Anaerobic oxalate degradation: widespread natural occurrence in aquatic sediments

Organic Ligand-Mediated Dissolution and Fractionation of Rare-Earth Elements (REEs) from Carbonate and Phosphate Minerals

Global efforts to build a net-zero economy and the irreplaceable roles of rare-earth elements (REEs) in low-carbon technologies urge the understanding of REE occurrence in natural deposits, discovery of alternative REE resources, and development of green extraction technologies. Advancement in these directions requires comprehensive knowledge on geochemical behaviors of REEs in the presence of naturally prevalent organic ligands, yet much remains unknown about organic ligand-mediated REE mobilization/fractionation and related mechanisms. Herein, we investigated REE mobilization from representative host minerals induced by three representative organic ligands: oxalate, citrate, and the siderophore desferrioxamine B (DFOB). Reaction pH conditions were selected to isolate the ligand-complexation effect versus proton dissolution. The presence of these organic ligands displayed varied impacts, with REE dissolution remarkably enhanced by citrate, mildly promoted by DFOB, and showing divergent effects in the presence of oxalate, depending on the mineral type and reaction pH. Thermodynamic modeling indicates the dominant presence of REE-ligand complexes under studied conditions and suggests ligand-promoted REE dissolution to be the dominant mechanism, consistent with experimental data. In addition, REE dissolution mediated by these ligands exhibited a distinct fractionation toward heavy REE (HREE) enrichment in the solution phase, which can be mainly attributed to the formation of thermodynamically predicted more stable HREE-ligand complexes. The combined thermodynamic modeling and experimental approach provides a framework for the systematic investigation of REE mobilization, distribution, and fractionation in the presence of organic ligands in natural systems and for the design of green extraction technologies.

Assessment of Surface Water Quality in the Podu Iloaiei Dam Lake (North-Eastern Romania): Potential Implications for Aquaculture Activities in the Area

The Podu Iloaiei Dam Lake located on the Bahluet River from Bahlui hydrographic basin, north-eastern Romania, is one of the most important water resources used for aquaculture activities in the region of interest. In the present study, the chemical composition related to water-soluble ions and elements was assessed in both water and sediment samples collected from the area of interest during July 2017 and October 2017, representative months for warm and cold seasons, respectively. Water-soluble ions (H3C2O2−, HCO2−, C2O42−, F−, Cl−, NO2−, Br−, NO3−, SO42−, Li+, Na+, NH4+, K+, and Ca2+) were analyzed by ion chromatography, while inductively coupled plasma mass spectrometry was used to quantify water-soluble fractions of elements (Be, B, Mg, Al, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, Rb, Sr, Mo, Ru, Pd, Ag, Cd, Sn, Sb, Te, Ba, Ir, Tl, Pb, Bi, and U). Evidence was obtained on the contributions of both anthropogenic and natural (pedologic) related sources in controlling the chemical composition of the water and sediment samples in the area. Analysis of Piper diagrams revealed the existence of CO32−/HCO3− and Ca2+/Mg2+ as dominant species for the sediment samples. The interest water pool was found to be oligotrophic over the warm period and eutrophic over the cold period. Overall, abundances and the association of chemical species in the area seemed to be controlled by a complex interplay between the water body’s main characteristics, meteorological factors, and anthropogenic activities. Moreover, the present results suggest that precautions should be taken for physicochemical parameter monitoring and prevention acts for surface water quality assurance in order to control the potential negative influence of some chemical parameters on fish productivity. Reported data also have a high potential to be used by experts in the field of developing lake water management policies for a sustainable exploitation of various aquatic systems.

Diversity and ecology of oxalotrophic bacteria

Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed.

Oxalate-degrading microorganisms or oxalate-degrading enzymes: which is the future therapy for enzymatic dissolution of calcium-oxalate uroliths in recurrent stone disease?

Renal urolithiasis is a pathological condition common to a multitude of genetic, physiological and nutritional disorders, ranging from general hyperoxaluria to obesity. The concept of quickly dissolving renal uroliths via chemolysis, especially calcium-oxalate kidney stones, has long been a clinical goal, but yet to be achieved. Over the past 25 years, there has been a serious effort to examine the prospects of using plant and microbial oxalate-degrading enzymes known to catabolize oxalic acid and oxalate salts. While evidence is emerging that bacterial probiotics can reduce recurrent calcium-oxalate kidney stone disease by lowering systemic hyperoxaluria, the possible use of free oxalate-degrading enzyme therapy remains a challenge with several hurdles to overcome before reaching clinical practice.

Investigation of the synergistic effects for p-nitrophenol mineralization by a combined process of ozonation and electrolysis using a boron-doped diamond anode

Electrolysis and ozonation are two commonly used technologies for treating wastewaters contaminated with nitrophenol pollutants. However, they are often handicapped by their slow kinetics and low yields of total organic carbon (TOC) mineralization. To improve TOC mineralization efficiency, we combined electrolysis using a boron-doped diamond (BDD) anode with ozonation (electrolysis-O3) to treat a p-nitrophenol (PNP) aqueous solution. Up to 91% TOC was removed after 60 min of the electrolysis-O3 process. In comparison, only 20 and 44% TOC was respectively removed by individual electrolysis and ozonation treatment conducted under similar reaction conditions. The result indicates that when electrolysis and ozonation are applied simultaneously, they have a significant synergy for PNP mineralization. This synergy can be mainly attributed to (i) the rapid degradation of PNP to carboxylic acids (e.g., oxalic acid and acetic acid) by O3, which would otherwise take a much longer time by electrolysis alone, and (ii) the effective mineralization of the ozone-refractory carboxylic acids to CO2 by OH generated from multiple sources in the electrolysis-O3 system. The result suggests that combining electrolysis with ozonation can provide a simple and effective way to mutually compensate the limitations of the two processes for degradation of phenolic pollutants.

A review of environmental characteristics and effects of low-molecular weight organic acids in the surface ecosystem

Low molecular weight organic acids (LMWOAs) are prevalent on the earth's surface. They are vital intermediate products during metabolic pathways of organic matter and participate in the tricarboxylic acid cycle during life activities. Photochemical reactions are pivotal for LMWOAs' origination and play a large role in determining their diversity and their ultimate fate. Within the long time that organic matter is preserved in sediments, it can be decomposed and converted to release organic and inorganic pollutants as well as C, N, and P nutrients, which are of potential ecological risk in causing secondary pollution to lake water. The sediment pool is a comprehensive and complex compartment closely associated with overlying water by various biochemical processes, during which LMWOAs play critical roles to transport and transform elements. This article elucidates geochemical behaviors of LMWOAs in the surface environment in details, taking natural water, soil, and aerosol as examples, focusing on reviewing research developments on sources and characteristics, migration and mineralization of LMWOAs and relevant environmental effects. Simultaneously, this review article depicts the categories and contents of LMWOAs or their contribution to DOC in environmental media, and evaluates their importance during organic matter early diagenesis. Through concluding and discussing the conversion mechanisms and influencing factors, the next research orientations on LMWOAs in lake ecosystems are determined, mainly concerning relationships with hydrochemical parameters and microorganisms, and interactions with pollutants. This will enrich the knowledge on organic matter degradation and related environmental effects, and help reconstruct a theoretical framework for organic compound succession and influencing factors, providing basic data for lake eutrophication and ecological risk assessment, conducive to better control over water pollution and proper management of water quality.

Oxalate degradation in a bioelectrochemical system: reactor performance and microbial community characterization

The aim of this work was to investigate the feasibility of using oxalate at the anode in a continuous reactor. Complete oxalate removal was observed, albeit at a maximum coulombic efficiency of 33.9±0.4%. At the cathode side, there was an increase in pH from 8 to 11 showing production of caustic. Analysis of the microbial community demonstrated a clear shift during reactor start-up, resulting in enrichment of microorganisms belonging to Bacteroidetes, Firmicutes, Mollicutes, and β and γ-Proteobacteria. Methane was produced throughout the experiment; Archaea belonging to the Methanosarcinacea, Methanomicrobiaceae and Methanosaetaceae were identified as key representatives.

Acetogenesis in the energy-starved deep biosphere - a paradox?

Under anoxic conditions in sediments, acetogens are often thought to be outcompeted by microorganisms performing energetically more favorable metabolic pathways, such as sulfate reduction or methanogenesis. Recent evidence from deep subseafloor sediments suggesting acetogenesis in the presence of sulfate reduction and methanogenesis has called this notion into question, however. Here I argue that acetogens can successfully coexist with sulfate reducers and methanogens for multiple reasons. These include (1) substantial energy yields from most acetogenesis reactions across the wide range of conditions encountered in the subseafloor, (2) wide substrate spectra that enable niche differentiation by use of different substrates and/or pooling of energy from a broad range of energy substrates, (3) reduced energetic cost of biosynthesis among acetogens due to use of the reductive acetyl CoA pathway for both energy production and biosynthesis coupled with the ability to use many organic precursors to produce the key intermediate acetyl CoA. This leads to the general conclusion that, beside Gibbs free energy yields, variables such as metabolic strategy and energetic cost of biosynthesis need to be taken into account to understand microbial survival in the energy-depleted deep biosphere.

Methylmercury decomposition in sediments and bacterial cultures: involvement of methanogens and sulfate reducers in oxidative demethylation

Demethylation of monomethylmercury in freshwater and estuarine sediments and in bacterial cultures was investigated with CH(3)HgI. Under anaerobiosis, results with inhibitors indicated partial involvement of both sulfate reducers and methanogens, the former dominating estuarine sediments, while both were active in freshwaters. Aerobes were the most significant demethylators in estuarine sediments, but were unimportant in freshwater sediments. Products of anaerobic demethylation were mainly CO(2) as well as lesser amounts of CH(4). Acetogenic activity resulted in fixation of some CO(2) produced from CH(3)HgI into acetate. Aerobic demethylation in estuarine sediments produced only CH(4), while aerobic demethylation in freshwater sediments produced small amounts of both CH(4) and CO(2). Two species of Desulfovibrio produced only traces of CH(4) from CH(3)HgI, while a culture of a methylotrophic methanogen formed traces of CO(2) and CH(4) when grown on trimethylamine in the presence of the CH(3)HgI. These results indicate that both aerobes and anaerobes demethylate mercury in sediments, but that either group may dominate in a particular sediment type. Aerobic demethylation in the estuarine sediments appeared to proceed by the previously characterized organomercurial-lyase pathway, because methane was the sole product. However, aerobic demethylation in freshwater sediments as well as anaerobic demethylation in all sediments studied produced primarily carbon dioxide. This indicates the presence of an oxidative pathway, possibly one in which methylmercury serves as an analog of one-carbon substrates.

Characteristics and distribution of low molecular weight organic acids in the sediment porewaters in Bosten Lake, China

The composition and vertical profiles of low molecular-weight organic acids (LMWOAs) and the contribution of them to dissolved organic matter (DOM) in sediment porewaters in Bosten Lake, Xinjiang, China were investigated. The results showed that total concentration of LMWOAs was up to 94.5 micromol/L and their proportion in DOM was 5.6%, suggesting that LMWOAs were important chemical components in DOM in lake sediment porewaters. Among the seven LMWOAs, pyruvic and acetic acid had the highest concentrations with 26.30 and 8.31 micromol/L, accounting for 51.4% and 14.92% of LMWOAs, respectively. Trifluoroacetic and sorbic acid had the lowest concentrations, indicating that the compositions of LMWOAs in relative reducing environments were largely different from those reported in glacier, atmosphere and soils. The concentrations of lactic, acetic, formic, sorbic and oxalic acid decreased with increasing depth, probably relating to stronger microbial activities in the initial stage of early diagenesis. Trifluoroacetic acid was mainly anthropogenic with its concentration, showing a diffusive trend from the surface to bottom sediments. The concentrations of lactic acid and nitrate generally showed a consistent profile. The increasing concentration of pyruvic acid in the vertical profile was just opposite to that of sulfate, revealing a significant negative relationship between them. Oxalic acid remained constant except for an obvious peak at 6 cm depth. The results indicated the diversities in sources and behaviors for various LMWOAs during early diagenesis in sediments.

Anaerobic biodegradability and methanogenic toxicity of key constituents in copper chemical mechanical planarization effluents of the semiconductor industry

Copper chemical mechanical planarization (CMP) effluents can account for 30-40% of the water discharge in semiconductor manufacturing. CMP effluents contain high concentrations of soluble copper and a complex mixture of organic constituents. The aim of this study is to perform a preliminary assessment of the treatability of CMP effluents in anaerobic sulfidogenic bioreactors inoculated with anaerobic granular sludge by testing individual compounds expected in the CMP effluents. Of all the compounds tested (copper (II), benzotriazoles, polyethylene glycol (M(n) 300), polyethylene glycol (M(n) 860) monooleate, perfluoro-1-octane sulfonate, citric acid, oxalic acid and isopropanol) only copper was found to be inhibitory to methanogenic activity at the concentrations tested. Most of the organic compounds tested were biodegradable with the exception of perfluoro-1-octane sulfonate and benzotriazoles under sulfate reducing conditions and with the exception of the same compounds as well as Triton X-100 under methanogenic conditions. The susceptibility of key components in CMP effluents to anaerobic biodegradation combined with their low microbial inhibition suggest that CMP effluents should be amenable to biological treatment in sulfate reducing bioreactors.

Oxalotrophic bacteria

Oxalic acid and its salts are widespread in nature, as they are produced by many species of plants, algae and fungi. The bacteria, which are capable of using oxalate as a sole carbon and energy source, are described as being "oxalotrophic". Oxalotrophic bacteria do not constitute a homogeneous taxonomic group, but they do constitute a well-defined physiological group. A limited number of aerobic bacteria which are able to utilize oxalate as sole carbon and energy source have been completely described. Most of them are facultative methylotrophs and/or facultative hydrogen-oxidizing chemolithoautotrophs. In this review, the current status of the taxonomy and biodiversity of oxalotrophic bacteria in various environments, and aspects of their biotechnological potential, are briefly summarized.

Oxalate- and Glyoxylate-Dependent Growth and Acetogenesis by Clostridium thermoaceticum

The acetogenic bacterium Clostridium thermoaceticum ATCC 39073 grew at the expense of the two-carbon substrates oxalate and glyoxylate. Other two-carbon substrates (acetaldehyde, acetate, ethanol, ethylene glycol, glycolaldehyde, glycolate, and glyoxal) were not growth supportive. Growth increased linearly with increasing substrate concentrations up to 45 mM oxalate and glyoxylate, and supplemental CO 2 was not required for growth. Oxalate and glyoxylate yielded 4.9 and 9.4 g, respectively, of cell biomass (dry weight) per mol of substrate utilized. Acetate was the major reduced end product recovered from oxalate and glyoxylate cultures. 14 C labeling studies showed that oxalate was subject to decarboxylation, and product analysis indicated that oxalate was utilized by the following reaction: 4 - OOC-COO - + 5H 2 O → CH 3 COO - + 6HCO 3 - + OH - . Oxalate- and glyoxylate-dependent growth produced lower acetate concentrations per unit of cell biomass synthesized than did H 2 -, CO-, methanol-, formate-, O -methyl-, or glucose-dependent growth. Protein profiles of oxalate-grown cells were dissimilar from protein profiles of glyoxylate-, CO-, or formate-grown cells, suggesting induction of new proteins for the utilization of oxalate. C. thermoaceticum DSM 2955 and Clostridium thermoautotrophicum JW 701/3 also grew at the expense of oxalate and glyoxylate. However, oxalate and glyoxylate did not support the growth of C. thermoaceticum OMD (a nonautotrophic strain) or six other species of acetogenic bacteria tested.

Dissimilatory Selenate Reduction Potentials in a Diversity of Sediment Types

We measured potential rates of bacterial dissimilatory reduction of 75 SeO 4 2− to 75 Se 0 in a diversity of sediment types, with salinities ranging from freshwater (salinity = 1 g/liter) to hypersaline (salinity = 320 g/liter and with pH values ranging from 7.1 to 9.8. Significant biological selenate reduction occurred in all samples with salinities from 1 to 250 g/liter but not in samples with a salinity of 320 g/liter. Potential selenate reduction rates (25 nmol of SeO 4 2− per ml of sediment added with isotope) ranged from 0.07 to 22 μmol of SeO 4 2− reduced liter −1 h −1 . Activity followed Michaelis-Menten kinetics in relation to SeO 4 2− concentration ( K m of selenate = 7.9 to 720 μM). There was no linear correlation between potential rates of SeO 4 2− reduction and salinity, pH, concentrations of total Se, porosity, or organic carbon in the sediments. However, potential selenate reduction was correlated with apparent K m for selenate and with potential rates of denitrification ( r = 0.92 and 0.81, respectively). NO 3 − , NO 2 − , MoO 4 2− , and WO 4 2− inhibited selenate reduction activity to different extents in sediments from both Hunter Drain and Massie Slough, Nev. Sulfate partially inhibited activity in sediment from freshwater (salinity = 1 g/liter) Massie Slough samples but not from the saline (salinity = 60 g/liter) Hunter Drain samples. We conclude that dissimilatory selenate reduction in sediments is widespread in nature. In addition, in situ selenate reduction is a first-order reaction, because the ambient concentrations of selenium oxyanions in the sediments were orders of magnitude less than their K m s.

Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract

This report describes a new group of anaerobic bacteria that degrade oxalic acid. The new genus and species, Oxalobacter formigenes, are inhabitants of the rumen and also of the large bowel of man and other animals where their actions in destruction of oxalic acid may be of considerable importance to the host. Isolates from the rumen of a sheep, the cecum of a pig, and from human feces were all similar Gram-negative, obligately anaerobic rods, but differences between isolates in cellular fatty acid composition and in serologic reaction were noted. Measurements made with type strain OxB indicated that 1 mol of protons was consumed per mol of oxalate degraded to produce approximately 1 mol of CO2 and 0.9 mol of formate. Substances that replaced oxalate as a growth substrate were not found.