Publications in peer reviewed journals

7 Publications found
  • Electrochemical enrichment of marine denitrifying bacteria to enhance nitrate metabolization in seawater

    De La Fuente MJ, de la Iglesia R, Farías L, Daims H, Lukumbuzya M, Vargas I
    2021 - J Environ Chem Eng, 9: 105604


    High concentrations of nitrate from industrial discharges to coastal marine environments are a matter of concern owing to their ecological consequences. In the last years, Bioelectrochemical Denitrification Systems (BEDS) have emerged as a promising nitrate removal technology. However, they still have limitations, such as the enrichment strategy for specific microbial communities in the electrodes under natural conditions. In this study, three-electrode electrochemical cells were used to test microbial enrichment from natural seawater by applying three reported potentials associated with the dissimilatory denitrification process (-130, -260, and -570 mV vs. Ag/AgCl). The microbial community analysis showed that by applying -260 mV (vs. Ag/AgCl) to the working electrode, it was possible to significantly enrich denitrifying microorganisms, specifically Marinobacter, in comparison with the control. Furthermore, -260 mV (vs. Ag/AgCl) led to a significantly higher nitrate removal than other conditions, which, combined with cyclic voltammetry analysis, suggested that the polarized electrodes worked as external electron donors for nitrate reduction. Hence, this work demonstrates for the first time that it is possible to enrich marine denitrifying microorganisms by applying an overpotential of -260 mV (vs. Ag/AgCl) without the need for a culture medium, the addition of an exogenous electron donor (i.e., organic matter) or a previously enriched inoculum.

  • Recently photoassimilated carbon and fungal-delivered nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica

    Mayerhofer W, Schintlmeister A, Dietrich M, Gorka S, Wiesenbauer J, Martin V, Gabriel R, Reipert S, Weidinger M, Clode P, Wagner M, Woebken D, Richter A, Kaiser C
    2021 - New Phytologist, in press


    Almost all land plants deliver recently assimilated carbon to mycorrhizal fungi, and receive nutrients in return. The controls of this exchange are, however, not yet fully understood. Here, we investigated if carbon for nitrogen exchange in the ectomycorrhizal symbiosis of Fagus sylvatica is regulated based on reciprocal rewards, and at which spatial scales such a reward mechanism operates.

    We set up a two-source tracing experiment with young ectomycorrhizal beech trees. We analysed the short-time distribution of isotopically labelled recent photosynthates (13CO2) and fungi-delivered nitrogen (15N) across the root system, as well as at the microscopic, cellular scale within an individual mycorrhizal root tip.

    While plants showed only limited control on directing photosynthates towards roots associated with N-delivering fungi, nano-scale secondary ion mass spectrometry (NanoSIMS) analysis of an individual ectomycorrhizal root tip revealed a strong spatial correlation between the distribution of plant-fixed C and fungi-delivered nitrogen. 

    Our results provide first evidence for a reciprocal exchange of C for N between plants and ectomycorrhizal fungi operating at the cellular scale in the ectomycorrhizal tissue. That suggests that individual hyphae emanating from a root tip, that are actively foraging for nutrients may be specifically supported by a greater share of recent photosynthates. 

  • Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration

    Yang Y, Herbold CW, Jung MY, Qin W, Cai M, Du H, Lin JG, Li X, Li M, Gu JD.
    2021 - Water Research, in press


    Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox while the dominance of WS9 specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.

  • Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.

    Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG, Loy A, Wasmund K
    2021 - ISME J, In press


    Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

  • Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment

    Pelikan C, Wasmund K, Glombitza C, Hausmann H, Herbold CW, Flieder M, Loy A
    2021 - ISME J, 15: 833-847


    Microorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions and genomic features of bacteria that degraded 13C-labelled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within five days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within ten days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.

  • Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting.

    Mueller AJ, Jung MY, Strachan CR, Herbold CW, Kirkegaard RH, Wagner M, Daims H
    2021 - ISME J, 15: 732–745


    Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.

  • Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.

    Mooshammer M, Kitzinger K, Schintlmeister A, Ahmerkamp S, Nielsen JL, Nielsen PH, Wagner M
    2021 - ISME J, 1: 348-353


    Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP-based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labeled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labeled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A nanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.

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