Accessibility of humic-associated Fe to a microbial siderophore: implications for bioavailability

Drivers to improve metal(loid) phytoextraction with a focus on microbial degradation of dissolved organic matter in soils

Bioaugmentation of soils can increase the mobilization of metal(loid)s from the soil-bearing phases. However, once desorbed, these metal(loid)s are mostly complexed to the dissolved organic matter (DOM) in the soil solution, which can restrict their availability to plants (roots mainly taking up the free forms) and then the phytoextraction performances. Firstly the main drivers influencing phytoextraction are reminded, then the review focuses on the DOM role. After having reminding the origin, the chemical structure and the lability of DOM, the pool of stable DOM (the most abundant in the soil) most involved in the complexation of metal(loid)s is addressed in particular by focusing on carboxylic and/or phenolic groups and factors controlling metal(loid) complexation with DOM. Finally, this review addresses the ability of microorganisms to degrade metal(loid)-DOM complexes as an additional lever for increasing the pool of free metal(loid) ions, and then phytoextraction performances, and details the origin of microorganisms and how they are selected. The development of innovative processes including the use of these DOM-degrading microorganisms is proposed in perspectives.

Interactions between Humic Substances and Microorganisms and Their Implications for Nature-like Bioremediation Technologies

The state of the art of the reported data on interactions between microorganisms and HSs is presented herein. The properties of HSs are discussed in terms of microbial utilization, degradation, and transformation. The data on biologically active individual compounds found in HSs are summarized. Bacteria of the phylum Proteobacteria and fungi of the phyla Basidiomycota and Ascomycota were found to be the main HS degraders, while Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were found to be the predominant phyla in humic-reducing microorganisms (HRMs). Some promising aspects of interactions between microorganisms and HSs are discussed as a feasible basis for nature-like biotechnologies, including the production of enzymes capable of catalyzing the oxidative binding of organic pollutants to HSs, while electron shuttling through the utilization of HSs by HRMs as electron shuttles may be used for the enhancement of organic pollutant biodegradation or lowering bioavailability of some metals. Utilization of HSs by HRMs as terminal electron acceptors may suppress electron transfer to CO2, reducing the formation of CH4 in temporarily anoxic systems. The data reported so far are mostly related to the use of HSs as redox compounds. HSs are capable of altering the composition of the microbial community, and there are environmental conditions that determine the efficiency of HSs. To facilitate the development of HS-based technologies, complex studies addressing these factors are in demand.

Rhizobactin B is the preferred siderophore by a novel Pseudomonas isolate to obtain iron from dissolved organic matter in peatlands

Bacteria often release diverse iron-chelating compounds called siderophores to scavenge iron from the environment for many essential biological processes. In peatlands, where the biogeochemical cycle of iron and dissolved organic matter (DOM) are coupled, bacterial iron acquisition can be challenging even at high total iron concentrations. We found that the bacterium Pseudomonas sp. FEN, isolated from an Fe-rich peatland in the Northern Bavarian Fichtelgebirge (Germany), released an unprecedented siderophore for its genus. High-resolution mass spectrometry (HR-MS) using metal isotope-coded profiling (MICP), MS/MS experiments, and nuclear magnetic resonance spectroscopy (NMR) identified the amino polycarboxylic acid rhizobactin and a novel derivative at even higher amounts, which was named rhizobactin B. Interestingly, pyoverdine-like siderophores, typical for this genus, were not detected. With peat water extract (PWE), studies revealed that rhizobactin B could acquire Fe complexed by DOM, potentially through a TonB-dependent transporter, implying a higher Fe binding constant of rhizobactin B than DOM. The further uptake of Fe-rhizobactin B by Pseudomonas sp. FEN suggested its role as a siderophore. Rhizobactin B can complex several other metals, including Al, Cu, Mo, and Zn. The study demonstrates that the utilization of rhizobactin B can increase the Fe availability for Pseudomonas sp. FEN through ligand exchange with Fe-DOM, which has implications for the biogeochemical cycling of Fe in this peatland.

The nature of dissolved organic matter determines the biosorption capacity of Cu by algae

The role of dissolved organic matter (DOM) on the biochemical behavior and toxicity of heavy metals in water is very important but complex and unclear. The present work extracted DOM from a natural water and separated it into three fractions, namely humic acid (HA), fulvic acid (FA) and transphilic acid (TPA). Optical detection showed that HA had most aromatic ring skeletons, FA had more aromatic ring hydrophilic groups, and TPA had the largest number of hydroxyl or carboxyl groups. Their effects on the toxicity of Cu by Chlorella pyrenoidosa depended on types and concentration of DOM. In the case of algal exposure to 0.003 mM initial Cu concentration, the final algal optical density increased from 0.317 of the control group to 0.345, 0.645 and 0.435 in the presence of 20, 10 mg L^-1 HA, and 10 mg L^-1 TPA, respectively, but were suppressed to 0.246, 0.117 and 0.234 in the presence of 10, 20 mg L^-1 FA and 20 mg L^-1 TPA. Most adsorption isotherms lost the linearity in the presence of HA, FA and TPA. The adsorbed Cu increased from 0.242 to 0.477 mmol g^-1, following the order of increased concentration of HA, FA, and TPA. The formation of ternary complex and the multi-layer adsorption were proposed to explain the significant enhancement adsorption of Cu in the presence of FA and TPA. This study showed that the type and the density of effective functional groups in DOM determined its effects on Cu toxicity and bioavailability to algae.

Assessing bioavailability of complex chemical mixtures in contaminated soils: Progress made and research needs

Understanding the distribution, behaviour and interactions of complex chemical mixtures is key for providing the evidence necessary to make informed decisions and implement robust remediation strategies. Much of the current risk assessment frameworks applied to manage land contamination are based on total contaminant concentrations and the exposure assessments embedded within them do not explicitly address the partitioning and bioavailability of chemical mixtures. These oversights may contribute to an overestimation of both the eco-toxicological effects of the fractions and the mobility of contaminants. In turn, this may limit the efficacy of risk frameworks to inform targeted and proportionate remediation strategies. In this review we analyse the science surrounding bioavailability, its regulatory inclusion and the challenges of incorporating bioavailability in decision making process. While a number of physical and chemical techniques have proven to be valuable tools for estimating bioavailability of organic and inorganic contaminants in soils, doubts have been cast on its implementation into risk management soil frameworks mainly due to a general disagreement on the interchangeable use of bioavailability and bioaccessibility, and the associated methods which are still not standardised. This review focuses on the role of biotic and abiotic factors affecting bioavailability along with soil physicochemical properties and contaminant composition. We also included advantages and disadvantages of different extraction techniques and their implications for bioavailability quantitative estimation. In order to move forward the integration of bioavailability into site-specific risk assessments we should (1) account for soil and contaminant physicochemical characteristics and their effect on bioavailability; (2) evaluate receptor's potential exposure and uptake based on mild-extraction; (3) adopt a combined approach where chemical-techniques are used along with biological methods; (4) consider a simplified and cost-effective methodology to apply at regulatory and industry setting; (5) use single-contaminant exposure assessments to inform and predict complex chemical mixture behaviour and bioavailability.

A universal assay for the detection of siderophore activity in natural waters

Siderophores, a family of biogenic metal chelating agents, play critical roles in the biogeochemical cycling of Fe and other metals by facilitating their solubilization and uptake in circumneutral to alkaline oxic environments. However, because of their small concentrations (ca. nM) and large number of molecular structures, siderophore detection and quantification in environmental samples requires specialized equipment and expertise, and often requires pre-concentration of samples, which may introduce significant bias. The "universal" CAS assay, which was originally designed for use in bacterial cultures, quantifies the iron chelating function of a pool of siderophores but only at concentrations (>2 µM) well above the concentrations estimated to be present in marine, freshwater, and soil samples. In this manuscript, we present a high sensitivity modification of this universal assay (HS-CAS) suitable for detecting and quantifying siderophore activity in the nM concentration range, allowing for direct quantitation of siderophore reactivity in transparent aqueous samples.

Synergistic Effects between Biogenic Ligands and a Reductant in Fe Acquisition from Calcareous Soil

Organisms have developed different strategies to cope with environmental conditions of low Fe availability based on the exudation of reducing, ligating, and acidifying compounds. In the context of Fe acquisition from soil, the effects of these reactive compounds have generally been considered independent and additive. However, highly efficient Fe acquisition strategies may rely on synergistic effects between reactive exudates. In the present study, we demonstrate that synergistic effects between biogenic ligands and a reductant (ascorbate) can occur in Fe mobilization from soil. Synergistic Fe mobilization was found for all ligands examined (desferrioxamine B (DFOB), 2'-deoxymugineic acid (DMA), esculetin, and citrate). The size and duration of the synergistic effect on Fe mobilization varied with ligand: larger effects were observed for the sideorphores compared to esculetin and citrate. For DFOB, the synergistic effect lasted for the 168 h duration of the experiment; for DMA, an initial synergistic effect turned into an antagonistic effect after 4 h because of enhanced mobilization of competing metals; and for esculetin and citrate, the synergistic effect was temporary (less than 24 h). Our results demonstrate that synergistic effects greatly enhance the reactivity of mixtures of compounds known to be exuded in response to Fe limitation. These synergistic effects could be decisive for the survival of plants and microorganisms under conditions of low Fe availability.

Sphagnum-dominated bog systems are highly effective yet variable sources of bio-available iron to marine waters

Iron is a micronutrient of particular interest as low levels of iron limit primary production of phytoplankton and carbon fluxes in extended regions of the world's oceans. Sphagnum-peatland runoff is extraordinarily rich in dissolved humic-bound iron. Given that several of the world's largest wetlands are Sphagnum-dominated peatlands, this ecosystem type may serve as one of the major sources of iron to the ocean. Here, we studied five near-coastal creeks in North Scotland using freshwater/seawater mixing experiments of natural creek water and synthetic seawater based on a (59)Fe radiotracer technique combined with isotopic characterization of dissolved organic carbon by Accelerator Mass Spectrometry. Three of the creeks meander through healthy Sphagnum-dominated peat bogs and the two others through modified peatlands which have been subject to artificial drainage for centuries. The results revealed that, at the time of sampling (August 16-24, 2014), the creeks that run through modified peatlands delivered 11-15μg iron per liter creek water to seawater, whereas the creeks that run through intact peatlands delivered 350-470μg iron per liter creek water to seawater. To find out whether this humic-bound iron is bio-available to marine algae, we performed algal growth tests using the unicellular flagellated marine prymnesiophyte Diacronema lutheri and the unicellular marine green alga Chlorella salina, respectively. In both cases, the riverine humic material provided a highly bio-available source of iron to the marine algae. These results add a new item to the list of ecosystem services of Sphagnum-peatlands.

Determination of size-dependent metal distribution in dissolved organic matter by SEC-UV/VIS-ICP-MS with special focus on changes in seawater

Iron is an essential micronutrient for all marine organisms, but it is also a growth limiting factor as the iron concentrations in the open ocean are below 1 nmol/L in sea water iron is almost entirely bound to organic ligands of the dissolved organic matter fraction, which are mostly of unknown structure. The input from rivers was traditionally considered as less important due to estuarine sedimentation processes of the mainly colloidal iron particles. However, recent studies have shown that this removal is not complete and riverine input may represent an important iron source in the open ocean. In this context, iron transport by land-derived natural organic matter (NOM), and dissolved organic matter (DOM) have been identified as carrier mechanisms for riverine iron. The aim of this work is to characterize complexes containing iron and other metals in waters simulating estuarine conditions in order to help understand which role iron-DOM compounds play in the open ocean. A method based on size-exclusion chromatography (SEC) with sequential UV/VIS and ICP-MS detection was developed for investigation of DOM size distribution and for assessment of the size-dependent metal distribution in NOM-rich surface water. Furthermore, sample matrix experiments were also performed revealing a dependence of DOM size distribution upon seawater concentration and different compounds present in seawater. Finally, efforts toward determination of DOM size with standardization with typical SEC standards indicate that only relative comparisons are possible with this approach, and that the sample matrix composition strongly influences obtained results.

River-derived humic substances as iron chelators in seawater

The speciation of iron(III) in oxic seawater is dominated by its hydrolysis and sedimentation of insoluble iron(III)-oxyhydroxide. As a consequence, many oceanic areas have very low iron levels in surface seawater which leads to iron deficiency since phytoplankton require iron as a micronutrient in order to grow. Fortunately, iron solubility is not truly as low as Fe(III) solubility measurements in inorganic seawater would suggest, since oceanic waters contain organic molecules which tend to bind the iron and keep it in solution. Various iron-binding organic ligands which combine to stabilize dissolved iron have been detected and thoroughly investigated in recent years. However, the role of iron-binding ligands from terrestrial sources remains poorly constrained. Blackwater rivers supply large amounts of natural organic material (NOM) to the ocean. This NOM (which consists mainly of vascular plant-derived humic substances) is able to greatly enhance iron bioavailability in estuaries and coastal regions, however, breakdown processes lead to a rapid decrease of river-derived NOM concentrations with increasing distance from land. It has therefore been argued that the influence of river-derived NOM on iron biogeochemistry in offshore seawater does not seem to be significant. Here we used a standard method based on ⁵⁹Fe as a radiotracer to study the solubility of Fe(III)-oxyhydroxide in seawater in the presence of riverine NOM. We aimed to address the question how effective is freshwater NOM as an iron chelator under open ocean conditions where the concentration of land-derived organic material is about 3 orders of magnitude smaller than in coastal regions, and does this iron chelating ability vary between NOM from different sources and between different size fractions of the river-borne NOM. Our results show that the investigated NOM fractions were able to substantially enhance Fe(III)-oxyhydroxide solubility in seawater at concentrations of the NOM ≥ 5 μg L^- 1. Terrigenous NOM concentrations ≥ 5 μg L^- 1 are in no way unusual in open ocean surface waters especially of the Arctic and the North Atlantic Oceans. River-derived humic substances could therefore play a greater role as iron carriers in the ocean than previously thought.

13C Nuclear Magnetic Resonance and Electron Paramagnetic Spectroscopic Comparison of Hydrophobic Acid, Transphilic Acid, and Reverse Osmosis May 2012 Isolates of Organic Matter from the Suwannee River

Dissolved organic matter (DOM) is found in most natural waters at concentrations low enough to make DOM isolation methodologies critical to full analytical characterization and preservation. During the last few decades, two major protocols have been developed for the extraction of DOM isolates from natural waters. These methods utilize XAD resins and reverse osmosis (RO). In this work, the hydrophobic acid (May 2012 HPOA) and transphilic acid (May 2012 TPIA) isolates from XAD-8 and XAD-4 resins, respectively, were compared with the RO (May 2012 RO) natural organic matter isolate of the Suwannee River water using ¹³C nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopies. ¹³C NMR analysis showed that the May 2012 RO isolate could be viewed as a hybrid of the more hydrophobic May 2012 HPOA isolate and more hydrophilic May 2012 TPIA isolate. The May 2012 HPOA isolate is shown to be higher in alkyl and aromatic moieties, while the May 2012 TPIA isolate is higher in O-alkyl moieties. EPR analysis revealed that the May 2012 TPIA and, in particular, May 2012 HPOA isolates had higher radical concentrations than the May 2012 RO isolate. It is postulated that some of the radical concentrations came from the use of base during the isolation procedures, especially in the XAD method.