Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability

Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances

Extracellular polymeric substances (EPS) are produced by microorganisms and interact to form a complex matrix called biofilm. In soils, EPS are important contributors to the microbial necromass and, thus, to soil organic carbon (SOC). Amino sugars (AS) are used as indicators for microbial necromass in soil, although the origin of galactosamine and mannosamine is largely unknown. However, indications exist that they are part of EPS. In this study, two bacteria and two fungi were grown in starch medium either with or without a quartz matrix to induce EPS production. Each culture was separated in two fractions: one that directly underwent AS extraction (containing AS from both biomass and EPS), and another that first had EPS extracted, followed then by AS determination (exclusively containing AS from EPS). We did not observe a general effect of the quartz matrix neither of microbial type on AS production. The quantified amounts of galactosamine and mannosamine in the EPS fraction represented on average 100% of the total amounts of these two AS quantified in cell cultures, revealing they are integral parts of the biofilm. In contrast, muramic acid and glucosamine were also quantified in the EPS, but with much lower contribution rates to total AS production, of 18% and 33%, respectively, indicating they are not necessarily part of EPS. Our results allow a meaningful ecological interpretation of mannosamine and galactosamine data in the future as indicators of microbial EPS, and also attract interest of future studies to investigate the role of EPS to SOC and its dynamics.

Bio-Characterization and Liquid Chromatography-Mass Spectrometry Analysis of Exopolysaccharides in Biofilm-Producing Cyanobacteria Isolated from Soil Crust: Exploring the Potential of Microalgal Biomolecules

Exopolysaccharide-producing cyanobacterial strains in biological soil crusts are described, in addition to their chemical properties and antioxidant and flocculation activities. The EPSs from Pudukkottai blackish biological soil crusts (PBBSCs) showed significant amounts of total soluble proteins (0.1687 mg/mL) and carbohydrates (0.8056 mg/mL) compared with the Ariyalur blackish biological soil crusts (ABBSCs). LC-MS analysis of the cyanobacterial polysaccharides revealed the presence of natural sugars such as ribose and glucose/mannose, and uronic acids. The FTIR spectrum showed specific peak for OH and -NH stretching, C-H stretching, and carboxylic acids as the dominant groups in EPS. The in vitro DPPH assay of EPSs from PBBSCs showed 74.3% scavenging activity. Furthermore, the reducing power was determined to be 0.59 ata 500 mg/mL concentration, respectively. The extracted EPSs from the biological soil crust flocculated Kaolin clay suspension maximum at 500 mg/mL. Consequently, the cyanobacterial strain and exopolysaccharide characterization from the sacred forest's biological soil crust were analyzed for their bioactive potential, bio-crust diversity, and distribution.

Chemodiversity of soil organic matters determines biodegradation of polychlorinated biphenyls by a graphene oxide-assisted bacterial agent

A promising strategy for degrading persistent organic pollutants (POPs) in soil is amendment with nanomaterial-assisted functional bacteria. However, the influence of soil organic matter chemodiversity on the performance of nanomaterial-assisted bacterial agents remains unclear. Herein, different types of soil (Mollisol soil, MS; Ultisol soil, US; and Inceptisol soil, IS) were inoculated with a graphene oxide (GO)-assisted bacterial agent (Bradyrhizobium diazoefficiens USDA 110, B. diazoefficiens USDA 110) to investigate the association between soil organic matter chemodiversity and stimulation of polychlorinated biphenyl (PCB) degradation. Results indicated that the high-aromatic solid organic matter (SOM) inhibited PCB bioavailability, and lignin-dominant dissolved organic matter (DOM) with high biotransformation potential was a favored substrate for all PCB degraders, which led to no stimulation of PCB degradation in MS. Differently, high-aliphatic SOM in US and IS promoted PCB bioavailability. The high/low biotransformation potential of multiple DOM components (e.g., lignin, condensed hydrocarbon, unsaturated hydrocarbon, etc.) in US/IS further resulted to the enhanced PCB degradation by B. diazoefficiens USDA 110 (up to 30.34%) /all PCB degraders (up to 17.65%), respectively. Overall, the category and biotransformation potential of DOM components and the aromaticity of SOM collaboratively determine the stimulation of GO-assisted bacterial agent on PCB degradation.

Exploring the Role of Bacterial Extracellular Polymeric Substances for Sustainable Development in Agriculture

The incessant need to increase crop yields has led to the development of many chemical fertilizers containing NPK (nitrogen-phosphorous-potassium) which can degrade soil health in the long term. In addition, these fertilizers are often leached into nearby water bodies causing algal bloom and eutrophication. Bacterial secondary metabolites exuded into the extracellular space, termed extracellular polymeric substances (EPS) have gained commercial significance because of their biodegradability, non-toxicity, and renewability. In many habitats, bacterial communities faced with adversity will adhere together by production of EPS which also serves to bond them to surfaces. Typically, hygroscopic, EPS retain moisture in desiccating conditions and modulate nutrient exchange. Many plant growth-promoting bacteria (PGPR) combat harsh environmental conditions like salinity, drought, and attack of pathogens by producing EPS. The adhesive nature of EPS promotes soil aggregation and restores moisture thus combating soil erosion and promoting soil fertility. In addition, these molecules play vital roles in maintaining symbiosis and nitrogen fixation thus enhancing sustainability. Thus, along with other commercial applications, EPS show promising avenues for improving agricultural productivity thus helping to address land scarcity as well as minimizing environmental pollution.

Metagenomic insights into the fungal assemblages of the northwest Himalayan cold desert

Psychrophilic fungi are a critical biotic component in cold deserts that serves a central role in nutrient recycling and biogeochemical cycles. Despite their ecological significance, culture-independent studies on psychrophilic mycobiome are limited. In the present study, the fungal diversity patterns across the Drass, an Indian cold desert in the Himalaya, were indexed by targeted amplicon pyrosequencing (ITS). In the Drass dataset, Ascomycota was represented by 92 genera, while 22 genera represented Basidiomycota. The most abundant genus was Conocybe (20.46%). Most of the identified genera were reported in the literature to be prolific extracellular hydrolytic enzyme producers. To identify whether the Drass fungal assemblages share similarities to other cold deserts, these were further compared to Antarctic and Arctic cold deserts. Comparative analysis across the three cold deserts indicated the dominance of Dikarya (Ascomycota and Basidiomycota). The observed alpha diversity, Shannon index as well as Pielou's evenness was highest in the Antarctic followed by Drass and Arctic datasets. The genera Malassezia, Preussia, Pseudogymnoascus, Cadophora, Geopora, Monodictys, Tetracladium, Titaea, Mortierella, and Cladosporium were common to all the cold deserts. Furthermore, Conocybe was represented predominantly in Drass. Interestingly, the genus Conocybe has not been previously reported from any other studies on Antarctic or Arctic biomes. To the best of our knowledge, this is the first fungal metagenome study in Drass soil. Our analysis shows that despite the similarities of low temperature among the cold deserts, a significant differential abundance of fungal communities prevails in the global cold deserts.

Soil organic carbon, extracellular polymeric substances (EPS), and soil structural stability as affected by previous and current land-use

While soil microbial ecology, soil organic carbon (SOC) and soil physical quality are widely understood to be interrelated - the underlying drivers of emergent properties, from land management to biochemistry, are hotly debated. Biological binding agents, microbial exudates, or 'extracellular polymeric substances' (EPS) in soil are now receiving increased attention due to several of the existing methodological challenges having been overcome. We applied a recently developed approach to quantify soil EPS, as extracellular protein and extracellular polysaccharide, on the well-characterised soils of the Highfield Experiment, Rothamsted Research, UK. Our aim was to investigate the links between agricultural land use, SOC, transient binding agents known as EPS, and their impacts on soil physical quality (given by mean weight diameter of water stable aggregates; MWD). We compared the legacy effects from long-term previous land-uses (unfertilised grassland, fertilised arable, and fallow) which were established > 50 years prior to investigation, crossed with the same current land-uses established for a duration of only 2.5 years prior to sampling. Continuously fallow and grassland soils represented the poorest and greatest states of structural integrity, respectively. Total SOC and N were found to be affected by both previous and current land-uses, while extractable EPS and MWD were driven primarily by the current land-use. Land-use change between these two extremes (fallow → grass; grass → fallow) resulted in smaller SOC differences (64% increase or 37% loss) compared to MWD (125% increase or 78% loss). SOC concentration correlated well to MWD (adjusted R 2 = 0.72) but the greater SOC content from previous grassland was not found to contribute directly to the current stability (p < 0.05). Our work thus supports the view that certain distinct components of SOC, rather than the total pool, have disproportionately important effects on a soil's structural stability. EPS-protein was more closely related to aggregate stability than EPS-polysaccharide (p values of 0.002 and 0.027, respectively), and ranking soils with the 5 greatest concentrations of EPS-protein to their corresponding orders of stability (MWD) resulted in a perfect match. We confirmed that both EPS-protein and EPS-polysaccharide were transient fractions: supporting the founding models for aggregate formation. We suggest that management of transient binding agents such as EPS -as opposed to simply increasing the total SOC content- may be a more feasible strategy to improve soil structural integrity and help achieve environmental objectives.

Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide-producing bacteria during soil formation

Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post-mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide-producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide-producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase.

Nitrogen fertilization modifies organic transformations and coatings on soil biogeochemical interfaces through microbial polysaccharides synthesis

The soil-water interfaces (SWI) in soil pores are hotspots for organic matter (OM) transformation. However, due to the heterogeneous and opaque nature of soil microenvironment, direct and continuous tracing of interfacial reactions, such as OM transformations and formation of organo-mineral associations, are rare. To investigate these processes, a new soil microarray technology (SoilChips) was developed and used. Homogeneous 800-μm-diameter SoilChips were constructed by depositing a dispersed Oxisol A horizon suspension on a patterned glass. Dissolved organic matter from the original soil was added on the SoilChips to mimic SWI processes. The effects of ammonium fertilization (90 mg N kg^-1 soil) on chemical composition of SWIs were evaluated via X-ray photoelectron spectroscopy. Over 21 days, ammonium addition increased OM coatings at SWIs and modified the OM chemical structure with more alcoholic- and carboxylic-C compared to the unfertilized control. Molecular modeling of OM composition at SWIs showed that N fertilization mainly facilitated the microbial production of glucans. We demonstrated that N availability modifies the specific OM molecular processing and its immobilization on SWIs, thereby providing a direct insight into biogeochemical transformation of OM at micro-scale.

Soil biofilm formation enhances microbial community diversity and metabolic activity

Biofilms have been extensively studied in aquatic and clinical environments. However, the complexity of edaphic microenvironment hinders the advances toward understanding the environmental functionalities and ecological roles of soil biofilms. In this work, artificial soil was employed to investigate the soil biofilm formation and corresponding impacts on community structure and microbial activities. Our results showed that extracellular polymeric substances (EPS) production was significantly enhanced and micro-meter sized cell aggregates formed with high glucose amendment. Biofilm development exhibited significant effects on the soil microbial processes. 16S rRNA gene sequencing demonstrated the soils with biofilms and free-living cells shared similar microbial communities. But the Shannon diversity and evenness indices of communities with soil biofilms were significantly enhanced by 18.2% and 17.1%. The soil with biofilms also revealed a rapid response to nutrient provision and robust microbial activity, which consumed 65.4% more oxygen in the topsoil (0-1.5 mm). Kinetic respiration analysis showed that the enhanced metabolic activity was attributed to 23-times more active microbes in soil biofilms. In summary, this study revealed that soil biofilms can sustain a diverse and robust community to drive soil biogeochemical processes.

Biochar combined with compost to reduce the mobility, bioavailability and plant uptake of 2,2',4,4'-tetrabrominated diphenyl ether in soil

Biochar application to soil is recognised for its capacity to immobilise pollutants (through sorption) while composted inputs can accelerate the biodegradation of organic pollutants. However, little is known about the influence of combined incorporation on plant uptake of organic pollutants. Therefore, we investigated the effects of maize straw-derived biochar (MSB), compost derived from maize straw and pig manure (SMC), and their combination (MSB-SMC) as soil amendments on bioavailability of 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) and carrot (Daucus carota L.) uptake in a horticultural soil. We found that biochar alone performed well in reducing BDE-47 bioavailability, but was less effective at degrading the pollutant. Conversely, addition of compost stimulated BDE-47 biodegradation. MSB-SMC enhanced BDE-47 biodegradation in soil, reduced contamination of carrot roots, and caused significant reductions in soil extractable BDE-47. The combination of contrasting approaches to remediation thus resulted in the most favorable outcome for a contaminated soil: immobilisation of contaminant from vegetable crops (via biochar) with simultaneous bioremediation of the growing medium. These findings point towards an effective strategy for reducing plant uptake of PDBEs through the combined use of biochar and compost as soil amendment - reducing mobility and facilitating degradation of the accessible contaminant fractions.

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.

Trichoderma-Azotobacter biofilm inoculation improves soil nutrient availability and plant growth in wheat and cotton

Microbial biofilms are gaining importance in agriculture, due to their multifaceted agronomic benefits and resilience to environmental fluctuations. This study focuses on comparing the influence of single inoculation-Azotobacter chroococcum (Az) or Trichoderma viride (Tv) and their biofilm (Tv-Az), on soil and plant metabolic activities in wheat and cotton grown under Phytotron conditions. Tv-Az proved superior to all the other treatments in terms of better colonisation, plant growth attributes and 10-40% enhanced availability of macronutrients and micronutrients in the soil, over control. Confocal and scanning electron microscopy showed that the cells attached to the root tips initially, followed by their proliferation along the surface of the roots. Soil polysaccharides, proteins and dehydrogenase activity showed several fold enhancement in Tv-Az biofilm inoculated samples. Time course studies revealed that the population of Az and Tv in the rhizoplane and rhizosphere was significantly higher with a 0.14-0.31 log colony-forming unit (CFU) increase in the biofilm-inoculated treatment in both crops. Enhancement in soil biological activities was facilitated by the improved colonisation of the biofilm, due to the synergistic association between Tv and Az. This demonstrates the utility of Tv-Az biofilm as a multifunctional plant growth promoting and soil fertility enhancing option in agriculture.

Development of Alditol Acetate Derivatives for the Determination of 15N-Enriched Amino Sugars by Gas Chromatography-Combustion-Isotope Ratio Mass Spectrometry

Amino sugars can be used as indices to evaluate the role of soil microorganisms in active nitrogen (N) cycling in soil. This paper details the assessment of the suitability of gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) for the analysis of ¹⁵N-enriched amino sugars as alditol acetate derivatives prior to application of a novel ¹⁵N stable isotope probing (SIP) approach to amino sugars. The efficient derivatization and cleanup of alditol acetate derivatives for GC was achieved using commercially available amino sugars, including glucosamine, mannosamine, galactosamine, and muramic acid, as laboratory standards. A VF-23ms stationary phase was found to produce optimal separations of all four compounds. The structure of the alditol acetate derivatives was confirmed using gas chromatography/mass spectrometry (GC/MS). For GC-C-IRMS determinations, implementation of a two-point normalization confirmed the optimal carrier gas flow rate to be 1.7 mL min^-1. Linearity of δ¹⁵N value determinations up to δ¹⁵N_t of 469 ± 3.1‰ (where δ¹⁵N_t is the independently measured δ¹⁵N value) was confirmed when 30 nmol N was injected on-column, with the direction of deviation from δ¹⁵N_t at low sample amount dependent on the ¹⁵N abundance of the analyte. Observed between- and within-run memory effects were significant ( P < 0.007) when a highly enriched standard (469 ± 3.1‰) was run; therefore, analytical run order and variation in ¹⁵N enrichment of analytes within the same sample must be considered. The investigated parameters have confirmed the isotopic robustness of alditol acetate derivatives of amino sugars for the GC-C-IRMS analysis of ¹⁵N-enriched amino sugars in terms of linearity over an enrichment range (natural abundance to 469 ± 3.1‰) with on-column analyte amount over 30 nmol N.

Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities

Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.

Effect of extracellular polymeric substance components on the sorption behavior of 2,2',4,4'-tetrabromodiphenyl ether to soils: Kinetics and isotherms

Microbial extracellular polymeric substances (EPS) and persistent organic pollutants (POPs) commonly exist in the soil environment. Currently, there is a knowledge gap regarding the effect of EPS on the fate of POPs in soil. In the present study, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) was used as a model compound to investigate the effects of bovine serum albumin (BSA) and sodium alginate (SA) - mimicking the main components of EPS - on sorption of POPs to soils, through batch experiments. Irrespective of the concentration of BSA: the addition of BSA did enhance the sorption capacity of BDE-47 to soils, due to generation of more sorption sites. For SA, it increased the sorption capacity of BDE-47 at low BDE-47 concentrations, while the presence of SA negatively affected sorption of BDE-47 at high BDE-47 concentrations. The partition effect dominates the sorption of BDE-47 to soils, but after adding either BSA or SA, the sorption of BDE-47 to soils is dominated by surface sorption. Film diffusion and intra-particle diffusion were also involved in the sorption process with and without BSA or SA, with the latter being the rate-limiting step. The heterogeneous surface and nonlinear sorption behavior of BDE-47 to soils increased in the presence of either BSA or SA. The FTIR spectra indicated that the aromatic CC, H-bonds and OH groups may be involved in the sorption process. Therefore, BSA enhanced the retention of BDE-47 to soil, while SA's influence on BDE-47 sorption to soil depended on the concentration of BDE-47.

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.