Electrogenic sulfur oxidation mediated by cable bacteria and its ecological effects

At the sediment-water interfaces, filamentous cable bacteria transport electrons from sulfide oxidation along their filaments towards oxygen or nitrate as electron acceptors. These multicellular bacteria belonging to the family Desulfobulbaceae thus form a biogeobattery that mediates redox processes between multiple elements. Cable bacteria were first reported in 2012. In the past years, cable bacteria have been found to be widely distributed across the globe. Their potential in shaping the surface water environments has been extensively studied but is not fully elucidated. In this review, the biogeochemical characteristics, conduction mechanisms, and geographical distribution of cable bacteria, as well as their ecological effects, are systematically reviewed and discussed. Novel insights for understanding and applying the role of cable bacteria in aquatic ecology are summarized.

Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis

The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.

Carbon and hydrogen stable isotope fractionation due to monooxygenation of short-chain alkanes by butane monooxygenase of Thauera butanivorans Bu-B1211

Multi element compound-specific stable isotope analysis (ME-CSIA) is a tool to assess (bio)chemical reactions of molecules in the environment based on their isotopic fingerprints. To that effect, ME-CSIA concepts are initially developed with laboratory model experiments to determine the isotope fractionation factors specific for distinct (bio)chemical reactions. Here, we determined for the first time the carbon and hydrogen isotope fractionation factors for the monooxygenation of the short-chain alkanes ethane, propane, and butane. As model organism we used Thauera butanivorans strain Bu-B1211 which employs a non-haem iron monooxygenase (butane monooxygenase) to activate alkanes. Monooxygenation of alkanes was associated with strong carbon and hydrogen isotope effects: εbulkC = -2.95 ± 0.5 ‰ for ethane, -2.68 ± 0.1 ‰ for propane, -1.19 ± 0.18 ‰ for butane; εbulkH = -56.3 ± 15 ‰ for ethane, -40.5 ± 2.3 ‰ for propane, -14.6 ± 3.6 ‰ for butane. This resulted in lambda (Λ ≈ εHbulk/εCbulk) values of 16.2 ± 3.7 for ethane, 13.2 ± 0.7 for propane, and 11.4 ± 2.8 for butane. The results show that ME-CSIA can be used to track the occurrence and impact of monooxygenase-dependent aerobic processes converting short-chain alkanes in natural settings like marine and terrestrial seeps, gas reservoirs, and other geological formations impacted by natural gas.

Antibiotic resistance indicator genes in biofilm and planktonic microbial communities after wastewater discharge

The spread of bacteria with antibiotic resistance genes (ARGs) in aquatic ecosystems is of growing concern as this can pose a risk of transmission to humans and animals. While the impact of wastewater treatment plant (WWTP) effluent on ARG abundance in surface waters has been studied extensively, less is known about the fate of ARGs in biofilms. The proximity and dense growth of microorganisms in combination with the accumulation of higher antibiotic concentrations in biofilms might render biofilms a reservoir for ARGs. Seasonal parameters such as water temperature, precipitation, and antibiotic concentrations should be considered as well, as they may further influence the fate of ARGs in aquatic ecosystems. Here we investigated the effect of WWTP effluent on the abundance of the sulfonamide resistance genes sul1 and sul2, and the integrase gene intI1 in biofilm and surface water compartments of a river in Germany with a gradient of anthropogenic impact using quantitative PCR. Furthermore, we analyzed the bacterial community structure in both compartments via 16S rRNA gene amplicon sequencing, following the river downstream. Additionally, conventional water parameters and sulfonamide concentrations were measured, and seasonal aspects were considered by comparing the fate of ARGs and bacterial community diversity in the surface water compartment between the summer and winter season. Our results show that biofilm compartments near the WWTP had a higher relative abundance of ARGs (up to 4.7%) than surface waters (<2.8%). Sulfonamide resistance genes were more persistent further downstream (>10 km) of the WWTP in the hot and dry summer season than in winter. This finding is likely a consequence of the higher proportion of wastewater and thus wastewater-derived microorganisms in the river during summer periods. We observed distinct bacterial communities and ARG abundance between the biofilm and surface water compartment, but even greater variations when considering seasonal and spatiotemporal parameters. This underscores the need to consider seasonal aspects when studying the fate of ARGs in aquatic ecosystems.

Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India

Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.

Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist

The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO₂ via beta oxidation and the oxidative Wood-Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps. Etymology: Desulfosarcina aeriophaga, aério (Greek): gas; phágos (Greek): eater; D. aeriophaga: a gas eating or gas feeding Desulfosarcina.

Comparative proteomics unravelled the hexachlorocyclohexane (HCH) isomers specific responses in an archetypical HCH degrading bacterium Sphingobium indicum B90A

Hexachlorocyclohexane (HCH) is a persistent organochlorine pesticide that poses threat to different life forms. Sphingobium indicum B90A that belong to sphingomonad is well-known for its ability to degrade HCH isomers (α-, β-, γ-, δ-), but effects of HCH isomers and adaptive mechanisms of strain B90A under HCH load remain obscure. To investigate the responses of strain B90A to HCH isomers, we followed the proteomics approach as this technique is considered as the powerful tool to study the microbial response to environmental stress. Strain B90A culture was exposed to α-, β-, γ-, δ-HCH (5 mgL^-1) and control (without HCH) taken for comparison and changes in whole cell proteome were analyzed. In β- and δ-HCH-treated cultures growth decreased significantly when compared to control, α-, and γ-HCH-treated cultures. HCH residue analysis corroborated previous observations depicting the complete depletion of α- and γ-HCH, while only 66% β-HCH and 34% δ-HCH were depleted from culture broth. Comparative proteome analyses showed that β- and δ-HCH induced utmost systemic changes in strain B90A proteome, wherein stress-alleviating proteins such as histidine kinases, molecular chaperons, DNA binding proteins, ABC transporters, TonB proteins, antioxidant enzymes, and transcriptional regulators were significantly affected. Besides study confirmed constitutive expression of linA, linB, and linC genes that are crucial for the initiation of HCH isomers degradation, while increased abundance of LinM and LinN in presence of β- and δ-HCH suggested the important role of ABC transporter in depletion of these isomers. These results will help to understand the HCH-induced damages and adaptive strategies of strain B90A under HCH load which remained unravelled to date.

Iron corrosion by methanogenic archaea characterized by stable isotope effects and crust mineralogy

Carbon and hydrogen stable isotope effects associated with methane formation by the corrosive archaeon Methanobacterium strain IM1 were determined during growth with hydrogen and iron. Isotope analyses were complemented by structural, elemental and molecular composition analyses of corrosion crusts. During growth with H₂ , strain IM1 formed methane with average δ¹³ C of -43.5‰ and δ² H of -370‰. Corrosive growth led to methane more depleted in ¹³ C, with average δ¹³ C ranging from -56‰ to -64‰ during the early and the late growth phase respectively. The corresponding δ² H were less impacted by the growth phase, with average values ranging from -316 to -329‰. The stable isotope fractionation factors, α 13 C CO 2 / CH 4 , were 1.026 and 1.042 for hydrogenotrophic and corrosive growth respectively. Corrosion crusts formed by strain IM1 have a domed structure, appeared electrically conductive and were composed of siderite, calcite and iron sulfide, the latter formed by precipitation of sulfide (from culture medium) with ferrous iron generated during corrosion. Strain IM1 cells were found attached to crust surfaces and encrusted deep inside crust domes. Our results may assist to diagnose methanogens-induced corrosion in the field and suggest that intrusion of sulfide in anoxic settings may stimulate corrosion by methanogenic archaea via formation of semiconductive crusts.

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses

Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used ¹³C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein–stable isotope probing. The detection of ¹³C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.

Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer

High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.

Dual C-Cl isotope analysis for characterizing the anaerobic transformation of α, β, γ, and δ-hexachlorocyclohexane in contaminated aquifers

Hexachlorocyclohexanes (HCHs) are widespread and persistent environmental pollutants, which cause heavy contamination in soil, sediment and groundwater. An anaerobic consortium, which was enriched on β-HCH using a soil sample from a contaminated area of a former pesticide factory, was capable to transform α, β, γ, and δ-HCH via tetrachlorocyclohexene isomers stoichiometrically to benzene and chlorobenzene. The carbon and chlorine isotope enrichment factors (ε_C and ε_Cl) of the dehalogenation of the four isomers ranged from -1.9 ± 0.3 to -6.4 ± 0.7‰ and from -1.6 ± 0.2 to -3.2 ± 0.6‰, respectively, and the correlation of δ³⁷Cl and δ¹³C (Λ values) of the four isomers ranged from 1.1 ± 0.1 to 2.4 ± 0.2. The evaluation of Λ and the apparent kinetic isotope effects (AKIE) for carbon and chlorine may lead to the hypothesis that the two eliminated chlorine atoms of α- and γ-HCH were in axial positions, the same as for the β-HCH conformer which has six chlorine atoms in axial positions after ring flip. The dichloroelimination of δ-HCH resulted in distinct AKIE and Λ values as one chlorine atom is in axial whereas the other chlorine atoms are in the equatorial positions. Significant chlorine and carbon isotope fractionations of HCH isomers were observed in the samples from a contaminated aquifer (Bitterfeld, Germany). The ³⁷Cl/³⁵Cl and ¹³C/¹²C isotope fractionation patterns of HCH isomers from laboratory experiments were used diagnostically in a model to characterize microbial dichloroelimination in the field study. The comparison of isotope fractionation patterns indicates that the transformation of HCH isomers at the field was mainly governed by microbial dichloroelimination transformation.

Dual C-Cl Isotope Analysis for Characterizing the Reductive Dechlorination of α- and γ-Hexachlorocyclohexane by Two Dehalococcoides mccartyi Strains and an Enrichment Culture

Hexachlorocyclohexanes (HCHs) are persistent organic contaminants that threaten human health. Microbial reductive dehalogenation is one of the most important attenuation processes in contaminated environments. This study investigated carbon and chlorine isotope fractionation of α- and γ-HCH during the reductive dehalogenation by three anaerobic cultures. The presence of tetrachlorocyclohexene (TeCCH) indicated that reductive dichloroelimination was the first step of bond cleavage. Isotope enrichment factors (ε_C and ε_Cl) were derived from the transformation of γ-HCH (ε_C, from -4.0 ± 0.5 to -4.4 ± 0.6 ‰; ε_Cl, from -2.9 ± 0.4 to -3.3 ± 0.4 ‰) and α-HCH (ε_C, from -2.4 ± 0.2 to -3.0 ± 0.4 ‰; ε_Cl, from -1.4 ± 0.3 to -1.8 ± 0.2 ‰). During α-HCH transformation, no enantioselectivity was observed, and similar ε_c values were obtained for both enantiomers. The correlation of ¹³C and ³⁷Cl fractionation (Λ = Δδ¹³C/Δδ³⁷Cl ≈ ε_C/ε_Cl) of γ-HCH (from 1.1 ± 0.3 to 1.2 ± 0.1) indicates similar bond cleavage during the reductive dichloroelimination by the three cultures, similar to α-HCH (1.7 ± 0.2 to 2.0 ± 0.3). The different isotope fractionation patterns during reductive dichloroelimination and dehydrochlorination indicates that dual-element stable isotope analysis can potentially be used to evaluate HCH transformation pathways at contaminated field sites.

Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis

Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (¹³C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.

Enantiomer and Carbon Isotope Fractionation of α-Hexachlorocyclohexane by Sphingobium indicum Strain B90A and the Corresponding Enzymes

Chiral organic contaminants, like α-hexachlorocyclohexane (α-HCH), showed isotope fractionation and enantiomer fractionation during biodegradation. This study aims to understand the correlation between these two processes. Initial tests of α-HCH degradation by six Sphingobium strains (with different LinA variants) were conducted. Results showed variable enantiomer selectivity over the time course. In contrast, constant enantiomer selectivity was observed in experiments employing (i) cell suspensions, (ii) crude extracts, or (iii) LinA1 and LinA2 enzymes of strain B90A for α-HCH degradation in enzyme activity assay buffer. The average value of enantioselectivity (ES) were -0.45 ± 0.03 (cell suspensions), -0.60 ± 0.05 (crude extracts), and 1 (LinA1) or -1 (LinA2). The average carbon isotope enrichment factors (ε_c) of (+)α- and (-)α-HCH were increased from cells suspensions (-6.3 ± 0.1‰ and -2.3 ± 0.03‰) over crude extracts (-7.7 ± 0.4‰ and -3.4 ± 0.02‰) to purified enzymes (-11.1 ± 0.3‰ and -3.8 ± 0.2‰). The variability of ES and the ε_c were discussed based on the effect of mass transport and degradation rates. Our study demonstrates that enantiomer and isotope fractionation of α-HCH are two independent processes and both are affected by underlying reactions of individual enzymes and mass transport to a different extent.

H2 Kinetic Isotope Fractionation Superimposed by Equilibrium Isotope Fractionation During Hydrogenase Activity of D. vulgaris Strain Miyazaki

We determined ²H stable isotope fractionation at natural abundances associated with hydrogenase activity by whole cells of Desulfovibrio vulgaris strain Miyazaki F expressing a NiFe(Se) hydrogenase. Inhibition of sulfate reduction by molybdate inhibited the overall oxidation of hydrogen but still facilitated an equilibrium isotope exchange reaction with water. The theoretical equilibrium isotope exchange δ²H-values of the chemical exchange reaction were identical to the hydrogenase reaction, as confirmed using three isotopically different waters with δ²H-values of – 62, +461, and + 1533‰. Expected kinetic isotope fractionation of hydrogen oxidation by non-inhibited cells was also superimposed by an equilibrium isotope exchange. The isotope effects were solely catalyzed biotically as hydrogen isotope signatures did not change in control experiments without cells of D. vulgaris Miyazaki.

Carbon and hydrogen isotopic fractionation during abiotic hydrolysis and aerobic biodegradation of phthalate esters

We systematically investigated the changes of carbon and hydrogen isotope signatures of three phthalate esters (PAEs) during (i) abiotic hydrolysis over the pH range of 2, 7 and 10, and (ii) aerobic biodegradation initiated by hydrolysis by Rhodococcus opacus strain DSM 43250. Significant carbon isotopic fractionation was exhibited under all investigated conditions. Hydrogen isotopic fractionation was observed in some experiments and is hypothesized to be a secondary isotope effect due to the absence of a hydrogen bond cleavage during hydrolysis. Dual stable isotope analysis (Λ = Δδ²H/Δδ¹³C) resulting from abiotic hydrolysis and aerobic biodegradation showed similar magnitudes for dimethyl phthalate (DMP) and diethyl phthalate (DEP). The calculated carbon apparent kinetic isotope effects (AKIE_C) for the hydrolytic pathway (CO bond cleavage) of PAEs fall within an expected range of 1.03-1.09, with the exception of lower AKIE_C values for dibutyl phthalate (DBP) during hydrolysis at pH 2 and aerobic biodegradation. The lower AKIE_C of DBP at pH 2 and aerobic biodegradation is likely related to a transition state from reactant-like to tetrahedral intermediate-like structure. Abiotic and biotic hydrolysis of PAEs resulted in similar AKIE_C and Λ values due to the CO bond cleavage pathway, indicating the potential of dual isotope analysis to detect and quantify hydrolytic processes of PAEs in the environment. The pronounced primary carbon and typically low secondary or absent hydrogen isotopic fractionation might form a typical pattern to identify the hydrolytic reaction of PAEs in the environment. The characteristic Λ values of the hydrolytic reaction were different from Λ values of chemical oxidation of PAEs and showed diagnostic potential of dual HC isotope analysis to analyze reactions.

Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep

Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps^1-3, and through ethane-dependent sulfate reduction in slurries^4-7. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown⁸. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name 'Candidatus Argoarchaeum ethanivorans'; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography-tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by 'Candidatus Syntrophoarchaeum'⁹. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO₂ occurs through the oxidative Wood-Ljungdahl pathway. The identification of an archaeon that uses ethane (C₂H₆) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (C_nH_2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps^10-12 suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.

Carbon and hydrogen stable isotope analysis for characterizing the chemical degradation of tributyl phosphate

Tributyl phosphate (TBP) belongs to the group of trialkyl substituted organophosphate esters. Its chemical reactivity depends on the stability of various chemical bonds. TBP was used as a model compound for the development of a concept using stable isotope fractionation associated with bond cleavage reactions for better understanding the fate of TBP in the environment. Carbon isotope enrichment factors (ε_C) of TBP hydrolysis were found to be pH dependent (-3.8 ± 0.3‰ at pH 2, -4.6 ± 0.5‰ at pH 7, -2.8 ± 0.1‰ at pH 9, no isotope fractionation at pH 12), which is in accordance with the mode of a S_N2 hydrolytic bond cleavage. Hydrogen isotope fractionation was negligible as no H bond cleavage is involved during hydrolysis. The apparent carbon kinetic isotope effect (AKIE_C) ranged from 1.045 to 1.058. In contrast to hydrolysis, both carbon and hydrogen isotope fractionation were observed during radical oxidation of TBP by OH and SO₄^-, yielding ε_C from -0.9 ± 0.1‰ to -0.5 ± 0.1‰ and ε_H from -20 ± 2‰ to -11 ± 1‰. AKIE_C and AKIE_H varied from 1.007 to 1.011 and from 1.594 to 2.174, respectively. The correlation of ²H and ¹³C isotope fractionation revealed Λ values ranging from 17 ± 1 to 25 ± 6. Results demonstrated that the correlation of ²H and ¹³C isotope fractionation of TBP allowed to identify radical reactions and to distinguish them from hydrolysis. The presented dual isotope analysis approach has diagnostic value for characterizing the chemical transformation of TBP in the environment.

Aqueous photodegradation of substituted chlorobenzenes: Kinetics, carbon isotope fractionation, and reaction mechanisms

Substituted chlorobenzenes are the basic substructure of many surface water contaminants. In this study, the isotope fractionation and reaction mechanisms involved during the aqueous direct and indirect photodegradation of CH₃-, Cl-, and NO₂- substituted chlorobenzenes were investigated in laboratory experiments. Only 4-nitrochlorobenzene showed slow but isotopically fractionating direct photolysis. During indirect photodegradation using UV/H₂O₂-generated OH radicals, the pseudo first-order reaction rate constants increased in the order of the NO₂- < Cl- < CH₃- substituted chlorobenzenes. The most pronounced carbon enrichment factors were observed for nitrochlorobenzenes (up to -4.8 ± 0.5‰), whereas the lowest were for chlorotoluenes (≤-1.0 ± 0.1‰). As the substituents became more electron-withdrawing, the activation energy barrier increased, leading to slower reaction rates, and the transition state changed to a more symmetrical or less reactant-like structure, resulting in larger apparent kinetic isotope effects. The results suggest that the rate-determining step in the reaction with OH radicals was the addition of the electrophile to the benzene ring. Even though further research is needed to quantify isotope fractionation during other transformation processes, these results showed evidence that compound specific isotope analysis can be used as a diagnostic tool for the fate of substituted chlorobenzenes in water.

A patchwork pathway for oxygenase-independent degradation of side chain containing steroids

The denitrifying betaproteobacterium Sterolibacterium denitrificans serves as model organism for studying the oxygen-independent degradation of cholesterol. Here, we demonstrate its capability of degrading various globally abundant side chain containing zoo-, phyto- and mycosterols. We provide the complete genome that empowered an integrated genomics/proteomics/metabolomics approach, accompanied by the characterization of a characteristic enzyme of steroid side chain degradation. The results indicate that individual molybdopterin-containing steroid dehydrogenases are involved in C25-hydroxylations of steroids with different isoprenoid side chains, followed by the unusual conversion to C26-oic acids. Side chain degradation to androsta-1,4-diene-3,17-dione (ADD) via aldolytic C-C bond cleavages involves acyl-CoA synthetases/dehydrogenases specific for the respective 26-, 24- and 22-oic acids/-oyl-CoAs and promiscuous MaoC-like enoyl-CoA hydratases, aldolases and aldehyde dehydrogenases. Degradation of rings A and B depends on gene products uniquely found in anaerobic steroid degraders, which after hydrolytic cleavage of ring A, again involves CoA-ester intermediates. The degradation of the remaining CD rings via hydrolytic cleavage appears to be highly similar in aerobic and anaerobic bacteria. Anaerobic cholesterol degradation employs a composite repertoire of more than 40 genes partially known from aerobic degradation in gammaproteobacteria/actinobacteria, supplemented by unique genes that are required to circumvent oxygenase-dependent reactions.

Compound Specific and Enantioselective Stable Isotope Analysis as Tools To Monitor Transformation of Hexachlorocyclohexane (HCH) in a Complex Aquifer System

Technical hexachlorocyclohexane (HCH) mixtures and Lindane (γ-HCH) have been produced in Bitterfeld-Wolfen, Germany, for about 30 years until 1982. In the vicinity of the former dump sites and production facilities, large plumes of HCHs persist within two aquifer systems. We studied the natural attenuation of HCH in these groundwater systems through a combination of enantiomeric and carbon isotope fractionation to characterize the degradation of α-HCH in the areas downstream of a former disposal and production site in Bitterfeld-Wolfen. The concentration and isotope composition of α-HCH from the Quaternary and Tertiary aquifers were analyzed. The carbon isotope compositions were compared to the source signal of waste deposits for the dumpsite and highly contaminated areas. The average value of δ¹³C at dumpsite was -29.7 ± 0.3 ‰ and -29.0 ± 0.1 ‰ for (-) and (+)α-HCH, respectively, while those for the β-, γ-, δ-HCH isomers were -29.0 ± 0.3 ‰, -29.5 ± 0.4 ‰, and -28.2 ± 0.2 ‰, respectively. In the plume, the enantiomer fraction shifted up to 0.35, from 0.50 at source area to 0.15 (well T1), and was found accompanied by a carbon isotope enrichment of 5 ‰ and 2.9 ‰ for (-) and (+)α-HCH, respectively. The established model for interpreting isotope and enantiomer fractionation patterns showed potential for analyzing the degradation process at a field site with a complex history with respect to contamination and fluctuating geochemical conditions.

Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments

Fungal–bacterial interactions are highly diverse and contribute to many ecosystem processes. Their emergence under common environmental stress scenarios however, remains elusive. Here we use a synthetic microbial ecosystem based on the germination of Bacillus subtilis spores to examine whether fungal and fungal-like (oomycete) mycelia reduce bacterial water and nutrient stress in an otherwise dry and nutrient-poor microhabitat. We find that the presence of mycelia enables the germination and subsequent growth of bacterial spores near the hyphae. Using a combination of time of flight- and nanoscale secondary ion mass spectrometry (ToF- and nanoSIMS) coupled with stable isotope labelling, we link spore germination to hyphal transfer of water, carbon and nitrogen. Our study provides direct experimental evidence for the stimulation of bacterial activity by mycelial supply of scarce resources in dry and nutrient-free environments. We propose that mycelia may stimulate bacterial activity and thus contribute to sustaining ecosystem functioning in stressed habitats.

The maintenance of bacterial and fungal activity is essential for ecosystem functioning, particularly in dry soils where the two phyla co-exist. Here, Worrich and colleagues show experimentally that mycelia traffic water and nutrients and thereby stimulate bacterial activity in stressful conditions.

Evaluation of the performance of high temperature conversion reactors for compound-specific oxygen stable isotope analysis

In this study conversion conditions for oxygen gas chromatography high temperature conversion (HTC) isotope ratio mass spectrometry (IRMS) are characterised using qualitative mass spectrometry (IonTrap). It is shown that physical and chemical properties of a given reactor design impact HTC and thus the ability to accurately measure oxygen isotope ratios. Commercially available and custom-built tube-in-tube reactors were used to elucidate (i) by-product formation (carbon dioxide, water, small organic molecules), (ii) 2nd sources of oxygen (leakage, metal oxides, ceramic material), and (iii) required reactor conditions (conditioning, reduction, stability). The suitability of the available HTC approach for compound-specific isotope analysis of oxygen in volatile organic molecules like methyl tert-butyl ether is assessed. Main problems impeding accurate analysis are non-quantitative HTC and significant carbon dioxide by-product formation. An evaluation strategy combining mass spectrometric analysis of HTC products and IRMS ¹⁸O/¹⁶O monitoring for future method development is proposed.

Carbon, Hydrogen and Chlorine Stable Isotope Fingerprinting for Forensic Investigations of Hexachlorocyclohexanes

Multielemental stable isotope analysis of persistent organic pollutants (POPs) has the potential to characterize sources, sinks, and degradation processes in the environment. To verify the applicability of this approach for source identification of hexachlorocyclohexane (HCHs), we provide a data set of carbon, hydrogen, and chlorine stable isotope ratios (δ¹³C, δ²H, δ³⁷Cl) of its main stereoisomers (α-, β-, δ- and γ-HCHs) from a sample collection based on worldwide manufacturing. This sample collection comprises production stocks, agricultural and pharmaceutical products, chemical waste dumps, and analytical-grade material, covering the production time period from the late 1960s until now. Stable isotope ratios of HCHs cover the ranges from -233‰ to +1‰, from -35.9‰ to -22.7‰, and from -6.69‰ to +0.54‰ for δ²H, δ¹³C, and δ³⁷Cl values, respectively. Four groups of samples with distinct multielemental stable isotope fingerprints were differentiated, most probably as a result of purification and isolation processes. No clear temporal trend in the isotope compositions of HCHs was found at the global scale. The multielemental stable isotope fingerprints facilitate the source identification of HCHs at the regional scale and can be used to assess transformation processes. The data set and methodology reported herein provide basic information for the assessment of environmental field sites contaminated with HCHs.

Thermophilic archaea activate butane via alkyl-coenzyme M formation

The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors, all of which are believed to be specific for C₁-compounds. Here we show that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C₄ hydrocarbon butane. The archaea, proposed genus 'Candidatus Syntrophoarchaeum', show the characteristic autofluorescence of methanogens, and contain highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase. We detect butyl-coenzyme M, indicating archaeal butane activation analogous to the first step in anaerobic methane oxidation. In addition, Ca. Syntrophoarchaeum expresses the genes encoding β-oxidation enzymes, carbon monoxide dehydrogenase and reversible C₁ methanogenesis enzymes. This allows for the complete oxidation of butane. Reducing equivalents are seemingly channelled to HotSeep-1, a thermophilic sulfate-reducing partner bacterium known from the anaerobic oxidation of methane. Genes encoding 16S rRNA and methyl-coenzyme M reductase similar to those identifying Ca. Syntrophoarchaeum were repeatedly retrieved from marine subsurface sediments, suggesting that the presented activation mechanism is naturally widespread in the anaerobic oxidation of short-chain hydrocarbons.

Lessons learned from the microbial ecology resulting from different inoculation strategies for biogas production from waste products of the bioethanol/sugar industry

BACKGROUND

During strategic planning of a biogas plant, the local availability of resources for start-up and operation should be taken into consideration for a cost-efficient process. Because most bioethanol/sugar industries in Brazil are located in remote areas, the use of fresh cattle manure from local farms could be a solution for the inoculation of the biogas process. This study investigated the diversity and dynamics of bacterial and archaeal communities and the performance of biogas reactors inoculated with manure and a mixed inoculum from different biogas reactors as for a controlled start-up until steady state.

RESULTS

Laboratory-scale biogas reactors were fed semi-continuously with sugarcane filter cake alone (mono-digestion) or together with bagasse (co-digestion). At the initial start-up, the reactors inoculated with the mixed inoculum displayed a less diverse taxonomic composition, but with higher presence of significant abundances compared to reactors inoculated with manure. However, in the final steady state, the communities of the differently inoculated reactors were very similarly characterized by predominance of the methanogenic genera Methanosarcina and Methanobacterium, the bacterial families Bacteroidaceae, Prevotellaceae and Porphyromonadaceae (phylum Bacteroidetes) and Synergistaceae (phylum Synergistetes). In the mono-digestion reactors, the methanogenic communities varied greater than in the co-digestion reactors independently of the inoculation strategy.

CONCLUSION

The microbial communities involved in the biogas production from waste products of the Brazilian bioethanol/sugar industry were relatively similar and stable at the reactor's steady phase independently of the inoculum source (manure or mixed inoculum). Therefore, the locally available manure can be used as inoculum for start-up of the biogas process, since it also contains the microbial resources needed. The strong fluctuation of methanogenic communities in mono-digestion reactors indicates higher risk of process instability than in co-digestion reactors.

Characterization of toluene and ethylbenzene biodegradation under nitrate-, iron(III)- and manganese(IV)-reducing conditions by compound-specific isotope analysis

Ethylbenzene and toluene degradation under nitrate-, Mn(IV)-, or Fe(III)-reducing conditions was investigated by compound specific stable isotope analysis (CSIA) using three model cultures (Aromatoleum aromaticum EbN1, Georgfuchsia toluolica G5G6, and a Azoarcus-dominated mixed culture). Systematically lower isotope enrichment factors for carbon and hydrogen were observed for particulate Mn(IV). The increasing diffusion distances of toluene or ethylbenzene to the solid Mn(IV) most likely caused limited bioavailability and hence resulted in the observed masking effect. The data suggests further ethylbenzene hydroxylation by ethylbenzene dehydrogenase (EBDH) and toluene activation by benzylsuccinate synthase (BSS) as initial activation steps. Notably, significantly different values in dual isotope analysis were detected for toluene degradation by G. toluolica under the three studied redox conditions, suggesting variations in the enzymatic transition state depending on the available TEA. The results indicate that two-dimensional CSIA has significant potential to assess anaerobic biodegradation of ethylbenzene and toluene at contaminated sites.

Characterization of phenol and cresol biodegradation by compound-specific stable isotope analysis

Microbial degradation of phenol and cresols can occur under oxic and anoxic conditions by different degradation pathways. One recent technique to take insight into reaction mechanisms is compound-specific isotope analysis (CSIA). While enzymes and reaction mechanisms of several degradation pathways have been characterized in (bio)chemical studies, associated isotope fractionation patterns have been rarely reported, possibly due to constraints in current analytical methods. In this study, carbon enrichment factors and apparent kinetic isotope effects (AKIEc) of the initial steps of different aerobic and anaerobic phenol and cresols degradation pathways were analyzed by isotope ratio mass spectrometry connected with liquid chromatography (LC-IRMS). Significant isotope fractionation was detected for aerobic ring hydroxylation, anoxic side chain hydroxylation, and anoxic fumarate addition, while anoxic carboxylation reactions produced small and inconsistent fractionation. The results suggest that several microbial degradation pathways of phenol and cresols are detectable in the environment by CSIA.

Improved Monitoring of Semi-Continuous Anaerobic Digestion of Sugarcane Waste: Effects of Increasing Organic Loading Rate on Methanogenic Community Dynamics

The anaerobic digestion of filter cake and its co-digestion with bagasse, and the effect of gradual increase of the organic loading rate (OLR) from start-up to overload were investigated. Understanding the influence of environmental and technical parameters on the development of particular methanogenic pathway in the biogas process was an important aim for the prediction and prevention of process failure. The rapid accumulation of volatile organic acids at high OLR of 3.0 to 4.0 gvs·L⁻¹·day⁻¹ indicated strong process inhibition. Methanogenic community dynamics of the reactors was monitored by stable isotope composition of biogas and molecular biological analysis. A potential shift toward the aceticlastic methanogenesis was observed along with the OLR increase under stable reactor operating conditions. Reactor overloading and process failure were indicated by the tendency to return to a predominance of hydrogenotrophic methanogenesis with rising abundances of the orders Methanobacteriales and Methanomicrobiales and drop of the genus Methanosarcina abundance.

Improvement of analytical method for chlorine dual-inlet isotope ratio mass spectrometry of organochlorines

RATIONALE

The development of compound-specific chlorine isotope analysis (Cl-CSIA) is hindered by the lack of international organochlorine reference materials with isotopic compositions expressed in the δ(37) Cl notation. Thus, a reliable off-line analytical method is needed, allowing direct comparison of the δ(37) Cl values of molecularly different organic compounds with that of ocean-water chloride, to refer measurement results to a Standard Mean Ocean Chloride (SMOC) scale.

METHODS

The analytical method included sealed-tube combustion of organochlorines, precipitation and subsequent conversion of formed inorganic chlorides into methyl chloride (CH3 Cl) for the determination of δ(37) Cl values by Dual-Inlet Isotope Ratio Mass Spectrometry (DI-IRMS). A sample preparation step most sensitive to the sample size - dissolution of the inorganic copper chlorides formed by combustion of organochlorines - was identified.

RESULTS

Recovery of 94 ± 5% of chlorine was reached by applying determined optimal conditions for the dissolution, implying good external precision of δ(37) Cl values (-0.18 ± 0.03‰, 1σ, n = 3). Validation of the optimized method by the analysis of the produced and initial CH3 Cl samples with known δ(37) Cl values vs SMOC resulted in a difference of 0.11 ± 0.04‰ (1σ, n = 3), confirming the external precision and accuracy of the entire method.

CONCLUSIONS

The efficiency of the sample preparation method for CH3 Cl-DI-IRMS analysis is independent both of the chemical structure of the chlorinated compound and of the amount of chlorine in the sample. This method has the potential to be applied to a broad range of chlorinated organic compounds, e.g. reference material for the calibration of methods for Cl-CSIA against SMOC.

The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment

The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in semiarid soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted semiarid soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation.

Carbon Stable Isotope Fractionation of Sulfamethoxazole during Biodegradation by Microbacterium sp. Strain BR1 and upon Direct Photolysis

Carbon isotope fractionation of sulfamethoxazole (SMX) during biodegradation by Microbacterium sp. strain BR1 (ipso-hydroxylation) and upon direct photolysis was investigated. Carbon isotope signatures (δ(13)C) of SMX were measured by LC-IRMS (liquid chromatography coupled to isotope ratio mass spectrometry). A new LC-IRMS method for the SMX metabolite, 3-amino-5-methylisoxazole (3A5MI), was established. Carbon isotope enrichment factors for SMX (ε(C)) were -0.6 ± 0.1‰ for biodegradation and -2.0 ± 0.1‰ and -3.0 ± 0.2‰ for direct photolysis, at pH 7.4 and pH 5, respectively. The corresponding apparent kinetic isotope effects (AKIE) for ipso-hydroxylation were 1.006 ± 0.001; these fall in the same range as AKIE in previously studied hydroxylation reactions. The differences in SMX and 3A5MI fractionation upon biotic and abiotic degradation suggest that compound specific stable isotope analysis (CSIA) is a suitable method to distinguish SMX reaction pathways. In addition, the study revealed that the extent of isotope fractionation during SMX photolytic cleavage is pH-dependent.

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.

Compound-specific isotope analysis as a tool to characterize biodegradation of ethylbenzene

This study applied one- and two-dimensional compound-specific isotope analysis (CSIA) for the elements carbon and hydrogen to assess different means of microbial ethylbenzene activation. Cultures incubated under nitrate-reducing conditions showed significant carbon and highly pronounced hydrogen isotope fractionation of comparable magnitudes, leading to nearly identical slopes in dual-isotope plots. The results imply that Georgfuchsia toluolica G5G6 and an enrichment culture dominated by an Azoarcus species activate ethylbenzene by anaerobic hydroxylation catalyzed by ethylbenzene dehydrogenase, similar to Aromatoleum aromaticum EbN1. The isotope enrichment pattern in dual plots from two strictly anaerobic enrichment cultures differed considerably from those for benzylic hydroxylation, indicating an alternative anaerobic activation step, most likely fumarate addition. Large hydrogen fractionation was quantified using a recently developed Rayleigh-based approach considering hydrogen atoms at reactive sites. Data from nine investigated microbial cultures clearly suggest that two-dimensional CSIA in combination with the magnitude of hydrogen isotope fractionation is a valuable tool to distinguish ethylbenzene degradation and may be of practical use for monitoring natural or technological remediation processes at field sites.

Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria

This study aimed to ascertain the functional and phylogenetic relationships within an m-xylene degrading sulfate-reducing enrichment culture, which had been maintained for several years in the laboratory with m-xylene as the sole source of carbon and energy. Previous studies indicated that a phylotype affiliated to the Desulfobacteraceae was the main m-xylene assimilating organism. In the present study, genes and gene products were identified by a metaproteogenomic approach using LC-MS/MS analysis of the microbial community, and 2426 peptides were identified from 576 proteins. In the metagenome of the community, gene clusters encoding enzymes involved in fumarate addition to a methyl moiety of m-xylene (nms, bss), as well as gene clusters coding for enzymes involved in modified beta-oxidation to (3-methyl)benzoyl-CoA (bns), were identified in two separate contigs. Additionally, gene clusters containing homologues to bam genes encoding benzoyl-CoA reductase (Bcr) class II, catalyzing the dearomatization of (3-methyl)benzoyl-CoA, were identified. Time-resolved protein stable isotope probing (protein-SIP) experiments using (13)C-labeled m-xylene showed that the respective gene products were highly (13)C-labeled. The present data suggested the identification of gene products that were similar to those involved in methylnaphthalene degradation even though the consortium was not capable of growing in the presence of naphthalene, methylnaphthalene or toluene as substrates. Thus, a novel branch of enzymes was found that was probably specific for anaerobic m-xylene degradation.

Rayleigh-based concept to tackle strong hydrogen fractionation in dual isotope analysis-the example of ethylbenzene degradation by Aromatoleum aromaticum

Compound-specific isotope analysis (CSIA) is a state-of-the-art analytical tool that can be used to establish and quantify biodegradation of pollutants such as BTEX compounds at contaminated field sites. Using isotopes of two elements and characteristic Lambda values (Λ) in dual-isotope-plots can provide insight into reaction mechanisms because kinetic isotope effects (KIEs) of both elements are reflected. However, the concept's validity in the case of reactions that show strong isotope fractionation needs to be examined. The anaerobic ethylbenzene degradation pathway of Aromatoleum aromaticum is initiated by the ethylbenzene dehydrogenase-catalyzed monohydroxylation of the benzylic carbon atom. Measurements of stable isotope ratios revealed highly pronounced hydrogen fractionation, which could not be adequately described by the classical Rayleigh approach. This study demonstrates the nonlinear behavior of hydrogen isotope ratios caused by anaerobic ethylbenzene hydroxylation both mathematically and experimentally, develops alternative dual plots to enable the comparison of reactions by considering the reacting atoms, and illustrates the importance of the stereochemical aspects of substrate and product for the quantification of hydrogen fractionation in an enzymatic reaction. With regard to field application, proposals for an improved CSIA evaluation procedure with respect to pronounced hydrogen enrichment are given.

Using compound-specific isotope analysis to assess the degradation of chloroacetanilide herbicides in lab-scale wetlands

Compound-specific isotope analysis (CSIA) is a promising tool to study the environmental fate of a wide range of contaminants including pesticides. In this study, a novel CSIA method was developed to analyse the stable carbon isotope signatures of widely used chloroacetanilide herbicides. The developed method was applied in combination with herbicide concentration and hydrochemical analyses to investigate in situ biodegradation of metolachlor, acetochlor and alachlor during their transport in lab-scale wetlands. Two distinct redox zones were identified in the wetlands. Oxic conditions prevailed close to the inlet of the four wetlands (oxygen concentration of 212±24μM), and anoxic conditions (oxygen concentrations of 28±41μM) prevailed towards the outlet, where dissipation of herbicides mainly occurred. Removal of acetochlor and alachlor from inlet to outlet of wetlands was 56% and 51%, whereas metolachlor was more persistent (23% of load dissipation). CSIA of chloroacetanilides at the inlet and outlet of the wetlands revealed carbon isotope fractionation of alachlor (εbulk=-2.0±0.3‰) and acetochlor (εbulk=-3.4±0.5‰), indicating that biodegradation contributes to the dissipation of both herbicides. This study is a first step towards the application of CSIA to evaluate the transport and degradation of chloroacetanilide herbicides in the environment.

Iron oxides stimulate microbial monochlorobenzene in situ transformation in constructed wetlands and laboratory systems

Natural wetlands are transition zones between anoxic ground and oxic surface water which may enhance the (bio)transformation potential for recalcitrant chloro-organic contaminants due to the unique geochemical conditions and gradients. Monochlorobenzene (MCB) is a frequently detected groundwater contaminant which is toxic and was thought to be persistent under anoxic conditions. Furthermore, to date, no degradation pathways for anoxic MCB removal have been proven in the field. Hence, it is important to investigate MCB biodegradation in the environment, as groundwater is an important drinking water source in many European countries. Therefore, two pilot-scale horizontal subsurface-flow constructed wetlands, planted and unplanted, were used to investigate the processes in situ contributing to the biotransformation of MCB in these gradient systems. The wetlands were fed with anoxic MCB-contaminated groundwater from a nearby aquifer in Bitterfeld, Germany. An overall MCB removal was observed in both wetlands, whereas just 10% of the original MCB inflow concentration was detected in the ponds. In particular in the gravel bed of the planted wetland, MCB removal was highest in summer season with 73 ± 9% compared to the unplanted one with 40 ± 5%. Whereas the MCB concentrations rapidly decreased in the transition zone of unplanted gravel to the pond, a significant MCB removal was already determined in the anoxic gravel bed of the planted system. The investigation of hydro-geochemical parameters revealed that iron and sulphate reduction were relevant redox processes in both wetlands. In parallel, the addition of ferric iron or nitrate stimulated the mineralisation of MCB in laboratory microcosms with anoxic groundwater from the same source, indicating that the potential for anaerobic microbial degradation of MCB is present at the field site.

Enantioselective carbon stable isotope fractionation of hexachlorocyclohexane during aerobic biodegradation by Sphingobium spp

Carbon isotope fractionation was investigated for the biotransformation of γ- and α- hexachlorocyclohexane (HCH) as well as enantiomers of α-HCH using two aerobic bacterial strains: Sphingobium indicum strain B90A and Sphingobium japonicum strain UT26. Carbon isotope enrichment factors (ε(c)) for γ-HCH (ε(c) = -1.5 ± 0.1 ‰ and -1.7 ± 0.2 ‰) and α-HCH (ε(c) = -1.0 ± 0.2 ‰ and -1.6 ± 0.3 ‰) were similar for both aerobic strains, but lower in comparison with previously reported values for anaerobic γ- and α-HCH degradation. Isotope fractionation of α-HCH enantiomers was higher for (+) α-HCH (ε(c) = -2.4 ± 0.8 ‰ and -3.3 ± 0.8 ‰) in comparison to (-) α-HCH (ε(c) = -0.7 ± 0.2 ‰ and -1.0 ± 0.6 ‰). The microbial fractionation between the α-HCH enantiomers was quantified by the Rayleigh equation and enantiomeric fractionation factors (ε(e)) for S. indicum strain B90A and S. japonicum strain UT26 were -42 ± 16% and -22 ± 6%, respectively. The extent and range of isomer and enantiomeric carbon isotope fractionation of HCHs with Sphingobium spp. suggests that aerobic biodegradation of HCHs can be monitored in situ by compound-specific stable isotope analysis (CSIA) and enantiomer-specific isotope analysis (ESIA). In addition, enantiomeric fractionation has the potential as a complementary approach to CSIA and ESIA for assessing the biodegradation of α-HCH at contaminated field sites.

Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP)

Current knowledge of the physiology and phylogeny of polycyclic aromatic hydrocarbon (PAH) degrading bacteria often relies on laboratory enrichments and isolations. In the present study, in situ microcosms consisting of activated carbon pellets (BACTRAP®s) were loaded with either (13) C-naphthalene or (13) C-fluorene and were subsequently exposed in the contaminant source and plume fringe region of a PAH-contaminated aquifer. Metaproteomic analysis and protein-stable isotope probing revealed Burkholderiales, Actinomycetales, and Rhizobiales as the most active microorganisms in the groundwater communities. Proteins identified of the naphthalene degradation pathway showed a relative (13) C isotope abundance of approximately 50 atom% demonstrating that the identified naphthalene-degrading bacteria gained at least 80% of their carbon by PAH degradation. Although the microbial community grown on the fluorene-BACTRAPs showed a structure similar to the naphthalene-BACTRAPs, the identification of fluorene degraders and degradation pathways failed in situ. In complementary laboratory microcosms, a clear enrichment in proteins related to Rhodococcus and possible fluorene degradation enzymes was observed. This result demonstrates the impact of laboratory conditions on microbial community structure and activity of certain species and underlines the need on in situ exploration of microbial community functions. In situ microcosms in combination with protein-stable isotope probing may be a significant tool for in situ identification of metabolic key players as well as degradation pathways.

Influence of mass transfer on stable isotope fractionation

Biodegradation of contaminants is a common remediation strategy for subsurface environments. To monitor the success of such remediation means a quantitative assessment of biodegradation at the field scale is required. Nevertheless, the reliable quantification of the in situ biodegradation process it is still a major challenge. Compound-specific stable isotope analysis has become an established method for the qualitative analysis of biodegradation in the field and this method is also proposed for a quantitative analysis. However, to use stable isotope data to obtain quantitative information on in situ biodegradation requires among others knowledge on the influence of mass transfer processes on the observed stable isotope fractionation. This paper reviews recent findings on the influence of mass transfer processes on stable isotope fractionation and on the quantitative interpretation of isotope data. Focus will be given on small-scale mass transfer processes controlling the bioavailability of contaminants. Such bioavailability limitations are known to affect the biodegradation rate and have recently been shown to affect stable isotope fractionation, too. Theoretical as well as experimental studies addressing the link between bioavailability and stable isotope fractionation are reviewed and the implications for assessing biodegradation in the field are discussed.

Protein-based stable isotope probing (protein-SIP) in functional metaproteomics

The community phenotype as the sum of molecular functions of organisms living in consortia strongly depends on interactions within these communities. Therefore, the analyses of the most significant molecules in terms of the phenotype, the proteins, have to be performed on samples without disrupting the meta-species environment. Due to the increasing genomic information, proteins provide insights into a potential molecular function and the phylogenetic structure of the community. Unfortunately, the lists of identified proteins are often based first on the technical capacity of the used methods or instruments, and second on the interpretation of them by the assignment of molecular functions to proteins in databases. Especially in non-model organisms the functions of many proteins are often not known and an increasing number of studies indicate a significant amount of uncertainty. To decrease the dependency on assumptions and to enable functional insights by metaproteome approaches, the metabolic labeling from an isotopically labeled substrate can be used. Since the metabolites deriving from the substrate are very rarely species-specific, the incorporation of the stable isotope into proteins can be used as a surrogate marker for metabolic activity. The degree of incorporation can be determined accurately on the peptide level by mass spectrometry; additionally, the peptide sequence provides information on the metabolic active species. Thereby, protein-stable isotope probing (protein-SIP) adds functional information to metaproteome approaches. The classical metaproteome approaches will be reviewed with an emphasis on their attempts towards functional interpretation. The gain from functional insights into metaproteomics by using metabolic labeling of stable isotopes of carbon, nitrogen, and sulfur is reviewed with a focus on the techniques of measurement, calculation of incorporation and data processing.

Monitoring of a simulated CO(2) leakage in a shallow aquifer using stable carbon isotopes

Artificial carbon dioxide leakage into a shallow aquifer was monitored using stable carbon isotope measurements at a field site near the town of Wittstock, Brandenburg, Germany. Approximately 400 000 L of CO(2) were injected into a shallow aquifer at 18 m depth over 10 days. The (13)C/ (12)C ratios of the CO(2) were measured in both groundwater and soil gas samples to monitor the distribution of the injected CO(2) plume and to evaluate the feasibility and reliability of this approach to detect potential CO(2) leakage, for example from carbon capture and storage (CCS) sites. The isotopic composition of the injected CO(2) (δ(13)C -30.5 ‰) was differentiable from the background CO(2) (δ(13)C -21.9 ‰) and the artificial CO(2) plume was monitored over a period spanning more than 204 days. The results demonstrate that this stable isotope monitoring approach can be used to identify CO(2) sources and detect potential CO(2) migration from CCS sites into overlying shallow aquifers or even into the upper subsurface. A significant difference between the isotope ratios of the natural background and the injected CO(2) is required for this monitoring approach to be effective.

Effects of high CO2 concentrations on ecophysiologically different microorganisms

We investigated the effect of increasing CO(2) concentrations on the growth and viability of ecophysiologically different microorganisms to obtain information for a leakage scenario of CO(2) into shallow aquifers related to the capture and storage of CO(2) in deep geological sections. CO(2) concentrations in the gas phase varied between atmospheric conditions and 80% CO(2) for the aerobic strains Pseudomonas putida F1 and Bacillus subtilis 168 and up to 100% CO(2) for the anaerobic strains Thauera aromatica K172 and Desulfovibrio vulgaris Hildenborough. Increased CO(2) concentrations caused prolonged lag-phases, and reduced growth rates and cell yields; the extent of this effect was proportional to the CO(2) concentration. Additional experiments with increasing CO(2) concentrations and increasing pressure (1-5000 kPa) simulated situations occurring in deep CO(2) storage sites. Living cell numbers decreased significantly within 24 h at pressures ≥1000 kPa, demonstrating a severe lethal effect for the combination of high pressure and CO(2).