Engineering soil organic matter quality: Biodiesel Co-Product (BCP) stimulates exudation of nitrogenous microbial biopolymers

Biodiesel Co-Product (BCP) is a complex organic material formed during the transesterification of lipids. We investigated the effect of BCP on the extracellular microbial matrix or ‘extracellular polymeric substance’ (EPS) in soil which is suspected to be a highly influential fraction of soil organic matter (SOM). It was hypothesised that more N would be transferred to EPS in soil given BCP compared to soil given glycerol. An arable soil was amended with BCP produced from either 1) waste vegetable oils or 2) pure oilseed rape oil, and compared with soil amended with 99% pure glycerol; all were provided with 15N labelled KNO3. We compared transfer of microbially assimilated 15N into the extracellular amino acid pool, and measured concomitant production of exopolysaccharide. Following incubation, the 15N enrichment of total hydrolysable amino acids (THAAs) indicated that intracellular anabolic products had incorporated the labelled N primarily as glutamine and glutamate. A greater proportion of the amino acids in EPS were found to contain 15N than those in the THAA pool, indicating that the increase in EPS was comprised of bioproducts synthesised de novo. Moreover, BCP had increased the EPS production efficiency of the soil microbial community (μg EPS per unit ATP) up to approximately double that of glycerol, and caused transfer of 21% more 15N from soil solution into EPS-amino acids. Given the suspected value of EPS in agricultural soils, the use of BCP to stimulate exudation is an interesting tool to consider in the theme of delivering sustainable intensification

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize

Modern breeding primarily targets crop yield traits and is likely to influence root-associated microbiomes, which play significant roles in plant growth and health. The relative importance of soil and cultivar factors in shaping root-associated microbiomes of modern maize (Zea mays L.) remains uncertain. We conducted a pot experiment in a controlled environment using three soils (Mollisol, Inceptisol, and Ultisol) and four contrasting cultivars, Denghai 605, Nonghua 816, Qiaoyu 8, and Zhengdan 958, which are widely planted in China. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities in the bulk soil, rhizosphere, and endosphere. Our results showed that the four cultivars had different shoot biomass and root exudate total organic carbon and organic acid contents. The microbiomes in the bulk soil, rhizosphere, and endosphere were different. We observed apparent community divergence between soils rather than cultivars, within which edaphic factors substantially contributed to microbiome variation. Moreover, permutational multivariate analysis of variance corroborated significant contributions of soil type but not cultivar on the root-associated microbiome structure. Differential abundance analysis confirmed that each soil presented a distinct root microbiome, while network analysis indicated different co-occurrence patterns of the root microbiome among the three soils. The core root microbiome members are implicated in plant growth promotion and nutrient acquisition in the roots. In conclusion, root-associated microbiomes of modern maize are much more controlled by soil characteristics than by cultivar root exudation. Our study is anticipated to help improve breeding strategies through integrative interactions of soils, cultivars, and their associated microbiomes

Effects of cropping systems upon the three-dimensional architecture of soil systems are modulated by texture

Soil delivers fundamental ecosystem functions via interactions between physical and biological processes mediated by soil structure. The structure of soil is also dynamic and modified by natural factors and management intervention. The aim of this study was to investigate the effects of different cropping systems on soil structure at contrasting spatial scales. Three systems were studied in replicated plot field experiments involving varying degrees of plant-derived inputs to the soil, viz. perennial (grassland), annual (arable), and no-plant control (bare fallow), associated with two contrasting soil textures (clayey and sandy). We hypothesized the presence of plants results in a greater range (diversity) of pore sizes and that perennial cropping systems invoke greater structural heterogeneity. Accordingly, the nature of the pore systems was visualised and quantified in 3D by X-ray Computed Tomography at the mm and μm scale. Plants did not affect the porosity of clay soil at the mm scale, but at the μm scale, annual and perennial plant cover resulted in significantly increased porosity, a wider range of pore sizes and greater connectivity compared to bare fallow soil. However, the opposite occurred in the sandy soil, where plants decreased the porosity and pore connectivity at the mm scale but had no significant structural effect at the μm scale. These data reveal profound effects of different agricultural management systems upon soil structural modification, which are strongly modulated by the extent of plant presence and also contingent on the inherent texture of the soil

BTW—Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data

Recent advances in Next-Generation Sequencing (NGS) make comparative analyses of the composition and diversity of whole microbial communities possible at a far greater depth than ever before. This brings new challenges, such as an increased dependence on computation to process these huge datasets. The demand on system resources usually requires migrating from Windows to Linux-based operating systems and prior familiarity with command-line interfaces. To overcome this barrier, we developed a fully automated and easy-to-install package as well as a complete, easy-to-follow pipeline for microbial metataxonomic analysis operating in the Windows Subsystem for Linux (WSL)—Bioinformatics Through Windows (BTW). BTW combines several open-access tools for processing marker gene data, including 16S rRNA, bringing the user from raw sequencing reads to diversity-related conclusions. It includes data quality filtering, clustering, taxonomic assignment and further statistical analyses, directly in WSL, avoiding the prior need of migrating from Windows to Linux. BTW is expected to boost the use of NGS amplicon data by facilitating rapid access to a set of bioinformatics tools for Windows users. Moreover, several Linux command line tools became more reachable, which will enhance bioinformatics accessibility to a wider range of researchers and practitioners in the life sciences and medicine. BTW is available in GitHub (https://github.com/vpylro/BTW). The package is freely available for noncommercial users

Extraction of extracellular polymeric substances (EPS) from red soils (Ultisols)

Extracellular polymeric substances (EPS) have many beneficial functions in soils. Accurate quantification of EPS in soils is crucial. Here, five methods were compared for their suitability for extraction of EPS from Ultisols: hot water extractable polysaccharide (HWEP), hot dilute acid extractable polysaccharide (HDAEP), easily extractable glomalin (EEG), sodium sulfide (SS) and cation exchange resin (CER) method. Humic-acid equivalent (HAE) was used as an indicator for extracellular contamination and ATP for quantifying intracellular contamination from cell lysis. Among the tested methods, CER resulted in EPS extraction with minimal contamination. Therefore, we propose that CER is currently the most appropriate method for extraction of EPS from Ultisols

Microbial formation and stabilisation of soil organic carbon is regulated by carbon substrate identity and mineral composition

The view that soil organic C (SOC) is formed mainly from non-metabolised and recalcitrant organic residues is being challenged by an emerging view that metabolic by-products form more stable associations with soil minerals. However, the effects of C substrate identity and soil mineral composition (and interactions) on microbial physiology and SOC formation are still not well understood. We added contrasting substrates (glucose, alanine and a mixture of glucose, alanine, and oxalic acid) into artificial soils of varying mineral composition (montmorillonite, kaolinite, and kaolinite plus goethite and hematite) for 12 weeks. We found that glucose led to 1.45 and 1.75 times more SOC formation than alanine and the mixed substrate, respectively. Montmorillonite based soils gained approximately 1.3 times more SOC compared to the other two soils. Compared with kaolinite-only soils, the inclusion of goethite and hematite had a positive effect on total SOC, extracellular C and biologically stable C when amended with alanine, but a negative effect on these SOC fractions when amended with glucose. Soils with greater SOC formation were associated with high microbial C use efficiency (CUE) and extracellular C, suggesting that spatial allocation by the microbial biomass is pivotal for creating stable SOC. Fungi-dominated soils typically had a higher CUE, which was positively correlated with the formation of new SOC. These results suggest that the identity of plant inputs will have a strong bearing on the formation of SOC via interactions with the soil microbial community and soil mineralogy

Environmental horticulture for domestic and community gardens – an integrated and applied research approach

This article presents an integrated and applied research approach to the unique and multi-disciplinary area of science referred to here as Environmental Horticulture. It does this by: a) providing an institutional perspective (The Royal Horticultural Society) on a research approach for this particular area, emphasising why domestic and community gardens are important in the context of global environmental threats; b) presenting four primary research focus areas and project examples, and; c) highlighting interdisciplinary linkages, future research needs, public engagement / knowledge sharing opportunities, and “Green Skills” development in the area of environmental horticulture. Research focus areas discussed are: 1) responding to the changing climate (adaptation, mitigation and resilience solutions in gardens); 2) “plants for purpose” (harnessing the potential of horticultural plant diversity, and gardening, to help regulate environmental conditions); 3) sustainability and climate risk reduction through effective and efficient resource management (reduction, re-use, recycling and repurposing); and 4) gardening and cultivated plant choice for human health and wellbeing. We argue that a key research priority is improving our understanding of the linkages and interactions between soil, water, plants, weather and people. These crucial linkages affect above and below ground processes, for both outdoor and indoor plants. They impact the effectiveness with which water and nutrient cycling takes place, the extent to which ecosystem services may be delivered, and the resultant capacity of gardens and gardening to provide environmental and human health benefits

Experimental evidence for the impact of phages on mineralization of soil-derived dissolved organic matter under different temperature regimes

Microbial mineralization of dissolved organic matter (DOM) plays an important role in regulating C and nutrient cycling. Viruses are the most abundant biological agents on Earth, but their effect on the density and activity of soil microorganisms and, consequently, on mineralization of DOM under different temperatures remains poorly understood. To assess the impact of viruses on DOM mineralization, we added soil phage concentrate (active vs. inactive phage control) to four DOM extracts containing inoculated microbial communities and incubated them at 18 °C and 23 °C for 32 days. Infection with active phages generally decreased DOM mineralization at day one and showed accelerated DOM mineralization later (especially from day 5 to 15) compared to that with the inactivated phages. Overall, phage infection increased the microbially driven CO2 release. Notably, while higher temperature increased the total CO2 release, the cumulative CO2 release induced by phage infection (difference between active phages and inactivated control) was not affected. However, higher temperatures advanced the response time of the phages but shortening its active period. Our findings suggest that bacterial predation by phages can significantly affect soil DOM mineralization. Therefore, higher temperatures may accelerate host-phage interactions and thus, the duration of C recycling

Aliphatic hydrocarbon enhances phenanthrene degradation by autochthonous prokaryotic communities from a pristine seawater

The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9^-14C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9^-14C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community—from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems