Phthalate acid esters (PAEs) are commonly used plastic additives, not chemically bound to the plastic that migrate into surrounding environments, posing a threat to environmental and human health. ...Dibutyl phthalate (DBP) and di(2-ethylhexyl) phthalate (DEHP) are two common PAEs found in agricultural soils, where degradation is attributed to microbial decomposition. Yet the impact of the plastic matrix on PAE degradation rates is poorly understood. Using 14C-labelled DBP and DEHP we show that migration from the plastic matrix into soil represents a key rate limiting step in their bioavailability and subsequent degradation. Incorporating PAEs into plastic film decreased their degradation in soil, DBP (DEHP) from 79% to 21% (9% to <1%), over four months when compared to direct application of PAEs. Mimicking surface soil conditions, we demonstrated that exposure to ultraviolet radiation accelerated PAE mineralisation twofold. Turnover of PAE was promoted by the addition of biosolids, while the presence of plants and other organic residues failed to promote degradation. We conclude that PAEs persist in soil for longer than previously thought due to physical trapping within the plastic matrix, suggesting PAEs released from plastics over very long time periods lead to increasing levels of contamination.
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•Method developed to study in-situ breakdown of phthalate acid esters (PAEs) in soil.•DBP migrated from the PVC plastic matrix and degraded much faster than DEHP.•Migration of DBP and DEHP from plastic is a key rate limiting step in degradation.•PAE degradation was accelerated by UV exposure and addition of some biosolids.•PAEs can persists in soil for longer than previously thought.
Dissolved organic matter (DOM) represents a key component of carbon (C) cycling in freshwater ecosystems. While the behaviour of bulk dissolved organic carbon (DOC) in aquatic ecosystems is well ...studied, comparatively little is known about the turnover of specific DOC compounds. The aim of this study was to investigate the persistence of
C-labelled low molecular weight (LMW) DOC at a wide range of concentrations (0.1 µM to 10 mM), in sediments and waters from oligotrophic and mesotrophic rivers within the same catchment. Overall, rates of DOC loss varied between compound groups (amino acids > sugars = organic acids > phenolics). Sediment-based microbial communities contributed to higher DOC loss from river waters, which was attributed, in part, to its greater microbial biomass. At higher DOC compound concentrations, DOC loss was greater in mesotrophic rivers in comparison to oligotrophic headwaters. A lag-phase in substrate use within sediments provided evidence of microbial growth and adaptation, ascribed here to the lack of inorganic nutrient limitation on microbial C processing in mesotrophic communities. We conclude that the higher microbial biomass and available inorganic nutrients in sediments enables the rapid processing of LMW DOC, particularly during high C enrichment events and in N and P-rich mesotrophic environments.
Dissolved organic matter (DOM) plays an important role in freshwater biogeochemistry. To investigate the influence of catchment character on the quality and quantity of DOM in freshwaters, 45 ...sampling sites draining subcatchments of contrasting soil type, hydrology, and land cover within one large upland-dominated and one large lowland-dominated catchment were sampled over a 1-yr period. Dominant land cover in each subcatchment included: arable and horticultural, blanket peatland, coniferous woodland, and improved, unimproved, acid, and calcareous grasslands. The composition of the C, N, and P pool was determined as a function of the inorganic nutrient species (NO₃⁻, NO₂⁻, NH₄⁺, and PO₄3−) and dissolved organic nutrient (dissolved organic carbon DOC, dissolved organic nitrogen DON, and dissolved organic phosphorus DOP) concentrations. DOM quality was assessed by calculation of the molar DOC : DON and DOC : DOP ratios and specific ultraviolet absorbance (SUVA254). In catchments with little anthropogenic nutrient inputs, DON and DOP typically composed > 80% of the total dissolved nitrogen (TDN) and total dissolved phosphorus (TDP) concentrations. By contrast, in heavily impacted agricultural catchments DON and DOP typically comprised 5–15% of TDN and 10–25% of TDP concentrations. Significant differences in DOC : DON and DOC : DOP ratios were observed between land cover class with significant correlations observed between both the DOC : DON and DOC : DOP molar ratios and SUVA254 (r
s = 0.88 and 0.84, respectively). Analysis also demonstrated a significant correlation between soil C : N ratio and instream DOC : DON/DOP (r
s = 0.79 and 0.71, respectively). We infer from this that soil properties, specifically the C : N ratio of the soil organic matter pool, has a significant influence on the composition of DOM in streams draining through these landscapes.
Abstract
Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be ...investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host–microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.
We identify research questions in the field of microbial ecology, with emerging themes that recognise vast microbial functions that could benefit humanity, and the need to integrate knowledge across organisms.
In fresh waters, the origins of dissolved organic matter (DOM) have been found to exert a fundamental control on its reactivity, and ultimately, its ecosystem functional role. A detailed ...understanding of landscape scale factors that control the export of DOM to aquatic ecosystems is, therefore, pivotal if the effects of DOM flux to fresh waters are to be fully understood. In this study we present data from a national sampling campaign across the United Kingdom in which we explore the variability in DOM composition in three broad landscape types defined by similar precipitation, geology, land use and management, hydrology, and nutrient enrichment status. We characterised samples from fifty-one sites, grouping them into one of three major underlying classifications: circumneutral streams underlain by clay and mudstone (referred to as ‘clay’), alkaline streams underlain by Cretaceous Chalk or by Carboniferous or Jurassic Limestone (‘limestone’), and acidic streams in peatland catchments underlain by a range of low permeability lithologies (‘peat’). DOM composition was assessed through organic matter stoichiometry (organic carbon: organic nitrogen; organic carbon: organic phosphorus; C/N(P)
DOM
) and metrics derived from ultra-violet (UV)/visible spectroscopic analysis of DOM such as specific UV absorption (a
254
nm; SUVA
254
). We found similar SUVA
254
, C/N
DOM
and DOM/a
254
relationships within classifications, demonstrating that despite a large degree of heterogeneity within environments, catchments with shared environmental character and anthropogenic disturbance export DOM with a similar composition and character. Improving our understanding of DOM characterisation is important to help predict shifts in stream ecosystem function, and ecological responses to enrichment or mitigation efforts and how these may result in species composition shifts and biodiversity loss in freshwater ecosystems.
Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments ...from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with
and
spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.
Rapidly assessing biodiversity is essential for environmental monitoring; however, traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based ...assessment offers enhanced scope for assessing biodiversity, while also increasing sampling efficiency and reducing processing time, compared to traditional methods. Here we investigated the effects of landuse and seasonality on headwater community richness and functional diversity, via spatio-temporal dynamics, using both eDNA and traditional sampling. We found that eDNA provided greater resolution in assessing biodiversity dynamics in time and space, compared to traditional sampling. Community richness was seasonally linked, peaking in spring and summer, with temporal turnover having a greater effect on community composition compared to localized nestedness. Overall, our assessment of ecosystem function shows that community formation is driven by regional resource availability, implying regional management requirements should be considered. Our findings show that eDNA based ecological assessment is a powerful, rapid and effective assessment strategy that enables complex spatio-temporal studies of community diversity and ecosystem function, previously infeasible using traditional methods.
The leaching of base cations in acidic soils can result in calcium (Ca2+) and magnesium (Mg2+) deficiencies, which are important for microbial cell function. We aimed to determine if microbial carbon ...use efficiency (CUE) and microbial biomass carbon (MBC) were limited in acidic soils due to a lack of base cations. Microbial CUE across a range of agricultural soils (n = 970; pHCa 3.4–7.9) treated with either deionised H2O (control) or a solution of 300 mM CaCl2 + 300 mM MgCl2 (+Base cations) was determined using a14C radioisotope tracer approach. Our results showed that the addition of base cations significantly increased microbial CUE (by up to 20%) at pHCa < 4.7; which coincided with a steep increase in exchangeable acidity. Base cation addition significantly increased MBC in nil-limed soils (pHCa 4.6) from 494 mg C kg−1 to 769 mg C kg−1 when plant residue was added, but not in limed soils (pHCa 6.2). Our findings indicate that the addition of base cations to highly acidic soils can increase microbial growth, thus aiding with carbon sequestration in these agricultural soils.
•Microbial biomass in acidic soils was limited by availability of base cations.•Microbial carbon use efficiency (CUE) declined below pHCa 5.5.•No evidence of Al3+ toxicity on microbial CUE after adding base cations.•Adding base cations overcomes microbial CUE limitations in acidic soils.
Herbal leys (multispecies swards) can potentially deliver greater agronomic and environmental benefits than conventional grass-clover swards in grazed agroecosystems. However, despite their ...popularity in agri-environment schemes, little is known about the effect of herbal leys on soil physical (e.g., porosity), chemical (e.g., carbon), and biological (e.g., soil fauna) characteristics. In the UK, a 2-ha replicated-field experiment utilising a herbal or grass-clover ley (n = 3 per sward) aimed to investigate the effect of sward type on soil quality. Each sward was rotationally grazed by weaned lambs (3.2 LU ha−1) over two grazing seasons, with soil physiochemical and biological characteristics assessed after 2-years using techniques such as X-ray micro-Computed Tomography (µCT) and microbial shallow shotgun sequencing. Soil chemical characteristics (e.g., pH) were unaffected by sward type. Similarly, topsoil (0–10 cm) organic carbon stocks measured after 2-years did not differ between the herbal (26.1 ± 1.1 t C ha−1) and grass-clover ley (25.7 ± 1.1 t C ha−1). X-ray µCT analysis revealed greater pore connectivity (Euler number) in grass-clover ley intact soil cores (0–10 cm depth, 7.5 cm width) than herbal ley cores dominated by Plantago lanceolata (p = 0.008). However, there was no sward-type difference in aggregate stability or general pore characteristics, determined using X-ray µCT, in air-dried 4 mm aggregates obtained from 0–5 or 5–10 cm depth, nor did sward type affect earthworm abundance, microbial community composition or the functional gene profile. This study is the first to explore the effects of a commercial herbal ley on physical, chemical, and biological soil quality indicators in a rotationally grazed sheep pasture. While no improvements in soil quality indicators were observed after 2-years, these findings have significant implications for agri-environment schemes promoting herbal leys to achieve soil quality and sustainability, with further research needed to optimise the seed mixture and management regime to deliver greater long-term below-ground ecosystem service benefits.
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•Increasing grassland species richness can improve soil quality.•X-ray µCT showed greatest pore connectivity in intact grass-clover ley cores.•Sward type did not affect soil physical or chemical characteristics.•Sward diversity did not affect earthworm abundance or microbial community composition.
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