The purpose of this study was a detailed characterization of Shewanella sp. O23S, a strain involved in arsenic transformation in ancient gold mine waters contaminated with arsenic and other heavy metals. Physiological analysis of Shewanella sp. O23S showed that it is a facultative anaerobe, capable of growth using arsenate, thiosulfate, nitrate, iron or manganite as a terminal electron acceptor, and lactate or citrate as an electron donor. The strain can grow under anaerobic conditions and utilize arsenate in the respiratory process in a broad range of temperatures (10–37 °C), pH (4–8), salinity (0%–2%), and the presence of heavy metals (Cd, Co, Cr, Cu, Mn, Mo, Se, V and Zn). Under reductive conditions this strain can simultaneously use arsenate and thiosulfate as electron acceptors and produce yellow arsenic (III) sulfide (As₂S₃) precipitate. Simulation of As-removal from water containing arsenate (2.5 mM) and thiosulfate (5 mM) showed 82.5% efficiency after 21 days of incubation at room temperature. Based on the obtained results, we have proposed a model of a microbially mediated system for self-cleaning of mine waters contaminated with arsenic, in which Shewanella sp. O23S is the main driving agent.

Organotin compounds (OTCs) are among the most hazardous substances found in the marine environment and can be determined by either the ISO 23161 method based on extraction with non-polar organic solvents and gas chromatography analysis or by the recently developed QuEChERS method coupled to liquid chromatography-mass spectrometry (LC-MS/MS). To date, the QuEChERS LC/MS and ISO 23161 methods have not been compared in terms of their fit-for-purpose and reliability in the determination of OTCs in bottom sediments. In the case of ISO 23161, due to a large number of interferences gas chromatography-mass spectrometry was not suitable for the determination of OTCs contrary to more selective determination by gas chromatography with an atomic emission detector. Moreover, it has been found that the derivatization of OTCs to volatile compounds, which required prior gas chromatography determination, was strongly affected by the sediments’ matrices. As a result, a large amount of reagent was needed for the complete derivatization of the compounds. Contrary to ISO 23161, the QuEChERS LC-MS/MS method did not require the derivatization of OTC and is less prone to interferences. Highly volatile and toxic solvents were not used in the QuEChERS LC-MS/MS method. This makes the method more environmentally friendly according to the principles of green analytical chemistry. QuEChERS LC-MS/MS is suitable for fast and reliable environmental monitoring of OTCs in bottom sediments from the Odra River estuary. However, determination of di- and monobutyltin by the QuEChERS LC-MS/MS method was not possible due to the constraints of the chromatographic system. Hence, further development of this method is needed for monitoring di- and monobutyltin in bottom sediments.

This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln³⁺)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by Alpha-, Beta-, and Gammaproteobacteria represented by the four orders Methylococcales, Nitrosomonadales, Rhizobiales, and Xanthomonadales. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with Nitrosomonadales and Rhizobiales, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.

This study describes for the first time the comprehensive characterization of tetrapyrrole cofactor biosynthetic pathways developed for bacterial community (BC) inhabiting shale rock. Based on the genomic and proteomic metadata, we have detailed the biosynthesis of siroheme, heme, cobalamin, and the major precursor uroporphyrinogen III by a deep BC living on a rock containing sedimentary tetrapyrrole compounds. The obtained results showed the presence of incomplete heme and cobalamin biosynthesis pathways in the studied BC. At the same time, the production of proteins containing these cofactors, such as cytochromes, catalases and sulfite reductase, was observed. The results obtained are crucial for understanding the ecology of bacteria inhabiting shale rock, as well as their metabolism and potential impact on the biogeochemistry of these rocks. Based on the findings, we hypothesize that the bacteria may use primary or modified sedimentary porphyrins and their degradation products as precursors for synthesizing tetrapyrrole cofactors. Experimental testing of this hypothesis is of course necessary, but its evidence would point to an important and unique phenomenon of the tetrapyrrole ring cycle on Earth involving bacteria.

Anaerobic digestion (AD) of waste biomass is primarily regarded as a technology for gaseous biofuel production. Depending on process configuration, AD enables the generation of biohydrogen, biomethane, and digestate with potential fertilization value. Although digestate from conventional single-stage (1SD) AD systems has been extensively investigated, digestate derived from two-stage (2SD) configurations remains largely overlooked and is commonly assumed to be equivalent. Here, we present the first interdisciplinary comparison of 1SD and 2SD molasses AD systems, integrating process performance, digestate chemistry, microbial composition, and fertilization response assessed in pot experiments.Operation across a range of hydraulic retention times showed that stages separation restructures carbon conversion pathways. The 2SD system achieved approximately 27% higher total energy recovery than the 1SD configuration and maintained stable operation at short HRTs inaccessible to 1SD system. Chemical analyses demonstrated that the 2SD system produced more mature digestates, characterized by low residual chemical oxygen demand, limited accumulation of fermentation intermediates and long-chain fatty acids, elevated pH, and a pronounced shift toward plant-available mineral nitrogen, whereas digestates from the 1SD system indicated ongoing fermentative processes. Metagenomic analysis revealed that 2SD digestates supported higher microbial diversity, greater archaeal abundance, and dominance of acetoclastic Methanosaetaceae, alongside enrichment of amino acid–degrading consortia, plant growth–promoting taxa (e.g., Alcaligenes and Liquorilactobacillus), and indole-derived auxin precursors. Pot experiments confirmed these differences, showing consistently higher plant biomass following fertilization with 2SD digestates.The two-stage AD enables integrated recovery of renewable energy and agronomically enhanced nutrients from carbon-rich wastes, supporting SDG goals.