassland systems

Grassland soils have been highlighted as a global soil carbon (C) sink, and have the potential to sequester additional C. Sequestration of C can occur through incorporation of soil organic carbon (SOC) within microaggregates and the silt and clay fractions. The distribution of SOC within macroaggregate fractions gives an insight into both SOC dynamics and its incorporation into the soil. Research to date on soil C has tended to focus on the topsoil (0–30 cm). While many studies have assessed the changes in aggregation and SOC dynamics after land use or management change, this paper assesses aggregation and SOC dynamics in the topsoil and subsoil of twenty-one temperate grassland sites covering four soil types (Haplic Luvisol, Haplic Stagnosol, Haplic Cambisol, Stagnic Cambisol). Results show that there are no differences in SOC between soil types in the surface 0–30 cm, except a decrease in the quantity of microaggregates within macroaggregates in Haplic Stagnosols. In the subsoil, the silt and clay fraction of clay-illuviated soils had a lower percentage of SOC. Soils with clay illuviation and reducing conditions had a decreased proportion of SOC in microaggregates and silt plus clay within small macroaggregates in the subsoil. This could be caused by a combination of (i) reduced incorporation of SOC into smaller fractions, because POM inputs could be limited due to soil saturation limiting root growth, and (ii) reduced mineralisation and subsequent incorporation of POM into microaggregates and silt plus clay within macroaggregates. These results enable elucidation of the mechanisms driving aggregate formation (and thus C sequestration in microaggregates and silt plus clay fractions) in topsoil and subsoil. This study shows that the dynamics of SOC in subsoil horizons is soil-type dependant and that differences between soil types cannot be elucidated when the sampling is limited to 30 cm. This suggests that the IPCC guidelines for SOC measurements should also include the sampling of subsoil horizons in order to get valuable information that allows discerning between soil types

The influence of aggregate size fraction and horizon position on microbial community composition

The influence of horizon position and aggregate size on bacterial and fungal community composition was determined. From nine sites, soils were collected from the top three horizon positions (H1, H2 and H3). Physical fractionation separated samples into large macroaggregate (LM, >2000 μm), macroaggregate (MAC, >250 μm), microaggregate (MIC, <250 μm), and silt and clay (SC, 53 μm) fractions. In all samples, the structure of the bacterial and fungal community composition was assessed via restriction fragment length polymorphism (T-RFLP), and for the four aggregate sizes from the top two horizons positions an in-depth analysis of the bacterial community was conducted using next generation sequencing (NGS). Bacterial and fungal communities both differed between aggregate-sizes. Changes in the composition of the bacterial and fungal communities also occurred among horizon positions, with a significant interaction between aggregate size and horizon position evident for the bacterial community. Using NGS, it was shown that aggregate-size had a significant effect on the bacterial community in both horizon positions at both the phyla and family taxonomic levels. MAC and MIC significantly differed in the % relative abundance of bacterial groups, potentially indicating differing predation pressures. These results indicate that both horizon position and aggregate size support distinct microbial communities. Understanding these parameters is critical in our comprehension of the patterns of microbial diversity in soil