Publications
2025
Journal Article
Soil pH modulates microbial nitrogen cycling under integrated soil-crop system management across agroecosystems. Soil Ecology Letters 7 (4), 250360 (2025)
Journal Article
Temperature increase in paddy soils remodels the relationship between the anaerobic food web and the Q10 of CH4 production. Molecular Ecology 34 (22), e70156 (2025)
Journal Article
Methylocystis hydrogenophila sp. nov.—A Type IIa Methanotrophic Bacterium Able to Utilize Hydrogen as an Alternative Energy Source. Microorganisms 10 (13), 2309; (2025)
Journal Article
Time-series metatranscriptomics reveals differential salinity effects on the methanogenic food web in paddy soil. mSystems 10 (8), e0001725 (2025)
Journal Article
Coevolution and cross-infection patterns between viruses and their host methanogens in paddy soils. ISME Communications 5 (1), ycaf088 (2025)
Journal Article
Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics (vol 12, 259, 2024). Microbiome 13 (1), 7 (2025)
Journal Article
Correction: Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics. Microbiome 13 (1), 7 (2025)
Journal Article
A global relationship between genome size and encoded carbon metabolic strategies of soil bacteria. Ecology Letters 28 (1), e70064 (2025)
2024
Journal Article
Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics. Microbiome 12 (1), 259 (2024)
Journal Article
Fulvic acid enhances nitrogen fixation and retention in paddy soils through microbial-coupled carbon and nitrogen cycling. Environmental Science & Technology 58 (42), pp. 18777 - 18787 (2024)
Journal Article
Exploring modes of microbial interactions with implications for methane cycling. FEMS Microbiology Ecology 100 (9), fiae112 (2024)
Journal Article
Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities. mSystems 9, e00095-24 (2024)
Journal Article
Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil. Microbiome 12, 39 (2024)
2023
Review Article
Harnessing biological nitrogen fixation in plant leaves. Trends in Plant Science 28 (12), pp. 1391 - 1405 (2023)
Journal Article
Asparagine uptake: a cellular strategy of Methylocystis to combat severe salt stress. Applied and Environmental Microbiology 89 (6), e0011323 (2023)
Journal Article
Soil microbial ecology through the lens of metatranscriptomics. Soil Ecology Letters 6 (3), 230217 (2023)
Journal Article
Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils. Science of the Total Environment 891, 164221 (2023)
2022
Journal Article
Methylocystis sp. strain SC2 acclimatizes to increasing NH4+ levels by a precise rebalancing of enzymes and osmolyte composition. mSystems 7 (5), e0040322 (2022)
Journal Article
Genome-resolved metagenomics reveals distinct phosphorus acquisition strategies between soil microbiomes. mSystems 7 (1), e0110721 (2022)
Journal Article
Genome-resolved metagenomics identifies the particular genetic traits of phosphate-solubilizing bacteria in agricultural soil. ISME Communications 2 (1), 17 (2022)
Journal Article
Peat-vermiculite alters microbiota composition towards increased soil fertility and crop productivity. Plant and Soil 470, pp. 21 - 34 (2022)
2021
Journal Article
Seasonality affects function and complexity but not diversity of the rhizosphere microbiome in European temperate grassland. Science of the Total Environment 784, 147036 (2021)
Journal Article
Shedding light on the functional role of the Ignavibacteria in Italian rice field soil: A meta-genomic/transcriptomic analysis. Soil Biology and Biochemistry 163, 108444 (2021)
Journal Article
Deciphering microbial mechanisms underlying soil organic carbon storage in a wheat-maize rotation system. Science of the Total Environment 788, 147798 (2021)
Journal Article
Metagenomic insights into nitrogen and phosphorus cycling at the soil aggregate scale driven by organic material amendments. Science of the Total Environment 785, 147329 (2021)
2020
Journal Article
Unexpected metabolic versatility among type II methanotrophs in the Alphaproteobacteria. BIOLOGICAL CHEMISTRY 401 (12), pp. 1469 - 1477 (2020)
Journal Article
Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs. METABOLIC ENGINEERING 61, pp. 181 - 196 (2020)
Journal Article
Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 70 (2), pp. 1240 - 1249 (2020)
2019
Journal Article
Metatranscriptomics reveals climate change effects on the rhizosphere microbiomes in European grassland. SOIL BIOLOGY & BIOCHEMISTRY 138, 107604 (2019)
Journal Article
Efficient Tandem LysC/Trypsin Digestion in Detergent Conditions. PROTEOMICS 19 (20), 1900136 (2019)
Journal Article
Community transcriptomics reveals drainage effects on paddy soil microbiome across all three domains of life. SOIL BIOLOGY & BIOCHEMISTRY 132, pp. 131 - 142 (2019)
Journal Article
Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph Methylospira mobilis as Revealed by the Complete Genome Sequence. MICROORGANISMS 7 (12), 683 (2019)
2018
Journal Article
Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil. MICROBIOME 6, 169 (2018)
Journal Article
Metatranscriptomics reveals the hydrolytic potential of peat-inhabiting Planctomycetes. ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY 111 (6), pp. 801 - 809 (2018)
Journal Article
Unusual Genomic Traits Suggest Methylocystis bryophila S285 to Be Well Adapted for Life in Peatlands. GENOME BIOLOGY AND EVOLUTION 10 (2), pp. 623 - 628 (2018)
Journal Article
Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis strain SC2. JOURNAL OF PROTEOME RESEARCH 17 (9), pp. 3086 - 3103 (2018)
2017
Journal Article
Response of Methylocystis sp Strain SC2 to Salt Stress: Physiology, Global Transcriptome, and Amino Acid Profiles. Applied and Environmental Microbiology 83 (20), UNSP e00866-17 (2017)
Journal Article
Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. Frontiers in Microbiology 8, 1023 (2017)
Journal Article
Short- Term Exposure of Paddy Soil Microbial Communities to Salt Stress Triggers Different Transcriptional Responses of Key Taxonomic Groups. Frontiers in Microbiology 8, 400 (2017)
Journal Article
Comparative Genomics of Four Isosphaeraceae Planctomycetes: A Common Pool of Plasmids and Glycoside Hydrolase Genes Shared by Paludisphaera borealis PX4(T), Isosphaera pallida IS1B(T), Singulisphaera acidiphila DSM 18658(T), and Strain SH-PL62. Frontiers in Microbiology 8, 412 (2017)
2016
Journal Article
Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Molecular Ecology 25 (19), pp. 4818 - 4835 (2016)
Journal Article
Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil. Environmental Microbiology 18 (9 Sp. Iss. SI), pp. 2825 - 2842 (2016)
Journal Article
Methylovulum psychrotolerans sp nov:, a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum. International Journal of Systematic and Evolutionary Microbiology 66, pp. 2417 - 2423 (2016)
2015
Journal Article
Differential Assemblage of Functional Units in Paddy Soil Microbiomes. PLOS ONE 10 (4), 0122221 (2015)
Conference Paper
Permanent managed grassland at future climate change: is there a connection between GHG emission and composition of plant and microbial communities? 4th International Conference on Agriculture and Horticulture (AGRI), Amsterdam, NETHERLANDS, February 15, 2015 - February 17, 2015. AGRICULTURE AND CLIMATE CHANGE - ADAPTING CROPS TO INCREASED UNCERTAINTY (AGRI 2015), pp. 156 - 157 (2015)
2014
Journal Article
Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp strain SC2. Environmental Microbiology 16 (10), pp. 3115 - 3127 (2014)
Journal Article
DAFGA: diversity analysis of functional gene amplicons. Bioinformatics 30 (19), pp. 2820 - 2821 (2014)
Journal Article
Gammaproteobacterial Methanotrophs Dominate Cold Methane Seeps in Floodplains of West Siberian Rivers. Applied and Environmental Microbiology 80 (19), pp. 5944 - 5954 (2014)
Book Chapter
Soil Metatranscriptomics. In: Omics in Soil Science (Vol. 5), pp. 63 - 93. Caister Academic Press, University of Firenze, Italy (2014)
2013
Journal Article
Genome Analysis Coupled with Physiological Studies Reveals a Diverse Nitrogen Metabolism in Methylocystis sp Strain SC2. PLoS ONE 8 (10), e74767 (2013)
Journal Article
Pyrosequencing-Based Assessment of the Bacteria Diversity in Surface and Subsurface Peat Layers of a Northern Wetland, with Focus on Poorly Studied Phyla and Candidate Divisions. PLoS ONE 8 (5), e63994 (2013)
2012
Journal Article
Complete Genome Sequence of Methylocystis sp Strain SC2, an Aerobic Methanotroph with High-Affinity Methane Oxidation Potential. Journal of Bacteriology 194 (21), pp. 6008 - 6009 (2012)
Journal Article
Complete Sequence Analysis of Two Methanotroph-Specific repABC-Containing Plasmids from Methylocystis sp Strain SC2. Applied and Environmental Microbiology 78 (12), pp. 4373 - 4379 (2012)
Journal Article
Linking activity, composition and seasonal dynamics of atmospheric methane oxidizers in a meadow soil. ISME Journal 6 (6), pp. 1115 - 1126 (2012)
Journal Article
Telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands. Frontiers in Microbiology 3, 146 (2012)
Journal Article
Activity and diversity of methane-oxidizing bacteria in glacier forefields on siliceous and calcareous bedrock. Biogeosciences 9 (6), pp. 2259 - 2274 (2012)
2011
Journal Article
Methyloferula stellata gen. nov., sp nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. International Journal of Systematic and Evolutionary Microbiology 61, pp. 2456 - 2463 (2011)
Journal Article
Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat. Environmental Microbiology 13 (7), pp. 1800 - 1814 (2011)
Journal Article
Acetate utilization as a survival strategy of peat-inhabiting Methylocystis spp. Environmental Microbiology Reports 3 (1), pp. 36 - 46 (2011)
2010
Journal Article
Extraction of mRNA from Soil. Applied and Environmental Microbiology 76 (17), pp. 5995 - 6000 (2010)
Journal Article
Complete Genome Sequence of Beijerinckia indica subsp indica. Journal of Bacteriology 192 (17), pp. 4532 - 4533 (2010)
Journal Article
Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella silvestris BL2. Journal of Bacteriology 192 (14), pp. 3840 - 3841 (2010)
Journal Article
Phylogenetic diversity and metagenomics of candidate division OP3. Environmental Microbiology 12 (5), pp. 1218 - 1229 (2010)
Journal Article
Bryobacter aggregatus gen. nov., sp nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria. International Journal of Systematic and Evolutionary Microbiology 60, pp. 301 - 306 (2010)
Journal Article
Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen, isolated from Italian rice field soil. International Journal of Systematic and Evolutionary Microbiology 60, pp. 2918 - 2923 (2010)
2009
Journal Article
Transcriptional activity of paddy soil bacterial communities. Environmental Microbiology 11, pp. 960 - 970 (2009)
2008
Journal Article
Two isozymes of particulate methane monooxygenase with different methane oxidation kinetics are found in Methylocystis sp. strain SC2. Proceedings of the National Academy of Sciences 105, pp. 10203 - 10208 (2008)
Journal Article
Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat. ISME Journal 2, pp. 551 - 560 (2008)
2007
Journal Article
Phylogenetic identity, growth-response time and rRNA operon copy number of soil bacteria indicate different stages of community succession. Environmental Microbiology 9, pp. 2464 - 2474 (2007)
Magazine Article
Rice Cluster I-Archaea - Methanproduzierende Mikroorganismen im Reisfeldboden. (2007)
Journal Article
Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing 'signature' fatty acids of type I methanotrophs. International Journal of Systematic and Evolutionary Microbiology 57, pp. 472 - 479 (2007)
Journal Article
Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450, pp. 879 - 882 (2007)
Journal Article
Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog. Journal of Systematic and Evolutionary Microbiology 57, pp. 2349 - 2354 (2007)
2006
Journal Article
Isolation of aerobic, gliding, xylanolytic and laminarinolytic bacteria from acidic Sphagnum peatlands and emended description of Chitinophaga arvensicola (Kämpfer et al. 2006). International Journal of Systematic and Evolutionary Microbiology 56, pp. 2761 - 2764 (2006)
Journal Article
Phylogenetic analysis and in situ identification of bacteria community composition in an acidic sphagnum peat bog. Applied and Environmental Microbiology 72, pp. 2110 - 2117 (2006)
Journal Article
Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Current Opinion in Biotechnology 17, pp. 262 - 267 (2006)
Journal Article
Genome of rice cluster I archaea - the key methane producers in the rice rhizosphere. Science 313, pp. 370 - 372 (2006)
Journal Article
Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog. International Journal of Systematic and Evolutionary Microbiology 56, pp. 1397 - 1402 (2006)
Journal Article
Structure and activity of bacterial community inhabiting rice roots and the rhizosphere. Environmental Microbiology 8 (8), pp. 1351 - 1360 (2006)
2005
Journal Article
First genome data from uncultured upland soil cluster alpha methanotrophs provide further evidence for a close phylogenetic relationship to Methylocapsa acidiphila B2 and for high-affinity methanotrophy involving particulate methane monooxygenase. Applied and Environmental Microbiology 71 (11), pp. 7472 - 7482 (2005)
Journal Article
Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environmental Microbiology 7 (3), pp. 382 - 395 (2005)
Journal Article
Methylotrophic autotrophy in Beijerinckia mobilis. Journal of Bacteriology 187, pp. 3884 - 3888 (2005)
Journal Article
Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniques. FEMS Microbiology Ecology 53, pp. 187 - 204 (2005)
Book Chapter
The genus Desulfospira. In: The Proteobacteria, pp. 984 - 987. Springer, New York (2005)
Book Chapter
The genus Desulfuromusa. In: The Proteobacteria, pp. 1010 - 1013. Springer, New York (2005)
2004
Journal Article
NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria. Microbiology 150, pp. 1301 - 1313 (2004)
Journal Article
Methylocella tundrae sp nov., a novel methanotrophic bacterium from acidic tundra peatlands. International Journal of Systematic and Evolutionary Microbiology 54, pp. 151 - 156 (2004)
Journal Article
Comparative analysis of the conventional and novel pmo (Particulate methane monooxygenase) Operons from Methylocystis strain SC2. Applied and Environmental Microbiology 70 (5), pp. 3055 - 3063 (2004)
2003
Journal Article
Wide distribution of a novel pmoA-like gene copy among type II methanotrophs, and its expression in Methylocystis strain SC2. Applied and Environmental Microbiology 69 (9), pp. 5593 - 5602 (2003)
Journal Article
Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. Environmental Microbiology 5 (8), pp. 691 - 705 (2003)
Journal Article
Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiology Ecology 43, pp. 299 - 308 (2003)
Journal Article
Strain FAc12, a dissimilatory iron-reducing member of the Anaeromyxobacter subgroup of Myxococcales. FEMS Microbiology Ecology 44, pp. 261 - 269 (2003)
2002
Journal Article
Characterization of three spiral-shaped purple nonsulfur bacteria isolated from coastal lagoon sediments, saline sulfur springs, and microbial mats: emended description of the genus Roseospira and description of Roseospira marina sp nov., Roseospira navarrensis sp nov., and Roseospira thiosulfatophila sp nov. Archives of Microbiology 178 (5), pp. 315 - 324 (2002)
Journal Article
Isolation of a Methylocystis strain containing a novel pmoA- like gene. FEMS Microbiology Ecology 41 (1), pp. 17 - 26 (2002)
Journal Article
Geovibrio thiophilus sp nov., a novel sulfur-reducing bacterium belonging to the phylum Deferribacteres. International Journal of Systematic and Evolutionary Microbiology 52, pp. 1341 - 1347 (2002)
Journal Article
Methylocapsa acidiphila gen. nov., sp nov., a novel methane- oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. International Journal of Systematic and Evolutionary Microbiology 52, pp. 251 - 261 (2002)
Book Chapter
Biodiversity in soils: Use of molecular methods for its characterization. In: The Encyclopedia of Environmental Microbiology, pp. 528 - 544. Wiley, New York (2002)
2001
Journal Article
A novel pmoA lineage represented by the acidophilic methanotrophic bacterium Methylocapsa acidophila B2. ARCHIVES OF MICROBIOLOGY 177 (1), pp. 117 - 121 (2001)
Journal Article
Opitutus terrae gen nov, sp nov, to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 51, pp. 1965 - 1968 (2001)