Manipulating exudate composition from root apices shapes the microbiome throughout the root system.

Certain soil microorganisms can improve plant growth, and practices that encourage their proliferation around the roots can boost production and reduce reliance on agrochemicals. The beneficial effects of the microbial inoculants currently used in agriculture are inconsistent or short-lived because their persistence in soil and on roots is often poor. A complementary approach could use root exudates to recruit beneficial microbes directly from the soil and encourage inoculant proliferation. However, it is unclear whether the release of common organic metabolites can alter the root microbiome in a consistent manner and if so, how those changes vary throughout the whole root system. In this study, we altered the expression of transporters from the ALUMINUM-ACTIVATED MALATE TRANSPORTER and the MULTIDRUG AND TOXIC COMPOUND EXTRUSION families in rice (Oryza sativa L.) and wheat (Triticum aestivum L.) and tested how the subsequent release of their substrates (simple organic anions, including malate, citrate, and γ-amino butyric acid) from root apices affected the root microbiomes. We demonstrate that these exudate compounds, separately and in combination, significantly altered microbiome composition throughout the root system. However, the root type (seminal or nodal), position along the roots (apex or base), and soil type had a greater influence on microbiome structure than the exudates. These results reveal that the root microbiomes of important cereal species can be manipulated by altering the composition of root exudates, and support ongoing attempts to improve plant production by manipulating the root microbiome.

The microbiomes on the roots of wheat (Triticum aestivum L.) and rice (Oryza sativa L.) exhibit significant differences in structure between root types and along root axes.

There is increasing interest in understanding how the microbial communities on roots can be manipulated to improve plant productivity. Root systems are not homogeneous organs but are comprised of different root types of various ages and anatomies that perform different functions. Relatively little is known about how this variation influences the distribution and abundance of microorganisms on roots and in the rhizosphere. Such information is important for understanding how root-microbe interactions might affect root function and prevent diseases. This study tested specific hypotheses related to the spatial variation of bacterial and fungal communities on wheat (Triticum aestivum L.) and rice (Oryza sativa L.) roots grown in contrasting soils. We demonstrate that microbial communities differed significantly between soil type, between host species, between root types, and with position along the root axes. The magnitude of variation between different root types and along individual roots was comparable with the variation detected between different plant species. We discuss the general patterns that emerged in this variation and identify bacterial and fungal taxa that were consistently more abundant on specific regions of the root system. We argue that these patterns should be measured more routinely so that localised root-microbe interactions can be better linked with root system design, plant health and performance.

Wastewater Treatment Processing of Silver Nanoparticles Strongly Influences Their Effects on Soil Microbial Diversity.

Silver nanoparticles (NPs) are entering soils with biosolids via wastewater treatment, and on-route, undergo changes (e.g., sulfidation) that alter silver bioavailability and toxicity. While additions of fresh Ag-NPs to soil have been show to influence bacterial diversity, it is unclear whether these effects are representative of realistic exposure pathways. To investigate the effects of wastewater treatment processing on the ecotoxicology of Ag-NPs, we ran sequencing batch reactors for 28 d to produce three batches of sludge: (1) a control, (2) Ag-NP sludge, and (3) AgNO3 sludge. The effects of processed silver on the diversity and composition of soil bacterial and fungal communities were compared to those of fresh Ag-NPs, Ag2S-NPs, and AgNO3, which were added with the control sludge, at two concentrations (1 and 10 mg Ag kg-1 dry soil) over time (3, 7, 30, and 90 d). The effects of processed Ag-NPs on the composition of soil bacterial communities were larger and more persistent than those of fresh Ag-NPs, Ag2S-NPs, and AgNO3. Treatment effects on fungi were relatively minor. These findings suggest that the potential ecological impacts of Ag-NPs entering soils via more realistic exposure pathways (e.g., sludge) are underestimated when extrapolated from studies that focus on applications of fresh Ag-NPs.

Silver Sulfide Nanoparticles Reduce Nitrous Oxide Emissions by Inhibiting Denitrification in the Earthworm Gut.

The accumulation of Ag2S in agricultural soil via application of Ag-containing sludge potentially affects the functioning of soil microorganisms and earthworms (EWs) due to the strong antimicrobial properties of Ag. This study examined the effects of Ag2S nanoparticles (Ag2S-NPs) on the EW-mediated (Eisenia fetida and Pontoscolex corethrurus) soil N cycle. We used 16S rRNA gene-based sequencing and quantitative polymerase chain reaction to examine the bacterial community and nitrification/denitrification-related gene abundance. The presence of either EWs or Ag significantly increased denitrification and N2O emissions. However, the addition of Ag2S to EW-inhabited soil reduced N2O emissions by 14-33%. Furthermore, Ag2S caused a low-dose stimulation but a high-dose inhibition to N2O flux from the EW gut itself. Accordingly, an increase in Ag in the EW gut caused a decrease in the relative abundance of denitrifiers in both the soil and the gut, especially for the dominant genus Bacillus. Ag2S also decreased the copy numbers of nitrification gene (nxrB) and denitrification genes (napA, nirS, and nosZ) in EW gut, leading to the observed decrease in N2O emissions. Collectively, applying Ag2S-containing sludge disturbs the denitrification function of the EW gut microbiota and the cycling of N in soil-based systems.

Soil chloride content influences the response of bacterial but not fungal diversity to silver nanoparticles entering soil via wastewater treatment processing.

Silver nanoparticles (NPs) are among the most widely used nanomaterials and are entering soil ecosystems, mainly via biosolids in agriculture. When added directly to soils, metallic Ag-NPs have been shown to affect microbial communities, which underpin important ecosystem functions. During wastewater treatment processing, metallic Ag-NPs are rapidly converted to Ag2S, which is relatively insoluble and less toxic. Furthermore, recent evidence indicates that silver bioavailability is influenced by soil chloride content. Hence there is a need to understand how Ag2S, which forms from Ag-NPs during wastewater treatment, influences soil microbial diversity at varying salinity. In this study, after adding Ag-NPs to sludge (with most converted to Ag2S), we then applied the sludge to soil and examined how salinity influences the effects of 0 mg, 1 mg and 10 mg kg-1 Ag on bacterial and fungal diversity over time. Using high-throughput phylogenetic marker gene sequencing of 16S rRNA gene and ITS2 amplicons, we demonstrate that, despite being theoretically less toxic, wastewater treatment processed Ag-NPs can affect the composition of soil bacterial and fungal communities, and influence bacterial alpha diversity. In addition, we found that silver-associated changes in bacterial community composition were affected by soil chloride content, with more acute responses to silver being observed in more saline soils. This work highlights that the release of Ag-NPs and their conversion into Ag2S prior to addition to soils via realistic exposure pathways can alter microbial diversity and that these effects may be influenced by soil chloride content.

Effects of carbon nanotubes and derivatives of graphene oxide on soil bacterial diversity.

Carbon nanotubes (CNTs), reduced graphene oxide (rGO) and ammonia-functionalized graphene oxide (aGO), are nanomaterials with useful properties, such as high tensile strength, elasticity and thermal conductivity. However, following their use, their release into the environment is inevitable. While CNTs have been shown to influence soil bacterial diversity, albeit only at concentrations far exceeding predicted rates of release, the effects of rGO have only been examined using pure bacterial cultures, and those of aGO are unknown. Here, we investigated the effects of CNTs, rGO and aGO, at three time points (7, 14 and 30days), and over a range of concentrations (1ng, 1µg and 1mgkg dry soil-1), on soil bacterial diversity using 16S rRNA amplicon sequencing. Graphite was included to facilitate comparisons with a similar and naturally occurring carbon material, while the inclusion of GO allowed the effects of GO modification to be isolated. Bacterial community composition, but not alpha diversity, was altered by all treatments except the low GO, low rGO and high aGO treatments on day 14 only. In all cases, the nanomaterials led to shifts in community composition that were of similar magnitude to those induced by graphite and GO, albeit with differences in the taxa affected. Our study highlights that carbon nanomaterials can induce changes in soil bacterial diversity, even at doses that are environmentally realistic.

Effects of graphene oxide and graphite on soil bacterial and fungal diversity.

Graphene oxide (GO) is an oxidized form of graphene that is relatively cheap and easy to produce. This has heralded its widespread use in a range of industries, with its likelihood of release into the environment increasing accordingly. In pure culture, GO has been shown to influence bacteria and fungi, but its effects on environmental microbial communities remain poorly characterized, despite the important ecosystem services that these organisms underpin. Here, we characterized the effects of GO and graphite, over time (7, 14 and 30 days) and at three concentrations (1 ng, 1 µg and 1 mg kg dry soil-1), on soil bacterial and fungal diversity using 16S rRNA and ITS2 gene amplicon sequencing. Graphite was included as a reference material as it is widely distributed in the environment. Neither GO or graphite had significant effects on the alpha diversity of microbial communities. The composition of bacterial and fungal communities, however, was significantly influenced by both materials at all doses. With the exception of the lowest GO dose on day 14, these effects were apparent for all treatments over the course of the experiment. Nonetheless, the effects of GO and graphite were of similar magnitude, albeit with some differences in the taxa affected.

The effects of glyphosate, glufosinate, paraquat and paraquat-diquat on soil microbial activity and bacterial, archaeal and nematode diversity.

In this study, we investigated the effects of one-off applications of glyphosate, glufosinate, paraquat, and paraquat-diquat on soil microbial diversity and function. All herbicides were added to soil as pure compounds at recommended dose and were incubated under laboratory conditions for 60 days. High-throughput phylogenetic marker gene sequencing revealed that none of the herbicides significantly influenced the richness, evenness and composition of bacterial and archaeal communities. Likewise, the diversity, composition and size of nematode communities were not significantly influenced by any of the herbicides. From a functional perspective, herbicides did not significantly affect fluorescein diacetate hydrolysis (FDA) and beta-glucosidase activities. Furthermore, the ability of soil organisms to utilise 15 substrates was generally unaffected by herbicide application. The only exception to this was a temporary impairment in the ability of soil organisms to utilise three organic acids and an amino acid. Given the global and frequent use of these herbicides, it is important that future studies evaluate their potential impacts on microbial communities in a wider-range of soils and environmental conditions.

Plasmacytoid dendritic cells protect from viral bronchiolitis and asthma through semaphorin 4a-mediated T reg expansion.

Respiratory syncytial virus-bronchiolitis is a major independent risk factor for subsequent asthma, but the causal mechanisms remain obscure. We identified that transient plasmacytoid dendritic cell (pDC) depletion during primary Pneumovirus infection alone predisposed to severe bronchiolitis in early life and subsequent asthma in later life after reinfection. pDC depletion ablated interferon production and increased viral load; however, the heightened immunopathology and susceptibility to subsequent asthma stemmed from a failure to expand functional neuropilin-1+ regulatory T (T reg) cells in the absence of pDC-derived semaphorin 4a (Sema4a). In adult mice, pDC depletion predisposed to severe bronchiolitis only after antibiotic treatment. Consistent with a protective role for the microbiome, treatment of pDC-depleted neonates with the microbial-derived metabolite propionate promoted Sema4a-dependent T reg cell expansion, ameliorating both diseases. In children with viral bronchiolitis, nasal propionate levels were decreased and correlated with an IL-6high/IL-10low microenvironment. We highlight a common but age-related Sema4a-mediated pathway by which pDCs and microbial colonization induce T reg cell expansion to protect against severe bronchiolitis and subsequent asthma.

Silver Nanoparticles Entering Soils via the Wastewater-Sludge-Soil Pathway Pose Low Risk to Plants but Elevated Cl Concentrations Increase Ag Bioavailability.

The widespread use of silver nanoparticles (Ag-NPs) results in their movement into wastewater treatment facilities and subsequently to agricultural soils via application of contaminated sludge. On-route, the chemical properties of Ag may change, and further alterations are possible upon entry to soil. In the present study, we examined the long-term stability and (bio)availability of Ag along the "wastewater-sludge-soil" pathway. Synchrotron-based X-ray absorption spectroscopy (XAS) revealed that ca. 99% of Ag added to the sludge reactors as either Ag-NPs or AgNO3 was retained in sludge, with ≥79% of this being transformed to Ag2S, with the majority (≥87%) remaining in this form even after introduction to soils at various pH values and Cl concentrations for up to 400 days. Diffusive gradients in thin films (DGT), chemical extraction, and plant uptake experiments indicated that the potential (bio)availability of Ag in soil was low but increased markedly in soils with elevated Cl, likely due to the formation of soluble AgClx complexes in the soil solution. Although high Cl concentrations increased the bioavailability of Ag markedly, plant growth was not reduced in any treatment. Our results indicate that Ag-NPs entering soils through the wastewater-sludge-soil pathway pose low risk to plants due to their conversion to Ag2S in the wastewater treatment process, although bioavailability may increase in saline soils or when irrigated with high-Cl water.

[Splitting into two lines: The historical development of the analytical and the gas ultracentrifuge]. / Zwei Entwicklungslinien einer Forschungstechnologie: Zur Geschichte der Analytischen Ultrazentrifugen und Gasultrazentrifugen.

In a historical perspective the ultracentrifuge is often taken as perfect example of a research technology according to Shinn and Joerges (Shinn and Joerges 2000, 2002). Research technologies are defined by a generic device, its own metrology and the interstitiality of the historical actors connected with the device. In our paper we give a detailed analysis of the development of the ultracentrifuge and thereby reveal two different lines of development: analytical ultracentrifuges and gas ultra centrifuges used for isotope separation. Surprisingly, we could not find any interstitial and transversal connections for these two lines. The lines end up with two different devices based on two different technical concepts. Moreover, the great majority of the actors stick to one line. These results are in accordance withother authors, who developed the concept of research technologies further and tried to sharpen their definition.