Environmental Microbiology Lab
At the Institute of Ecology and Earth Sciences, the environmental microbiology lab consists of researchers and doctoral students with backgrounds in environmental technology, microbiology, gene technology, and biogeography. Group's main research topics are related to the study of microbial activity and community structure in different natural habitats and engineered systems.
Currently, we carry research on microbial community structure and abundance of functional genes in wetland, peatland, forest, coastal and agricultural ecosystems. Treatment wetlands, constructed wetland-microbial electrochemical systems, and green roofs are some examples of the studied engineered environments. Besides, we work on the plants' microbiological communities in different systems.
We apply DNA and RNA-based molecular methods for characterising the phylogenetic and functional structure of microbial communities using next-generation sequencing (metagenomics, metatranscriptomics, metabarcoding) and quantify the abundance of microbial groups functional genes using quantitative PCR.
We have carried out studies in collaboration with different partners in Estonia and abroad.
Environmental microbiology research group - Media gallery
Some selected studies:
- Global perspective and microbiome
Mander, Ü., Öpik, M., & Espenberg, M. (2025). Global peatland greenhouse gas dynamics: State of the art, processes, and perspectives. New Phytologist, 246(1), 94–102. doi:10.1111/nph.20436
Bahram, M., Espenberg, M., Pärn, J., Lehtovirta-Morley, L., Anslan, S., . . . Mander, Ü. (2022). Structure and function of the soil microbiome underlying N2O emissions from global wetlands. Nature Communications, 13, 1430. doi:10.1038/s41467-022-29161-3
- Integrated microbiome and isotope analysis
Deb, S., Espenberg, M., Well, R., Bucha, M., Jakubiak, M., . . . Lewicka-Szczebak, D. (2025). N transformations in nitrate-rich groundwaters: Combined isotope and microbial approach. Biogeosciences, 22, 5535–5556. doi:10.5194/bg-22-5535-2025
Masta, M., Espenberg, M., Kuusemets, L., Pärn, J., Thayamkottu, S., . . . Mander, Ü. (2024). 15N tracers and microbial analyses reveal in situ N2O sources in contrasting water regimes on drained peatland forest. Pedosphere, 34(4), 749–758. doi:10.1016/j.pedsph.2023.06.006
Masta, M., Espenberg, M., Gadegaonkar, S. S., Pärn, J., Sepp, H., Kirsimae, K., . . . Mander, Ü. (2022). Integrated isotope and microbiome analysis indicates dominance of denitrification in N2O production after rewetting of drained fen peat. Biogeochemistry, 161(2), 119–136. doi:10.1007/s10533-022-00971-3
- Aboveground (leaves, stems, canopy soil) microbiome in tropical forests
Kazmi, F. A., Mander, Ü., Khanongnuch, R., Öpik, M., Ranniku, R., Soosaar, K., . . . Espenberg, M. (2025). Distinct microbial communities drive methane cycling in below-and above-ground compartments of tropical cloud forests growing on peat. Environmental Microbiome, 20(54), 1–13. doi:10.1186/s40793-025-00718-1
Kazmi, F. A., Mander, Ü., Ranniku, R., Öpik, M., Püssa, K., Soosaar, K., . . . Espenberg, M. (2025). Nitrogen cycling genes abundance in soil and aboveground compartments of tropical peatland cloud forests and a wetland on Réunion island. Scientific Reports, 15, 27155. doi:10.1038/s41598-025-12367-y
- Soil microbiome–plant interactions
Kuusemets, L., Mander, Ü., Escuer-Gatius, J., Astover, A., Kauer, K., Soosaar, K., & Espenberg, M. (2025). Interactions of fertilisation and crop productivity in soil nitrogen cycle microbiome and gas
emissions. SOIL, 11(1), 1–15. doi:10.5194/soil-11-1-2025
Espenberg, M., Pille, K., Yang, B., Maddison, M., Abdalla, M., Smith, P., . . . Mander, Ü. (2024). Towards an integrated view on microbial CH4, N2O and N2 cycles in brackish coastal marsh soils: A comparative analysis of two sites. Science of the Total Environment, 918, 170641. doi:10.1016/j.scitotenv.2024.170641
- Soil microbiome in temperate forest ecosystems
Reiss, K., Mander, Ü., Öpik, M., Sepp, S.-K., Kanger, K., Schindler, T., . . . Espenberg, M. (2025). Temporal and spatial dynamics of microbial communities and greenhouse gas flux responses to experimental flooding in riparian forest soils. FEMS Microbiology Ecology, 101(12), fiaf109. doi:10.1093/femsec/fiaf109
Kazmi, F. A., Espenberg, M., Pärn, J., Masta, M., Ranniku, R., Thayamkottu, S., & Mander, Ü. (2025). Meltwater of freeze-thaw cycles drives N2O-governing microbial communities in a drained peatland forest soil. Biology and Fertility of Soils, 61(3), 667–680. doi:10.1007/s00374-023-01790-w
- Soil microbiome in tropics
Midot, F., Goh, K. M., Liew, K. J., Lau, S. Y. L., Espenberg, M., Mander, Ü., & Melling, L. (2025). Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation. Applied and Environmental Microbiology, 91(1), e01986–24. doi:10.1128/aem.01986-24
Espenberg, M., Truu, M., Mander, Ü., Kasak, K., Nõlvak, H., Ligi, T., . . . Truu, J. (2018). Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils. Scientific Reports, 8, 4742. doi:10.1038/s41598-018-23032-y
- Nature-Based Solutions (NBS)
Choudhury, M. I., Espenberg, M., Hauber, M. M., Kasak, K., & Hylander, S. (2024). Application of floating beds constructed with woodchips for nitrate removal and plant growth in wetlands. Water, Air, Soil Pollution, 235, 493. doi:10.1007/s11270-024-07275-2
Gadegaonkar, S. S., Mander, Ü., & Espenberg, M. (2023). A state-of-the-art review and guidelines for enhancing nitrate removal in bio-electrochemical systems (BES). Journal of Water Process Engineering, 53, 103788. doi:10.1016/j.jwpe.2023.103788
Lust, R., Nerut, J., Gadegaonkar, S. S., Kasak, K., Espenberg, M., Visnapuu, T., & Mander, Ü. (2022). Single-chamber microbial electrosynthesis reactor for nitrate reduction from waters with a low electron donors’ concentration: From design and set-up to the optimal operating potential. Frontiers in Environmental Science, 10, 938631. doi:10.3389/fenvs.2022.938631
Teemusk, A., Espenberg, M., & Mander, Ü. (2022). Archaea rather than bacteria govern green roofs greenhouse gas production. Ecological Engineering, 176, 151723. doi:10.1016/j.ecoleng.2021.106530
Mander, Ü., Tournebize, J., Espenberg, M., Chaumont, C., Torga, R., Garnier, J., . . . Soosaar, K. (2021). High denitrification potential but low nitrous oxide emission in a constructed wetland treating nitrate-polluted agricultural run-off. Science of the Total Environment, 779, 146614. doi:10.1016/j.scitotenv.2021.146614
Gadegaonkar, S. S., Philippon, T., Rogińska, J. M., Mander, Ü., Maddison, M., Etienne, M., . . . Espenberg, M. (2020). Effect of Cathode Material and Its Size on the Abundance of Nitrogen Removal Functional Genes in Microcosms of Integrated Bioelectrochemical-Wetland Systems. Soil Systems, 4(3), 47. doi:10.3390/soilsystems4030047
- Restoration of wetlands
Gios, E., Verbruggen, E., Audet, J., Burns, R., Butterbach-Bahl, K., Espenberg, M., . . . Silvennoinen, H. M. (2024). Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology. Biogeochemistry, 609–629. doi:10.1007/s10533-024-01122-6
Mander, Ü., Espenberg, M., Melling, L., & Kull, A. (2024). Peatland restoration pathways to mitigate greenhouse gas emissions and retain peat carbon. Biogeochemistry, 167, 523–543. doi:10.1007/s10533-023-01103-1
Kasak, K., Espenberg, M., Anthony, T. L., Tringe, S. G., Valach, A. C., Hemes, K. S., . . . Baldocchi, D. D. (2021). Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential. Journal of Environmental Management, 299, 113562. doi:10.1016/j.jenvman.2021.113562
Espenberg, M., Truu, M., Truu, J., Maddison, M., Nõlvak, H., Järveoja, J., & Mander, Ü. (2016). Impact of Reed Canary Grass Cultivation and Mineral Fertilisation on the Microbial Abundance and Genetic Potential for Methane Production in Residual Peat of an Abandoned Peat Extraction Area. PLOS One, 11(9), e0163864. doi:10.1371/journal.pone.0163864
Our cooperation partners in Estonia and other parts of the world:
- Estonian University of Life Sciences
- Latvian National Forest Research Institute "Silava" (Latvia)
- University of Latvia (Latvia)
- Finnish Institute of Natural Resources (Luke) (Finland)
- University of Helsinki (Finland)
- Swedish University of Agricultural Sciences (Sweden)
- Linné University (Sweden)
- University of Rennes (France)
- University of Lorraine (France)
- French National Agricultural Research Institute (INRAE) (France)
- East China Normal University (Shanghai, China)
- Chungbuk National University (South Korea)
- University of Aberdeen (UK)
- University of East Anglia (UK)
- University of California, Berkeley (USA)
- National Taiwan University (Taiwan)
- National Ilan University (Taiwan)
Contact: [email protected]
Depending on the theme and students' interests, work may involve engineering, fieldwork, lab work, computer work (bioinformatics, statistics):
- Development, implementation and improvement of sustainable methods in different environments through the study of the microbial community
- Impact of wetland land use change on microbial community and biogeochemical cycles using sequencing (metagenomics, amplicon-based)
- Dynamics of the microbial nitrogen cycle in the deeper layers of peat soil in a drained forest by year
- Dynamics of the microbial carbon cycle in the peat soil in a drained forest by year
- The role of plants in emitting or sequestering methane (CH4) and nitrous oxide (N2O): microbiological analysis
- Design and development of microbiological methods for studying the carbon and nitrogen cycle
- Designing, installation and monitoring of bio-electrochemical systems treating nitrate polluted water
- A meta-analysis of the effectiveness of environmental technology methods
- Tropical peatlands and nutrient cycles
and many other themes. Just ask. We will find a way.
People
Laura Kuusemets, PhD student - Sustainable management of wetland forest nutrient cycling considering microbiome and greenhouse gas fluxes (Märgalade metsade toitainete ringluse jätkusuutlik juhtimine arvestades mikrobioomi ja kasvuhoonegaaside vooge)
Maret Hobolainen, PhD student - Dead wood decomposition rates in nature: major drivers and measurement techniques (Kõdupuidu lagunemiskiirus looduses: varieeruvuse allikad ja mõõtmine)
Kristel Reiss, PhD student - Global peatlands' nitrogen cycle microbiome analysis (Globaalsete turbaalade lämmastikuringe mikrobioomi analüüs)
Kien Yung Teo, PhD student - Carbon and nitrogen cycling in tropical peatlands from integrated microbiome, isotope and reactome analyses (Troopiliste soode süsiniku- ja lämmastikuringed integreeritud mikrobioom- ja isotoopanalüüsi ning reaktoomika alusel)
Si Chen, PhD student - Microbial patterns in forest phyllosphere and relations to greenhouse gases (Mikrobioloogiliste protsesside seosed kasvuhoonegaasidega metsade füllosfääris)
Amy Russell, PhD student - Wetlands under threat: Linking microbiomes, nitrous oxide emissions and climate change (Märgalad ohus: mikrobioomi, naerugaasi emissiooni ja kliimamuutuste seosed)
Matilda Touart, Undergraduate
Kreete Suve, Undergraduate
Kris Kontram, Undergraduate
3) Fahad Ali Kazmi - The role of microbiome in CH4 and N2O fluxes in temperate and tropical peatland forests (Mikrobioomi seosed metaani ja naerugaasi voogudega parasvöötme ja troopika soometsades) (2025)
2) Sharvari Sunil Gadegaonkar - Microbial and environmental factors affecting the nitrate removal efficiency from water in bioelectrochemical systems (Mikrobioloogiliste ja keskkonnategurite mõju nitraadi eemaldamisele veest bioelektrokeemilistes süsteemides) (2023)
1) Mohit Masta - Isotopologue and microbiome studies for N2O source attribution in peat soils (Soomuldade naerugaasi-allikate määramine isotopoloogiliste ja mikrobioloogiliste meetoditega) (2022)
12) Karmel Kikas - Comparison between microbial nitrogen cycling in tropical peat soils of swamp forests and oil palm plantation (Mikroobse lämmastikuringe võrdlus troopiliste soometsade ja õlipalmiistanduse turvasmuldades) (2025)
11) Si Chen - Microbial carbon and nitrogen cycle in tropical peatland forests and grasslands of Congo Basin (Mikrobioloogiline süsiniku- ja lämmastikuringe Kongo nõo troopilistes soometsades ja rohumaadel) (2025)
10) Hayden Nobis - Impact of afforestation on greenhouse gases from abandoned peat extraction areas in Estonia (Metsastamise mõju mahajäätud turbakaevandamise aladelt pärinevatele kasvuhoonegaasidele Eestis) (2025)
9) Kristel Reiss - Microbial community response to short-term flooding in a riparian forest (Lühiajalise üleujutuse mõju mulla mikrobioomile kaldaäärses lepikus) (2024)
8) Rasak Ayodeji Bello - Long-term monitoring and optimization of a continuous-flow bioelectrochemical reactor for the treatment of nitrate pollution in water (Pideva vooluga bioelektrokeemilise reaktori pikaajaline seire ja optimeerimine vee nitraadireostuse puhastamiseks) (2024)
7) Ikechukwu Timothy Ukah - Microbial nitrogen cycle in tropical cloud forest soils and canopy soils of Réunion island (Troopiliste pilvemetsade muldade ja võramuldade mikroobsed protsessid lämmastikuringes Réunioni saarel) (2024)
6) Esther Amalachukwu Nwume - Root traits and microbial community – indicators for environmental change in belowground (Juureparameetrid ja mikroobikooslus – keskkonnamuutuste indikaatorid mullas) (2023)
5) Laura Kuusemets -The effect of fertilisation and crop on the nitrogen cycle based on microbial analysis and N2O emissions (Väetamise ja põllukultuuride mõju lämmastikuringele mikrobioloogiliste analüüside ja N2O emissioonide põhjal) (2023)
4) Majid Farhadi - Design and startup of a continuous-flow bioelectrochemical reactor for treating nitrate pollution from water (Pideva vooluga bioelektrokeemilise reaktori disainimine ja käivitamine nitraadireostuse puhastamiseks veest) (2023)
3) Zane Ferch - Dynamics of soil microbial nitrogen cycle during a year-long study in a drained peatland forest (Turbamulla mikroobse lämmastikuringe dünaamika kuivendatud metsas aasta lõikes) (2022)
2) Kadri Kuusk - The genetic potential of nitrogen pollution removal in surface flow constructed wetlands (Lämmastikreostuse eemaldamise geneetiline potentsiaal vabaveelistes tehismärgalades) (2022)
1) Kristin Pille - Impact of different plant species on the microbial methane and nitrogen cycle and CH4 and N2O emissions on coasts affected by brackish water (Erinevate taimeliikide mõju mikrobioloogilisele metaani- ja lämmastikuringele ning CH4 ja N2O emissioonidele riimveest mõjutatud rannikul) (2020)
10) Sophie Saarts - Nitrogen-cycling microbiome of African tropical peat swamp forests’ phyllosphere (Aafrika troopiliste soometsade füllosfääri lämmastiku aineringe mikrobioom) (2025)
9) Lauri Eving - Microbial nitrogen cycle of Silver Birch (Betula pendula) in the soil-rhizosphere-plant-atmosphere continuum (Kase (Betula pendula) mikrobioloogiline lämmastikuringe muld-risosfäär-taim-atmosfäär kompleksis) (2025)
8) Monika Stjuf - Changes in nitrification and denitrification processes in agricultural soils with different arbuscular mycorrhizal fungal diversity (Nitrifikatsiooni- ja denitrifikatsiooniprotsesside muutused erineva arbuskulaar-mükoriissete seente mitmekesisusega põllumuldades) (2025)
7) Eliisabet Ojar - Comparison of different types of wastewater treatment systems for nitrogen removal: a systematic literature review (Erinevat tüüpi reoveepuhastite võrdlus lämmastikärastuseks: süstemaatiline kirjanduse ülevaade) (2024)
6) Karmel Kikas - Assessment of denitrification potential of prokaryotes and fungi in different ecosystems using the real-time PCR method (Prokarüootide ja seente denitrifikatsiooni potentsiaali hindamine erinevates ökosüsteemides reaalaja PCR meetodiga) (2023)
5) Liina Hints - Microbial nitrogen cycle and resulting nitrous oxide fluxes in Amazonian peatland soils (Amasoonase madaliku lääneosa palmisoode mulla mikrobiooom ja selle seos metaani ning dilämmastikoksiidi voogudega mullas) (2022)
4) Laura Kuusemets - Nitrification and denitrification processes in drained and inundated peatland forest determined by real-time PCR and isotope methods (Nitrifikatsiooni ja denitrifikatsiooni protsesside määramine reaalaja PCR-i ja isotoopanalüüsi meetoditega kuivendatud ja üleujutatud kõdusoometsades) (2021)
3) Kristel Reiss - Microbial nitrogen cycle response to short-term flooding in a riparian forest soil (Lühiajalise üleujutuse mõju mulla mikrobioloogilisele lämmastikuringele kaldaäärses lepikus) (2021)
2) Kadri Kuusk - The microbiological potential of methane production and consumption on different types of green roofs (Metaani tootmise ja tarbimise mikrobioloogiline potentsiaal erinevat tüüpi haljaskatustel) (2020)
1) Kadri Saare - Characterisation of the population and diversity of archaea in Paistu hybrid constructed treatment wetland (Arhede arvukuse ja mitmekesisuse iseloomustamine Paistu hübriidse tehismärgala pinnasfiltrites) (2014)
Former team members
Lisa Collin (summer 2025, visiting lab assistant)
Enzo Lelandais (summer 2025, visiting lab assistant)
Mayang Christy Perdana (2023-2024, summer 2025, visiting PhD student)
Karmel Kikas (2021-2025, bachelor's & master's thesis)
Monika Stjuf (2023-2025, bachelor's thesis)
Hayden Nobis (2024-2025, master's thesis)
Sophie Saarts (2024-2025, bachelor's thesis)
Lauri Eving (2024-2025, bachelor's thesis)
Sushmita Deb (April & July 2024, visiting PhD student)
Eliisabet Ojar (2022-2024, bachelor's thesis)
Rasak Ayodeji Bello (2023-2024, master's thesis)
Ikechukwu Timothy Ukah (2023-2024, master's thesis)
Sharvari Sunil Gadegaonkar (2019-2023, PhD dissertation)
Esther Amalachukwu Nwume (2022-2023, master's thesis)
Majid Farhadi (2022-2023, master's thesis)
Jessyca Rodrigues Marques (summer 2023, visiting lab assistant)
Bastien Pallu (summer 2023, visiting lab assistant)
Mohit Masta (2020-2022, PhD dissertation)
Zane Ferch (2020-2022, master's thesis)
Kadri Kuusk (2019-2020 & 2021-2022, bachelor's & master's thesis)
Liina Hints (2021-2022, bachelor's thesis)
Kristin Pille (2019-2020, master's thesis)
