Cooperative microbial interactions drive spatial segregation in porous environments.

The role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.

Transcriptomic and metabolomic changes in lettuce triggered by microplastics-stress.

Microplastics (MPs) are a global threat to the environment, and plant uptake of MP particles (≤0.2 µm) is a particular cause for concern. However, physiological and molecular mechanisms underlying MP-induced growth inhibition need to be clarified. Towards this goal, we conducted a hydroponic experiment to investigate the accumulation of MPs, changes in physiology, gene expression, and metabolites in lettuce from a series of concentrations of fluorescence-labelled polystyrene MPs (0, 10, 20, 30, 40, 50 mg L-1, ∼0.2 µm). Our results showed that MPs accumulated in the lettuce root tips and leaf veins, resulting in the hypertonic injury of lettuce, and the down-regulation of genes related to ion homeostasis. Stress-related genes were up-regulated, and sphingolipid metabolism increased in response to MP additions, causing increased biosynthesis of ascorbic acid, terpenoid, and flavonoids in root exudates. Our findings provide a molecular-scale perspective on the response of leafy vegetables to MP-stress at a range of concentrations. This enables more comprehensive evaluation of the risks of MPs to human health and the ecological environment.

Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants.

The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.

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.

Influence of surface coatings on the adhesion of Shewanella oneidensis MR-1 to hematite.

The adhesion of dissimilatory iron reducing bacteria (DIRB) to iron oxides is an important process to initiate direct extracellular electron transfer. Iron oxides in natural environments are often coated by organic matter or silica (SiO2) which alters their surface physicochemical properties. To investigate the influence of these surface coatings, we characterized the dynamic adhesion processes of Shewanella oneidensis MR-1 to bare hematite, humic acid-coated hematite (hematite-HA), and SiO2-coated hematite (hematite-SiO2) using Quartz Crystal Microbalance with Dissipation (QCM-D). The molecular-level process and mechanism were investigated using in situ Attenuated Total Reflectance - Fourier Transform Infrared (ATR-FTIR) spectrometry. We found that MR-1 formed a rigid bacterial layer on bare hematite. Coating with HA or SiO2 decreased the surface cell density during the initial adhesion stage, and compromised the stability of the subsequent bacterial attachment. The FTIR combined with two-dimensional correlation spectroscopy (2D-COS) analysis showed that C-moieties of polysaccharides dominated interactions in initial adhesion on HA and SiO2-coated hematite. In the longer term, the HA coating hindered the adsorption of amide, but promoted the binding of polysaccharide C-moieties to hematite. We concluded that, in general, both the HA and SiO2 coatings reduced the attachment of MR-1 on hematite. These results advance our understanding of the roles of surface coatings on microbe-mineral interactions, which has significant implications for a series of biogeochemical processes in nature.

Risk Assessment of Agricultural Plastic Films Based on Release Kinetics of Phthalate Acid Esters.

Plastic films have become an integral part of fruit and vegetable production systems, but their release of phthalate acid esters (PAEs) is a threat to human health. The release kinetics of PAEs and measures of risk are still not well understood. We investigated 50 agricultural films, with concentrations ranging from 2.59 to 282,000 mg kg-1. The seven commercially available film types included were polyvinylchloride (PVC), metallocene polyethylene (mPE), ethylene vinyl acetate (EVA), polyolefin (PO), and three mulch films. Bis(2-ethylhexyl) phthalate (DEHP) was detected in most of films, and its release fitted well into the first-order kinetic model. The release rate of DEHP was negatively related to the film thickness. The potential carcinogenic risks of DEHP in the air of six kinds of plastic greenhouses to human health were estimated. We found that the carcinogenic risks associated with PVC and mPE greenhouse films warrant greater attention. Though EVA, PO greenhouse, and mulch films were lower risk, we advise keeping plastic greenhouses well ventilated during the first month of use to reduce direct human exposure to volatile PAEs.

Organic and inorganic model soil fractions instigate the formation of distinct microbial biofilms for enhanced biodegradation of benzo[a]pyrene.

This study conducted the sorption and biodegradation of benzo[a]pyrene (BaP) by microbial biofilm communities developed on proxies for materials typically found in soils. The half-life of BaP was 4.7 and 2.3 weeks for biofilms on the inorganic carrier (BCINOR, montmorillonite) and on the organic carrier (BCOR, humic acid), respectively. In contrast, the half-life was 7.0 weeks for specialized planktonic cultures (PK). The exposure to BaP caused the development of lipid inclusion bodies inside the bacteria of the PK systems and biofilms of the BCINOR, but not on the biofilms of the BCOR system. Interestingly, the BCOR displayed not only the greatest BaP sorption capacity but also the greatest bacterial density and membrane integrity and the shortest bacteria-to-bacteria distances, which were consistent with the increased production of cell surface extracellular polymeric substances on the BCOR. Both carriers caused a noticeable shift in the bacterial genera during the biodegradation of the BaP. The BCINOR selected for Rhodococcus, Brucella, Chitinophaga, and Labrys, whereas the BCOR favored Rhodococcus and Dokdonella. It indicated that ultra-structure and BaP degradation within the organic carrier-attached biofilms differed from the inorganic ones, and suggested that the microstructural heterogeneity and microbial biodiversity from biofilms on the organic carrier promoted biodegradation.

Reducing plant uptake of a brominated contaminant (2,2',4,4'­tetrabrominated diphenyl ether) by incorporation of maize straw into horticultural soil.

Application of crop residues is a conventional practice that contributes to crop production through nutrient returns and other benefits to soil health: driving soil physicochemical and biological functions. However, little is known about the impacts of straw residue incorporation on the bioavailability of organic pollutants and associated changes in microbial community structure in contaminated soils. In this study, maize straw was added to a soil contaminated with a model polybrominated diphenyl ether (BDE-47). A pot experiment was conducted and planted with carrot (Daucus carota L.). We found that straw addition greatly reduced the bioavailability of BDE-47, changed the bacterial community structure and affected a range of soil physiochemical properties. Moreover, the amount of BDE-47 that had accumulated in carrot roots and aboveground tissues was significantly reduced. This study may therefore describe an effective agronomic strategy to reduce the bioavailability of polybrominated diphenyl ethers (PBDEs) in a soil used to grow high value vegetable crops. This strategy draws on traditional wisdom and shows promise as a practical method to support horticultural production systems, remediate soils, and help to ensure food safety.

Extracellular polymeric substances (EPS) modulate adsorption isotherms between biochar and 2,2',4,4'-tetrabromodiphenyl ether.

Extracellular polymeric substances (EPS), chars and persistent organic pollutants (POPs) frequently coexist in the environment. However, a knowledge gap exists regarding their interactions. Therefore, we applied 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) as a model POP to investigate the influence of bovine serum albumin (BSA) and sodium alginate (SA) - representing protein and polysaccharide components of EPS - on POP adsorption to biochars. Surface activities of tested biochars were characterised using nuclear magnetic resonance, X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy. The adsorption capacities of BDE-47 on biochars were significantly improved by both EPS analogues: BSA at concentrations of only 5 mg L-1 and SA at 80 mg L-1 at ce = 1 Sw BDE-47 concentration. However, 80 mg L-1 BSA decreased the BDE-47 adsorption capacities on biochars at the tested BDE-47 concentrations. Chemisorption and pore filling mechanisms appeared to dominate the adsorption process of BDE-47 on maize straw and wheat straw biochars. After adding BSA (or SA), a hydrophobic partition effect was found to best explain the adsorption process and linearity of adsorption was enhanced. These results progress our understanding of bioavailability and migration of POPs: especially relevant to the water industry and biochar/EPS facilitated removal of these contaminants.

Changes in nitrogen related functional genes along soil pH, C and nutrient gradients in the charosphere.

The interface between biochar and soil differs from both the bulk soil and the biochar itself, and has been termed the "charosphere". However, a complete definition of the charosphere, including aspects of size, properties, functional reach and effects on soil processes, is still required. In this study, the distributions of functional genes related to the soil N cycle within the charosphere were investigated over a multi-sectional gradient. We found that concentrations of dissolved organic carbon (DOC), available phosphorus and exchangeable cations (Ca2+, Mg2+, K+) increased with proximity to the biochar surface (termed the 'near charosphere'). Similarly, the abundance of bacterial amoA was greater in the near charosphere, while archaeal amoA abundance was relatively homogenous. This taxonomic asymmetry resulted in a shift in the predominant ammonia-oxidizers from ammonia-oxidizing bacteria (AOB) to ammonia-oxidizing archaea (AOA) in the far charosphere. This was associated with other factors such as decreasing pH and carbon availability with increasing distance from the biochar. Moreover, the ratio of nosZ/(nirS + nirK) genes also showed functionally asymmetry in the charosphere: increasing with increasing distance from the biochar. This is the first study to map spatial distributions of a set functional genes related to soil N cycling in the soil around biochar. This exploration into the underlying heterogeneity of biochar-affected mechanisms of N transformation provides new insight into the functional geometry of the charosphere.

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.

Differences in bacterial composition between men's and women's restrooms and other common areas within a public building.

Humans distribute a wide range of microorganisms around building interiors, and some of these are potentially pathogenic. Recent research established that humans are the main drivers of the indoor microbiome and up to now significant literature has been produced about this topic. Here we analyzed differences in bacterial composition between men's and women's restrooms and other common areas within the same public building. Bacterial DNA samples were collected from restrooms and halls of a three-floor building from the Federal University of Pampa, RS, Brazil. The bacterial community was characterized by amplification of the V4 region of the 16S rRNA gene and sequencing. Throughout all samples, the most abundant phylum was Proteobacteria, followed by Actinobacteria, Bacteroidetes and Firmicutes. Beta diversity metrics showed that the structure of the bacterial communities were different among the areas and floors tested, however, only 6-9% of the variation in bacterial communities was explained by the area and floors sampled. A few microorganisms showed significantly differential abundance between men's and women's restrooms, but in general, the bacterial communities from both places were very similar. Finally, significant differences among the microbial community profile from different floors were reported, suggesting that the type of use and occupant demographic within the building may directly influence bacterial dispersion and establishment.

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.

Zinc toxicity stimulates microbial production of extracellular polymers in a copiotrophic acid soil.

The production of extracellular polymeric substances (EPS) is crucial for biofilm structure, microbial nutrition and proximal stability of habitat in a variety of environments. However, the production patterns of microbial EPS in soils as affected by heavy metal contamination remain uncertain. Here we investigate the extracellular response of the native microbial biomass in a grassland soil treated with refined glycerol or crude unrefined biodiesel co-product (BCP) with and without ZnCl2. We extracted microbial EPS and more readily soluble microbial products (SMP), and quantified total polysaccharide, uronic acid, and protein content in these respective extracts. Organic addition, especially BCP, significantly stimulated the production of EPS-polysaccharide and protein but had no impact on EPS-uronic acids, while in the SMP-fraction, polysaccharides and uronic acids were both significantly increased. In response to the inclusion of Zn2+, both EPS- and SMP-polysaccharides increased. This implies firstly that a tolerance mechanism of soil microorganisms against Zn2+ toxicity exists through the stimulation of SMP and EPS production, and secondly that co-products of biofuel industries may have value-added use in bioremediation efforts to support in-situ production of microbial biopolymers. Microbial films and mobile polymers are likely to impact a range of soil properties. The recent focus on EPS research in soils is anticipated to help contribute an improved understanding of biofilm dynamics in other complex systems - such as continuously operated bioreactors.

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.