@article{Karner2026,

title = {Gut microbial diversity and inferred capacity to produce short-chain fatty acids are associated with acute stress reactivity in healthy adults},

author = {Thomas Karner and Paul A.G. Forbes and David Berry and Isabella C. Wagner},

doi = {10.1016/j.ynstr.2026.100807},

issn = {2352-2895},

year  = {2026},

date = {2026-06-01},

urldate = {2026-06-00},

journal = {Neurobiology of Stress},

volume = {42},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cao2026,

title = {Defining the “Point of No Return”: Thickness-Dependent Fragmentation Controls Nonlinear Microplastics Emissions from Agricultural Mulch Films},

author = {Tianchi Cao and Xiaoxia Zhang and Yan Lin and Thilo Hofmann and Wei Chen},

doi = {10.1021/acs.est.6c00814},

issn = {1520-5851},

year  = {2026},

date = {2026-05-12},

journal = {Environ. Sci. Technol.},

volume = {60},

number = {18},

pages = {13645--13655},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2026b,

title = {Retreaded tires are an overlooked source of microplastics with distinct additive leaching and ecotoxicity},

author = {Hao Liu and Tianchi Cao and Yan Lin and Guoliang Shi and Kaiwei Huang and Zhi Cao and Tong Zhang and Thilo Hofmann and Wei Chen},

doi = {10.1038/s43247-026-03566-0},

issn = {2662-4435},

year  = {2026},

date = {2026-04-28},

urldate = {2026-04-28},

journal = {Commun Earth Environ},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>

                    Retreaded tires constitute a substantial segment of the commercial tire market and are an important source of tire wear particles (TWPs), yet the environmental risks of this major microplastic category remain uninvestigated. Here, we show that although the total additive mass is generally lower in TWPs from retreaded tires, these particles exhibit a markedly greater additive leaching potential, particularly for

                    <jats:italic>p</jats:italic>

                    -phenylenediamines (PPDs). Notably, the highly water-soluble additive

                    <jats:italic>N</jats:italic>

                    -isopropyl-

                    <jats:italic>N’</jats:italic>

                    -phenyl-p-phenylenediamine (IPPD), present at high concentrations in some retreaded-tire TWPs, is especially leachable. Correspondingly, leachates from retreaded-tire TWPs cause greater growth inhibition in

                    <jats:italic>Vibrio fischeri</jats:italic>

                    and

                    <jats:italic>Chlorella vulgaris</jats:italic>

                    than those from new or used tires. Furthermore, our numerical model projections under the Shared Socioeconomic Pathway 2 (SSP2) scenario show that global emissions of retreaded-tire TWPs could increase several hundred-fold by 2060. The substantial and growing risks identified in our study underscore the urgent need for broader investigations into the environmental impacts of these particles.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Seki2026,

title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum},

author = {David Seki and Shaul Pollak and Magdalena Kujawska and Raymond Kiu and Antia Acuna-Gonzalez and Lucy I. Crouch and Cassie R. Bakshani and Peter T. Chivers and Monique Mommers and Nils van Best and John Penders and Lindsay J. Hall},

doi = {10.1038/s41467-026-71764-7},

issn = {2041-1723},

year  = {2026},

date = {2026-04-22},

urldate = {2026-12-00},

journal = {Nat Commun},

volume = {17},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>

                    Infant gut microbiota development involves frequent colonization by

                    <jats:italic>Enterobacteriaceae</jats:italic>

                    , particularly

                    <jats:italic>Escherichia coli</jats:italic>

                    , yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that

                    <jats:italic>Bifidobacterium</jats:italic>

                    species are frequently shared within families, whereas

                    <jats:italic>E. coli</jats:italic>

                    derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between

                    <jats:italic>E. coli</jats:italic>

                    and

                    <jats:italic>Bifidobacterium bifidum</jats:italic>

                    are mutualistic in co-culture, where

                    <jats:italic>E. coli</jats:italic>

                    supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2′-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain

                    <jats:italic>E. coli</jats:italic>

                    growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating

                    <jats:italic>E. coli</jats:italic>

                    abundance within the infant host.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Treichel2026,

title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis},

author = {Nicole S. Treichel and Charlie Pauvert and Joana Séneca and Petra Pjevac and David Berry and John Penders and Thomas C. A. Hitch and Thomas Clavel},

doi = {10.1038/s41564-026-02334-2},

issn = {2058-5276},

year  = {2026},

date = {2026-04-21},

urldate = {2026-04-21},

journal = {Nat Microbiol},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1–50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5–1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5–81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vogel2026,

title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts},

author = {Margaret A Vogel and Fragkiskos Machairas and Sophia Ferchiou and Jay Osvatic and Hanin Alzubaidy and Joana Séneca and Bela Hausmann and Katja Klun and Jillian M Petersen},

doi = {10.1093/ismejo/wrag094},

issn = {1751-7370},

year  = {2026},

date = {2026-04-15},

urldate = {2026-04-15},

journal = {The ISME Journal},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a ‘three-way’ facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Ca. Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S rRNA gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Spieck2026,

title = {Cultivation‐Based Detection of a Novel High‐GC Nitrospira Derived From the Argentinian Copahue Volcano Area},

author = {Eva Spieck and Hanna Koch and Linnea F. M. Kop and Sabine Keuter and Marcel Malinowski and Katharina Sass and Wolfgang Sand and Edgardo Donati and Pablo Perez Garcia and Sebastian Lücker and Alejandra Giaveno},

doi = {10.1111/1462-2920.70290},

issn = {1462-2920},

year  = {2026},

date = {2026-04-03},

urldate = {2026-04-03},

journal = {Environmental Microbiology},

volume = {28},

number = {4},

publisher = {Wiley},

abstract = {<jats:title>ABSTRACT</jats:title>

                  <jats:p>

                    Nitrification is an essential process within the global nitrogen cycle and also occurs under extreme conditions, such as in geothermal environments. The nitrite‐oxidizing group

                    <jats:italic>Nitrospira</jats:italic>

                    represents key nitrifiers in these systems, as several species inhabit hot springs worldwide. Using different initial incubation temperatures, two novel moderately thermophilic

                    <jats:italic>Nitrospira</jats:italic>

                    enrichments,

                    <jats:italic>Nitrospira</jats:italic>

                    sp. Vd2 and

                    <jats:italic>Ca</jats:italic>

                    .

                    <jats:styled-content style="fixed-case">

                      N.

                      <jats:italic>neuquenensis</jats:italic>

                    </jats:styled-content>

                    E2OT, were obtained from sulfur‐rich mud pools in the geothermal field Las Máquinas (Neuquén Province, Argentina).

                    <jats:italic>Nitrospira</jats:italic>

                    sp. Vd2 belongs to the N.

                    <jats:italic>bockiana</jats:italic>

                    lineage V, whereas the second enrichment (E2OT) represents the novel taxonomic lineage VIII, together with cultures from Kamchatka (Kam‐Ns4a) and Garga hot springs (Ga3a). The vibrioid morphology of

                    <jats:italic>Ca</jats:italic>

                    .

                    <jats:styled-content style="fixed-case">

                      N.

                      <jats:italic>neuquenensis</jats:italic>

                    </jats:styled-content>

                    E2OT is strikingly different from all described, twisted rod‐shaped

                    <jats:italic>Nitrospira</jats:italic>

                    . Our study expands the knowledge of the taxonomic and genomic diversity of moderately thermophilic

                    <jats:italic>Nitrospira</jats:italic>

                    , by comparing the high‐quality draft genomes with those of previously described species. The recent discovery of quorum‐sensing genes outside the

                    <jats:italic>Nitrospira</jats:italic>

                    lineage II was confirmed for both Argentinian cultures. Notably, the genome GC contents of the enrichments Vd2 and E2OT are 60.6% and 69.4%, respectively. The latter is the highest observed for

                    <jats:italic>Nitrospira</jats:italic>

                    to date and might support thermotolerance up to 50°C.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schmelz2026,

title = {Host depletion kits improve microbiome analyses in environmental samples: Seagrass as a test case},

author = {Philipp Schmelz and Stefan Eckensperger and Jay Osvatic and Joana Séneca and Hanin Alzubaidy and Jillian Petersen},

doi = {10.1093/ismeco/ycag082},

issn = {2730-6151},

year  = {2026},

date = {2026-03-28},

urldate = {2026-03-28},

journal = {ISME Communications},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health, however such efforts are often hindered by the dominance of host-derived material in e.g., DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes (MAGs) with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krasenbrink2026,

title = {Sulfoquinovose degradation by cow rumen microbiota},

author = {Julia Krasenbrink and Song-Can Chen and Tomohisa Sebastian Tanabe and Hüseyin Sarikeçe and Pleun Meurs and Sabrina Borusak and Rahul Samrat and Guoqing Guan and Clara Priemer and Jay Osvatic and Joana Séneca and Bela Hausmann and Daan R Speth and Evelyne Selberherr and Wolfgang Wanek and David Schleheck and Marc Mussmann and Alexander Loy},

doi = {10.1093/ismejo/wrag069},

issn = {1751-7370},

year  = {2026},

date = {2026-03-27},

urldate = {2026-03-27},

journal = {ISME J},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kück2026,

title = {Host species-specific gene expression by a widespread and flexible chemosynthetic symbiont},

author = {A Carlotta Kück and Lukas Leibrecht and Isidora Morel-Letelier and Olivier Gros and Laetitia G E Wilkins and Benedict Yuen-Simović and Jillian M Petersen},

doi = {10.1093/ismejo/wrag065},

issn = {1751-7370},

year  = {2026},

date = {2026-03-24},

urldate = {2026-03-24},

journal = {The ISME Journal},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>Associations with microbial symbionts shape the ecology and evolution of almost all eukaryotes. One of their defining features is their specificity, but despite this, many symbioses show a degree of flexibility, with some symbiont species capable of colonizing multiple (often closely related) host species. Although widespread, the functional and evolutionary consequences of flexibility in host-symbiont pairings is poorly understood. Bivalves from the diverse, globally distributed, and ecologically important family Lucinidae are ideal for investigating this, as multiple host species can associate with the same symbiont species, often at the same location. We used metatranscriptomics to investigate the molecular responses of one symbiont species, Candidatus Thiodiazotropha endolucinida, in association with three different host species that co-occur in seagrass meadows in the Caribbean Sea. In replicated experiments, we identified host species-specific patterns of symbiont gene expression including those for key functions such as carbon fixation, cell division, and sulfide oxidation. Our work shows that the symbiont consistently responds in different ways to association with different host species. Because all samples were collected at the same site on the same day, and were thus exposed to the same environmental conditions, these differences are likely driven by host rather than environmental factors. In addition, host species had significantly different carbon isotope signatures, which were consistent with distinct modes of host-microbe interaction indicated by transcriptomics. Our results show that not only symbiont genotype, but also symbiont phenotype may enable coexistence of closely related host species, demonstrating the power of symbiosis in promoting and maintaining biodiversity.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2026,

title = {Per- and polyfluoroalkyl substances-driven enhancement of colloid-facilitated contaminant transport in groundwater},

author = {Jiameng Liu and Tianchi Cao and Tong Zhang and Thilo Hofmann and Wei Chen},

doi = {10.1016/j.watres.2026.125335},

issn = {0043-1354},

year  = {2026},

date = {2026-03-15},

urldate = {2026-03-00},

journal = {Water Research},

volume = {292},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid41766386,

title = {Arbuscular mycorrhizal fungal families and exploration-based guilds exhibit distinct responses to long-term N, P and K deficiencies and imbalances},

author = {Kian Jenab and Lauren Alteio and Ksenia Guseva and Stefan Gorka and Sean Darcy and Lucia Fuchslueger and Alberto Canarini and Victoria Martin and Julia Wiesenbauer and Felix Spiegel and Bruna Imai and Hannes Schmidt and Karin Hage-Ahmed and Erich M Pötsch and Andreas Richter and Jan Jansa and Christina Kaiser},

doi = {10.1111/nph.70969},

issn = {1469-8137},

year  = {2026},

date = {2026-03-02},

urldate = {2026-03-01},

journal = {New Phytol},

abstract = {Many agroecosystems face nitrogen (N), phosphorus (P) or potassium (K) deficiencies due to imbalanced or insufficient nutrient replenishment after biomass harvest. How this affects the symbiosis between plants and arbuscular mycorrhizal fungi (AMF) and the abundance of exploration-based AMF guilds (rhizophilic, edaphophilic and ancestral) remains largely unknown. We studied a 70-yr nutrient deficiency experiment in a managed grassland in central Austria, where aboveground biomass was harvested three times annually. N, P and K were fully, partially or not replenished, causing long-term nutrient deficiencies and imbalances. We analysed AMF communities in soil and roots by DNA/RNA amplicon sequencing and fatty acid biomarkers, alongside soil and plant community properties. Soil AMF communities were affected by N and P deficiencies, while root AMF communities were most susceptible to K deficiency, showing up to 50% biomass reduction, particularly when N was abundant. We observed a shift from rhizophilic to ancestral guilds under P deficiency in soil, and under K deficiency in roots. Families within each guild, particularly ancestral, showed differential responses, indicating complementary nutrient specializations at the family level. Our findings underscore the previously unrecognized role of K deficiency in AMF symbiosis and suggest the existence of nutrient-related functional subgroups within exploration-based AMF guilds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lee2026,

title = {Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase},

author = {Ui-Ju Lee and Joo-Han Gwak and Christiana Abiola and Seongjun Lee and Jin-Sun Yoo and Ok-Ja Si and Hyo Je Cho and Zhe-Xue Quan and Katharina Kitzinger and Holger Daims and Michael Wagner and Man-Young Jung and Sung-Keun Rhee},

doi = {10.1093/ismejo/wrag040},

issn = {1751-7370},

year  = {2026},

date = {2026-02-27},

urldate = {2026-02-27},

journal = {ISME J},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>Nitrite-oxidizing bacteria (NOB) use either periplasmic (pNXR) or cytoplasmic (cNXR) nitrite oxidoreductase to oxidize nitrite, and this distinction influences nitrite affinity and energy yield. cNXR-containing NOB have historically been considered low-affinity, copiotrophic nitrifiers adapted to high nitrite and neutral pH. Here, we report a previously uncharacterized pH- and substrate-dependent modulation of nitrite affinity in cNXR NOB that is not observed in pNXR NOB and is not a universal microbial trait. Nitrobacter winogradskyi Nb-255, grown at low nitrite (1 mM), had a high apparent affinity (Km(app) = 25.9 μM; specific affinity ao = 440.5 l g cells−1 h−1) comparable to oligotrophic pNXR NOB. However, when grown at high nitrite (10 mM), these cells showed a low affinity at pH 7.5 (Km(app) = 388.0 μM) but exhibited a rapid increase in affinity upon immediate exposure to pH 5.5 (Km(app) = 19.2 μM) without prior acid adaptation. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions, underscoring that this kinetic plasticity is unique to cNXR NOB. Kinetic inhibition assays revealed that this plasticity is mechanistically underpinned by a shift from a low-affinity nitrite/nitrate antiporter (NarK) to a high-affinity nitrite channel (NirC), coupled with enhanced HNO2 diffusion at low pH, together increasing intracellular nitrite availability. These findings establish that cNXR NOB can dynamically tune nitrite affinity via transporter-level regulation in response to nitrite concentration and pH. This novel mechanism provides a mechanistic explanation for the unexpected prevalence of Nitrobacter in acidic, low-nitrite environments, highlighting its ecological relevance.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2026,

title = {Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils},

author = {Baozhan Wang and Ping Gao and Ping Zhang and Yue Zheng and Xu Liu and Ning Ling and Jun Shan and Rongjiang Yao and Shuai Zhao and Zhiguo Zhang and Guibing Zhu and Man-Young Jung and Jianwen Zou and Xiaoyuan Yan and Sungeun Lee and Christina Hazard and Graeme W Nicol and Jizhong Zhou and Yunfeng Yang and Yongguan Zhu and David A Stahl and Michael Wagner and Yanzheng Gao and Jiandong Jiang and Wei Qin},

doi = {10.1093/ismejo/wrag037},

issn = {1751-7370},

year  = {2026},

date = {2026-02-20},

urldate = {2026-02-20},

journal = {ISME J},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus–host interaction strategies in a land-use–dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mohammadzadeh2026,

title = {Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems},

author = {Rokhsareh Mohammadzadeh and Alexander Mahnert and Tamara Zurabishvili and Lisa Wink and Christina Kumpitsch and Hansjoerg Habisch and Jannik Sprengel and Klara Filek and Polona Mertelj and Dominique Pernitsch and Kerstin Hingerl and Marija Durdevic and Gregor Gorkiewicz and Christian Diener and Alexander Loy and Dagmar Kolb and Christoph Trautwein and Tobias Madl and Christine Moissl-Eichinger},

doi = {10.1038/s41467-026-69711-7},

issn = {2041-1723},

year  = {2026},

date = {2026-02-20},

urldate = {2026-02-20},

journal = {Nat Commun},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:p>

                    The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea, an evolutionarily distinct group of microbes, in human disease remains elusive. By analyzing 19 independent clinical studies, we demonstrate that associations between Archaea and human diseases are widespread yet highly heterogeneous, with a pronounced and consistent enrichment of

                    <jats:italic>Methanobrevibacter smithii</jats:italic>

                    in colorectal cancer (CRC) patients. Metabolic modelling and in vitro co-culture identified distinct mutualistic interactions of

                    <jats:italic>M. smithii</jats:italic>

                    with CRC-causing bacteria such as

                    <jats:italic>Fusobacterium nucleatum</jats:italic>

                    , including metabolic enhancement. Metabolomics further reveal archaeal-derived compounds with tumor-modulating properties. Together, our results provide mechanistic insights into how the human gut archaeome may participate in CRC-associated microbial networks through metabolic cooperation with bacteria.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40897862,

title = {Cell membrane cholesterol affects serotonin transporter efflux due to altered transporter oligomerization},

author = {Deborah Rudin and Dino Luethi and Marco Niello and Jae-Won Yang and Isabella Burger and Walter Sandtner and Ruth Birner-Gruenberger and Gerhard J Schütz and Harald H Sitte},

doi = {10.1038/s41380-025-03201-y},

issn = {1476-5578},

year  = {2026},

date = {2026-02-01},

journal = {Mol Psychiatry},

volume = {31},

number = {2},

pages = {963--975},

abstract = {The human monoamine transporters (MATs) for serotonin (SERT), dopamine (DAT), and norepinephrine (NET) play a key role in neurotransmission by transporting neurotransmitters from the synaptic cleft back into the neuron. MATs are embedded in the cell membrane's lipid bilayer, encompassing cholesterol, phospholipids, and sphingolipids as main components. Membrane cholesterol association has been shown for all MATs impacting transporter conformation, substrate affinity, transport velocity, and turnover rates. In the present study, we compared the regulatory impact of cholesterol on the uptake and efflux function, binding affinity, and transporter oligomerization across all three MATs. We observed that cholesterol depletion impairs transporter-mediated uptake in human transporter-transfected HEK293 cells and reduces the binding affinity of all MATs. Electrophysiological investigations in SERT-expressing cells revealed that cholesterol alterations affect the transition of the transporter from the outward to the inward-facing conformation in the presence of substrate. Upon cholesterol depletion, FRET imaging and single molecule microscopy studies indicated altered oligomerization behavior exclusively for SERT. Interestingly, reduction of membrane cholesterol selectively increased amphetamine-induced efflux via SERT, while efflux via DAT and NET was reduced. This effect was diminished in a mutant with reduced PIP binding capacity. Hence, the increased efflux at SERT due to cholesterol depletion appears to depend on the ability of PIP to bind to SERT. Thus, we hypothesize that the interaction profile between cholesterol and MATs may fine-tune the transporter functionality and influence MAT-dependent disorders.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cuparencu2026,

title = {Integration of modern technologies to advance dietary assessment},

author = {Catalina Cuparencu and Christian Diener and Thomas Wilson and Sean M. Gibbons and Desiree A. Lucassen},

doi = {10.1038/s43016-025-01290-0},

issn = {2662-1355},

year  = {2026},

date = {2026-01-26},

urldate = {2026-01-00},

journal = {Nat Food},

volume = {7},

number = {1},

pages = {17--26},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Holub2026,

title = {Investigating Spectral Biomarker Candidates for Migratory Potential in Cancer Cells Using Micro-FTIR and O-PTIR Spectroscopy},

author = {Elisabeth Holub and Nikolaus Hondl and Kai-Lan Lin and Marjaana Parikainen and Cecilia Sahlgren and Bernhard Lendl and Georg Ramer},

doi = {10.1021/acsmeasuresciau.5c00132},

issn = {2694-250X},

year  = {2026},

date = {2026-01-21},

journal = {ACS Meas. Sci. Au},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sherman2026,

title = {Minor influence of climbing hall characteristics on rubber-derived compound contamination highlights a need for material-level solutions},

author = {Anya Sherman and Laura Lotteraner and Leah K. Maruschka and Thilo Hofmann},

doi = {10.1039/d5em00812c},

issn = {2050-7895},

year  = {2026},

date = {2026-01-06},

urldate = {2026-00-00},

journal = {Environ. Sci.: Processes Impacts},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>Climbing shoe abrasion generates fine rubber particles, leading to elevated concentrations of rubber-derived compounds (RDCs) in airborne particulate matter and settled dust of indoor climbing halls, in some cases comparable...</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lotteraner2026,

title = {The Importance of Being Thorough: How Data Analysis Choices Impact the Perceived Relationship between Pollutants and Predictors},

author = {Laura Lotteraner and Torsten Möller and Thilo Hofmann},

doi = {10.1016/j.watres.2025.124639},

issn = {0043-1354},

year  = {2026},

date = {2026-01-01},

urldate = {2026-01-00},

journal = {Water Research},

volume = {288},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bauchinger2025,

title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota},

author = {Franziska Bauchinger and David Berry},

editor = {Leluo Guan},

doi = {10.1093/femsec/fiaf118},

issn = {1574-6941},

year  = {2025},

date = {2025-12-22},

volume = {102},

number = {1},

publisher = {Oxford University Press (OUP)},

abstract = {Abstract

                  The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin, it is still unclear which species transcribe the respective genes. Here, we systematically analysed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized cooccurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although ~60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singleton2025,

title = {The Microflora Danica atlas of Danish environmental microbiomes},

author = {C. M. Singleton and T. B. N. Jensen and F. Delogu and K. S. Knudsen and E. A. Sørensen and V. R. Jørgensen and S. M. Karst and Y. Yang and M. Sereika and F. Petriglieri and S. Knutsson and S. M. Dall and R. H. Kirkegaard and J. M. Kristensen and C. K. Overgaard and B. J. Woodcroft and D. R. Speth and S. T. N. Aroney and and Henning C. Thomsen and Bent T. Christensen and Lis W. de Jonge and Anne-Cathrine S. Danielsen and Cecilie Hermansen and Mogens H. Greve and Rasmus Ejrnæs and Thomas A. Davidson and Signe Normand and Urs A. Treier and Bjarke Madsen and Andreas Schramm and Ian P. G. Marshall and Ann-Sofie Dam and Kasper U. Kjeldsen and Kai Finster and Philip F. Thomsen and Eva E. Sigsgaard and Martin J. Klepke and Marie Vestergård and Erik Aude and Lene Thomsen and Camilla Lemming and Rita Hørfarter and Marlene M. Jensen and Tobias G. Frøslev and Lone Gram and Peter B. Svendsen and Morten Dencker Schostag and Sanne Kjellerup and Torben L. Skovhus and Ditte A. Søborg and Kasper Reitzel and Jørgen F. Pedersen and Andrew Giguere and Inge S. Pedersen and Mads Sønderkær and Jes Vollertsen and Fan Liu and Peter Roslev and Niels Iversen and Kåre L. Nielsen and Nadieh de Jonge and Dan Bruhn and Jeppe L. Nielsen and Torsten N. Kristensen and Chenjing Jiang and Marta A. Nierychlo and Giulia Dottorini and M. Wagner and M. K. D. Dueholm and P. H. Nielsen and M. Albertsen},

doi = {10.1038/s41586-025-09794-2},

issn = {1476-4687},

year  = {2025},

date = {2025-12-03},

urldate = {2025-12-03},

journal = {Nature},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid41425875,

title = {Single-Mode Ring Resonator-Based Optomechanical Transducers for Advanced Atomic Force Sensing},

author = {Yide Zhang and Artem S Vorobev and Savda Sam and S Hadi Badri and Mauro David and Bernhard Lendl and Georg Ramer and Liam O'Faolain},

doi = {10.1021/acsphotonics.5c01914},

issn = {2330-4022},

year  = {2025},

date = {2025-12-01},

journal = {ACS Photonics},

volume = {12},

number = {12},

pages = {6778--6787},

abstract = {Atomic force microscopy (AFM) is a widely used technique for high-resolution imaging and force sensing, yet its performance is fundamentally constrained by the cantilever size, spring constants, and mechanical frequencies. To overcome these limitations, we present a compact and highly efficient single-mode ring resonator-based optomechanical transducer on an silicon-on-insulator (SOI) platform. Unlike conventional designs that rely on whispering gallery modes (WGMs) resonators, our approach ensures mode stability, facilitates straightforward signal interpretation, and enhances measurement reliability by eliminating mode-splitting effects and complex optical responses. Coupled with a picogram-scale cantilever, our system achieves exceptional displacement resolution of 6.7 × 10 m/Hz and force detection down to 5.0 × 10 N, providing a high-performance alternative to existing optomechanical AFM transducers. The tunable mechanical resonance frequency (1.3 to 22.5 MHz) and adjustable stiffness (0.46 to 3.54 N/m) enable precise force sensing across a broad range of applications, from soft matter characterization to high-speed imaging. Importantly, our results exhibit strong agreement with theoretical predictions, ensuring accurate and direct displacement measurements. Our results establish this single-mode optomechanical transducer as a robust, high-sensitivity platform for next-generation AFM and nanoscale sensing applications, offering a compact, scalable, and highly precise alternative to traditional free-space optical detection methods. The combination of high displacement resolution, mode stability, and tunable performance establishes this optomechanical transducer as a promising advancement in integrated nanoscale sensing and AFM applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Plöchl2025,

title = {A novel class of small-molecule inhibitors targeting bacteriophage infection},

author = {Konstantin Plöchl and Thomas Böttcher},

doi = {10.1039/d5cb00120j},

issn = {2633-0679},

year  = {2025},

date = {2025-12-01},

urldate = {2025-00-00},

journal = {RSC Chem. Biol.},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>Discovery of benzimidazylpyrazoles as a new class of synthetic bacteriophage antivirals provides a chemical tool enabling the study of disease-related phage–host interactions.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2025,

title = {Methane-cycling microbiomes in soils of the pan-Arctic and their response to permafrost degradation},

author = {Haitao Wang and Erik Lindemann and Patrick Liebmann and Milan Varsadiya and Mette Marianne Svenning and Muhammad Waqas and Sebastian Petters and Andreas Richter and Georg Guggenberger and Jiri Barta and Tim Urich},

doi = {10.1038/s43247-025-02765-5},

issn = {2662-4435},

year  = {2025},

date = {2025-12-00},

journal = {Commun Earth Environ},

volume = {6},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          The methane-cycling microbiomes play crucial roles in methane dynamics. However, little is known about their distributions on a pan-Arctic scale as well as their responses to the widespread permafrost degradation. Based on 621 datasets of 16S rRNA gene amplicons from intact permafrost soils across the pan-Arctic, we identified only 22 methanogen and 26 methanotroph phylotypes. Their relative abundances varied significantly between sites and soil horizons. Only four methanogen phylotypes were detected at all locations. Remarkably, the permafrost soil methane filter was almost exclusively dominated by some obligate methanotroph (Methylobacter-like) phylotypes. However, a case study in Alaska suggests that atmospheric methane oxidizing bacteria (Methylocapsa-like phylotypes) dominated methanotrophs in a drier condition after permafrost degradation. These findings point towards a few key microbes particularly relevant for future studies on Arctic methane dynamics in a warming climate and that under future dry conditions, increased atmospheric methane uptake in Arctic upland soils may occur.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krasenbrink2025,

title = {Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans},

author = {Julia Krasenbrink and Buck T. Hanson and Anna S. Weiss and Sabrina Borusak and Tomohisa Sebastian Tanabe and Michaela Lang and Georg Aichinger and Bela Hausmann and David Berry and Andreas Richter and Doris Marko and Marc Mussmann and David Schleheck and Bärbel Stecher and Alexander Loy},

doi = {10.1186/s40168-025-02175-x},

issn = {2049-2618},

year  = {2025},

date = {2025-12-00},

journal = {Microbiome},

volume = {13},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title> 

 <jats:sec> 

 <jats:title>Background</jats:title> 

 <jats:p>Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.</jats:p> 

 </jats:sec> 

 <jats:sec> 

 <jats:title>Results</jats:title> 

 <jats:p> 

 <jats:sup>13</jats:sup>CO<jats:sub>2</jats:sub> breath tests with germ-free C57BL/6 mice gavaged with <jats:sup>13</jats:sup>C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of <jats:italic>Agathobacter rectalis</jats:italic> and <jats:italic>Bilophila wadsworthia</jats:italic> in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. <jats:italic>Escherichia coli</jats:italic> and <jats:italic>Enterocloster clostridioformis</jats:italic> were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some <jats:italic>E. clostridioformis</jats:italic> genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived <jats:italic>E. clostridioformis</jats:italic> strain.</jats:p> 

 </jats:sec> 

 <jats:sec> 

 <jats:title>Conclusions</jats:title> 

 <jats:p>Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.</jats:p> 

 </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Weinberger2025b,

title = {Proteomic and metabolomic profiling of extracellular vesicles produced by human gut archaea},

author = {Viktoria Weinberger and Barbara Darnhofer and Himadri B. Thapa and Polona Mertelj and Régis Stentz and Emily Jones and Gerlinde Grabmann and Rokhsareh Mohammadzadeh and Tejus Shinde and Christina Karner and Jennifer Ober and Rokas Juodeikis and Dominique Pernitsch and Kerstin Hingerl and Tamara Zurabishvili and Christina Kumpitsch and Torben Kuehnast and Beate Rinner and Heimo Strohmaier and Dagmar Kolb and Kathryn Gotts and Thomas Weichhart and Thomas Köcher and Harald Köfeler and Simon R. Carding and Stefan Schild and Christine Moissl-Eichinger},

doi = {10.1038/s41467-025-60271-w},

issn = {2041-1723},

year  = {2025},

date = {2025-12-00},

journal = {Nat Commun},

volume = {16},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title> 

 <jats:p>Gastrointestinal bacteria interact with the host and each other through various mechanisms, including the production of extracellular vesicles (EVs). However, the composition and potential roles of EVs released by gut archaea are poorly understood. Here, we study EVs produced by four strains of human gut-derived methanogenic archaea: <jats:italic>Methanobrevibacter smithii</jats:italic> ALI, <jats:italic>M. smithii</jats:italic> GRAZ-2, <jats:italic>M. intestini</jats:italic>, and <jats:italic>Methanosphaera stadtmanae</jats:italic>. The size (~130 nm) and morphology of these EVs are comparable to those of bacterial EVs. Proteomic and metabolomic analyses reveal that the archaeal EVs are enriched in putative adhesins or adhesin-like proteins, free glutamic and aspartic acid, and choline glycerophosphate. The archaeal EVs are taken up by macrophages in vitro and elicit species-specific responses in immune and epithelial cell lines, including production of chemokines such as CXCL9, CXCL11, and CX3CL1. The EVs produced by <jats:italic>M. intestini</jats:italic> strongly induce pro-inflammatory cytokine IL-8 in epithelial cells. Future work should examine whether archaeal EVs play roles in the interactions of archaea with other gut microbes and with the host.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jancheva2025,

title = {A phage-selective trigger hints at an SOS-independent mechanism of prophage induction by oxidative stress},

author = {Magdalena Jancheva and Thi-Hong Nhung Nguyen and Felix Anderl and Shubham Joge and Jessica Neubauer and Clarissa Rominger-Baumann and Alexandra Walter and Golo Storch and Thomas Böttcher},

doi = {10.1039/d5sc04923g},

issn = {2041-6539},

year  = {2025},

date = {2025-11-29},

urldate = {2025-00-00},

journal = {Chem. Sci.},

publisher = {Royal Society of Chemistry (RSC)},

abstract = {<jats:p>

                    We report an SOS-independent mechanism of selective prophage induction in a poly-lysogenic

                    <jats:italic>Staphylococcus aureus</jats:italic>

                    host triggered by redox cycling of phenazine compounds.

                  </jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Speth2024,

title = {GlobDB: a comprehensive species-dereplicated microbial genome resource},

author = {Daan R Speth and Nick Pullen and Samuel T N Aroney and Benjamin L Coltman and Jay Osvatic and Ben J Woodcroft and Thomas Rattei and Michael Wagner},

editor = {Nicola Mulder},

doi = {10.1093/bioadv/vbaf280},

issn = {2635-0041},

year  = {2025},

date = {2025-11-09},

urldate = {2025-11-09},

journal = {Bioinfo Adv},

volume = {5},

number = {1},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

                  <jats:sec>

                    <jats:title>Motivation</jats:title>

                    <jats:p>Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Results</jats:title>

                    <jats:p>The GlobDB aggregates 14 independent genomic catalogues to provide a comprehensive database of species-dereplicated microbial genomes, with consistent taxonomy, annotations, and additional analysis resources. The GlobDB more than doubles the number of microbial species represented by genomes relative to the field standard genome taxonomy database.</jats:p>

                  </jats:sec>

                  <jats:sec>

                    <jats:title>Availability and implementation</jats:title>

                    <jats:p>The GlobDB is available at https://globdb.org/.</jats:p>

                  </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Holub2025,

title = {Not Just Better Resolution: A Detailed Study of the Signal Distribution in Mid-Infrared Optical Photothermal Imaging},

author = {Elisabeth Holub and Nikolaus Hondl and Sebastian Wöhrer and Bernhard Lendl and Georg Ramer},

doi = {10.1021/acs.analchem.5c03194},

issn = {1520-6882},

year  = {2025},

date = {2025-10-07},

urldate = {2025-10-07},

journal = {Anal. Chem.},

volume = {97},

number = {39},

pages = {21418--21427},

publisher = {American Chemical Society (ACS)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bayer2025,

title = {Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean},

author = {Barbara Bayer and Katharina Kitzinger and Nicola L. Paul and Justine B. Albers and Mak A. Saito and Michael Wagner and Craig A. Carlson and Alyson E. Santoro},

doi = {10.1038/s41561-025-01798-x},

issn = {1752-0908},

year  = {2025},

date = {2025-09-23},

journal = {Nat. Geosci.},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          Ammonia-oxidizing archaea are the most abundant chemolithoautotrophs in the ocean and are assumed to dominate carbon fixation below the sunlit surface layer. However, the supply of reduced nitrogen delivered from the surface in sinking particulate organic matter is insufficient to support the amount of nitrification required to sustain measured carbon fixation rates in the dark ocean. Here we attempt to reconcile this observed discrepancy by quantifying the contribution of ammonia oxidizers to dark carbon fixation in the eastern tropical and subtropical Pacific Ocean. We used phenylacetylene—a specific inhibitor of the ammonia monooxygenase enzyme—to selectively inhibit ammonia oxidizers in samples collected throughout the water column (60–600 m depth). We show that, despite their high abundances, ammonia oxidizers contribute only a small fraction to dark carbon fixation, accounting for 4–25% of the total depth-integrated rates in the eastern tropical Pacific. The highest contributions were observed within the upper mesopelagic zone (120–175 m depth), where ammonia oxidation could account for ~50% of dark carbon fixation at some stations. Our results challenge the current view that carbon fixation in the dark ocean is primarily sustained by nitrification and suggest that other microbial metabolisms, including heterotrophy, might play a larger role than previously assumed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kaiser2025,

title = {The role of ectomycorrhizal functional diversity in mediating soil carbon cycling under global change},

author = {Christina Kaiser and Mark A. Anthony},

doi = {10.1111/nph.70559},

issn = {1469-8137},

year  = {2025},

date = {2025-09-08},

journal = {New Phytologist},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40965358,

title = {Experimental and Theoretical Insights into Nanoscale AFM-IR Imaging of Complex Heterogeneous Structures},

author = {Yide Zhang and Ufuk Yilmaz and Artem S Vorobev and Simone Iadanza and Liam O'Faolain and Bernhard Lendl and Georg Ramer},

doi = {10.1021/acs.analchem.5c04707},

issn = {1520-6882},

year  = {2025},

date = {2025-09-01},

journal = {Anal Chem},

volume = {97},

number = {38},

pages = {21141--21149},

abstract = {Nanoscale chemical imaging enabled by atomic force microscopy-infrared spectroscopy (AFM-IR) provides valuable insights into the complex structures and chemical compositions of materials and biological samples. While AFM-IR has been applied to subsurface imaging, the underlying mechanisms, particularly in nonplanar geometries and complex heterogeneous structures, remain underexplored. This study presents a theoretical analysis and experimental validation of AFM-IR for imaging subsurface features within organic multilayer structures, uncovering how image broadening depends on whether the excitation occurs in the subsurface or the covering layer. An analytical model based on the sample geometry demonstrates that the lateral size of the absorber significantly impacts both the signal intensity and spatial resolution in AFM-IR chemical imaging. These findings are experimentally validated, and a more representative finite element method (FEM) model was subsequently created, resulting in strong agreement with the experimental data. The model reveals how irregular structures directly impact photothermal expansion, providing an explanation for the distinct image broadening observed with infrared excitation of different layers. Additionally, a linear relationship is observed between feature size, chemical images, and AFM-IR signal intensity. These findings contribute significantly to the understanding of the AFM-IR signal, providing insights into resolution and sensitivity, paving the way for more advanced nanoscale chemical imaging capabilities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sherman2025b,

title = {Uptake of tire-wear derived compounds by lettuce grown in three soils},

author = {Anya Sherman and Luzian Elijah Hämmerle and Evyatar Ben Mordechay and Benny Chefetz and Thilo Hofmann},

doi = {10.1016/j.envint.2025.109742},

issn = {0160-4120},

year  = {2025},

date = {2025-09-00},

journal = {Environment International},

volume = {203},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2025,

title = {Microbial iron oxide respiration coupled to sulfide oxidation},

author = {Song-Can Chen and Xiao-Min Li and Nicola Battisti and Guoqing Guan and Maria A. Montoya and Jay Osvatic and Petra Pjevac and Shaul Pollak and Andreas Richter and Arno Schintlmeister and Wolfgang Wanek and Marc Mussmann and Alexander Loy},

doi = {10.1038/s41586-025-09467-0},

issn = {1476-4687},

year  = {2025},

date = {2025-08-27},

journal = {Nature},

publisher = {Springer Science and Business Media LLC},

abstract = {Abstract

          Microorganisms have driven Earth’s sulfur cycle since the emergence of life1–6, yet the sulfur-cycling capacities of microorganisms and their integration with other element cycles remain incompletely understood. One such uncharacterized metabolism is the coupling of sulfide oxidation with iron(iii) oxide reduction, a ubiquitous environmental process hitherto considered to be strictly abiotic7,8. Here we present a comprehensive genomic analysis of sulfur metabolism across prokaryotes, and reveal bacteria that are capable of oxidizing sulfide using extracellular solid phase iron(iii). Based on a phylogenetic framework of over hundred genes involved in dissimilatory transformation of sulfur compounds, we recorded sulfur-cycling capacity in most bacterial and archaeal phyla. Metabolic reconstructions predicted co-occurrence of sulfur compound oxidation and iron(iii) oxide respiration in diverse members of 37 prokaryotic phyla. Physiological and transcriptomic evidence demonstrated that a cultivated representative, Desulfurivibrio alkaliphilus, grows autotrophically by oxidizing dissolved sulfide or iron monosulfide (FeS) to sulfate with ferrihydrite as an extracellular iron(iii) electron acceptor. The biological process outpaced the abiotic process at environmentally relevant sulfide concentrations. These findings expand the known diversity of sulfur-cycling microorganisms and unveil a biological mechanism that links sulfur and iron cycling in anoxic environments, thus highlighting the fundamental role of microorganisms in global element cycles.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rasoulimehrabani2025,

title = {Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting},

author = {Hamid Rasoulimehrabani and Sanaz Khadem and Adnan Hodžić and Miriam Philipp and Rebecca Gallo and Georgi Nikolov and Joana Séneca and Julia Ramesmayer and Patrik Sivulič and David Berry},

doi = {10.20517/mrr.2025.29},

issn = {2771-5965},

year  = {2025},

date = {2025-08-14},

journal = {Microbiome Res Rep.},

volume = {4},

number = {3},

publisher = {OAE Publishing Inc.},

abstract = {

          Background: Arabinogalactan is a complex plant-derived polysaccharide proposed to function as a selective prebiotic, yet the microbial taxa directly involved in its metabolism and the cooperative dynamics within the gut microbiota remain incompletely defined.

          

          Methods: Here, we combined community-level sequencing with targeted single-cell activity profiling to investigate how arabinogalactan shapes gut microbial composition and function. Fecal samples from ten healthy individuals were incubated ex vivo with arabinogalactan, and microbial responses were assessed using 16S rRNA gene amplicon sequencing alongside Raman-activated cell sorting (RACS) and coculture experiments.

          

          Results: Arabinogalactan consistently enriched Bifidobacterium and Gemmiger across donors, with Bifidobacterium also responding to galactose and Gemmiger and Blautia stimulated by arabinose, the two monosaccharide components of arabinogalactan. RACS enabled the selective isolation of metabolically active arabinogalactan responders, including Bifidobacterium longum (B. longum) and Faecalibacterium prausnitzii, along with other strains from the phyla Actinomycetota, Bacteroidota, and Bacillota. Notably, coculture experiments revealed that B. longum not only degraded arabinogalactan efficiently but also supported the growth of non-degrading species via metabolic cross-feeding. These cooperative interactions highlight B. longum as a keystone species in arabinogalactan utilization and suggest broader community-level benefits from its activity.

          

          Conclusion: Together, our findings demonstrate arabinogalactan’s bifidogenic effect and its potential to promote functionally important microbes within the gut ecosystem. This study also highlights the utility of RACS for linking microbial identity to function, enabling the targeted recovery of active strains from complex communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bale2025,

title = {Unusual Plastoquinones in Non‐Phototrophic Nitrifying Bacteria},

author = {Nicole J. Bale and Hayato Fujimura and Petra Pjevac and Michel Koenen and Hikaru Ikeda and Satohiro Itagaki and Yojiro Yamamoto and Johanna Palmetzhofer and Christopher J. Sedlacek and Hayk Palabikyan and Jaap S. Sinninghe Damsté and Michael Wagner and Hiroshi Shiigi and Holger Daims},

doi = {10.1111/1758-2229.70174},

issn = {1758-2229},

year  = {2025},

date = {2025-08-05},

urldate = {2025-08-00},

journal = {Environ Microbiol Rep},

volume = {17},

number = {4},

publisher = {Wiley},

abstract = {<jats:title>ABSTRACT</jats:title><jats:p>Isoprenoid quinones are important compounds in most organisms. They are essential in electron and proton transport in respiratory and photosynthetic electron transport chains, and additional functions include oxidative stress defence. The biologically most relevant quinones are naphthoquinones including menaquinone and benzoquinones including ubiquinone and plastoquinone. They differ in their polar headgroup structures, physicochemical properties, and distribution among organisms. Menaquinone is the most widespread quinone in prokaryotes, ubiquinone occurs only in bacteria of the phylum <jats:italic>Pseudomonadota</jats:italic> and eukaryotes, and plastoquinone exists in phototrophic <jats:italic>Cyanobacteria</jats:italic> and plants. We found that chemolithoautotrophic nitrifying bacteria of the genus <jats:italic>Nitrospira</jats:italic> (phylum <jats:italic>Nitrospirota</jats:italic>) exclusively possess unusual methyl‐plastoquinones with a standard redox potential below that of canonical plastoquinone and ubiquinone but above menaquinone, suggesting functional roles in reverse electron transport, ammonia oxidation, alternative energy metabolisms, and oxidative stress mitigation. This extends the known diversity of quinones and suggests that plastoquinone derivatives are essential in ecologically important, non‐phototrophic bacteria.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{FMKop2025,

title = {Comparative genome analysis reveals broad phylogenetic and functional diversity within the order Nitrospirales},

author = {Linnea F M Kop and Hanna Koch and Daan Speth and Claudia Lüke and Eva Spieck and Mike S M Jetten and Holger Daims and Sebastian Lücker},

doi = {10.1093/ismejo/wraf151},

issn = {1751-7370},

year  = {2025},

date = {2025-07-24},

urldate = {2025-07-22},

journal = {The ISME Journal},

volume = {19},

issue = {1},

pages = {wraf151},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title> 

 <jats:p>Nitrification, a key process in the nitrogen cycle, involves the oxidation of ammonia to nitrite and nitrate by a diverse group of chemolithoautotrophic microorganisms. The order Nitrospirales (referred to in literature as the genus Nitrospira), which includes both nitrite-oxidizing and complete ammonia-oxidizing bacteria, plays a central role in this process. We sequenced the genomes of nine Nitrospirales members, incorporating genomes from previously unsequenced taxonomic Nitrospirales lineages. A comprehensive genomic analysis of these new Nitrospirales was conducted, which included an examination of their habitat distribution, phylogenetic diversity, and functional capabilities. This was complemented by the construction of and comparison to a database of 446 non-redundant, high-quality Nitrospirales genomes. Our phylogenomic analysis uncovered the presence of additional unclassified lineages and provided a comparison between genome-based and 16S rRNA gene-based taxonomies. Whereas some Nitrospirales lineages seem to exhibit habitat preferences, others are found across a wide variety of ecosystems, suggesting a broad niche spectrum. This capacity to adapt to different environmental conditions is also reflected in the high variability and modularity of the respiratory chain and nitrogen assimilation mechanisms. Additionally, we found evidence of quorum sensing systems in species beyond lineage II, implying a broader ecological role for this communication mechanism within the Nitrospirales. Finally, we identified a set of conserved genes unique to nitrite oxidoreductase-containing Nitrospirales, providing insights into the emergence of this functional group. In conclusion, our study emphasizes the adaptability of the various nitrifying classes of the order Nitrospirales to diverse environments and reveals the presence of new taxonomic lineages.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40296371b,

title = {The Fecal Microbiome of IBD Patients Is Less Divertible by Bowel Preparation Compared to Healthy Controls: Results From a Prospective Study},

author = {Andreas Blesl and Lukas Binder and Bettina Halwachs and Franziska Baumann-Durchschein and Stefan Fürst and Patrizia Constantini-Kump and Heimo Wenzl and Gregor Gorkiewicz and Christoph Högenauer},

doi = {10.1093/ibd/izaf053},

issn = {1536-4844},

year  = {2025},

date = {2025-07-01},

journal = {Inflamm Bowel Dis},

volume = {31},

number = {7},

pages = {2007--2018},

abstract = {BACKGROUND: The fecal microbiome of patients with inflammatory bowel diseases (IBD) is characterized by longitudinal variability. It remains unknown if this is caused by decreased resilience of the microbiome to external factors. We investigated the influence of osmotic diarrhea induced by bowel preparation as a disruptive factor on the fecal microbiome in IBD patients and healthy comparators.nnMETHODS: We conducted a prospective, single-center study including IBD patients and healthy controls scheduled for colonoscopy with uniform bowel preparation. Fecal samples were collected at 7 time points prior, during, and until 3 months after the intervention. 16S rRNA was isolated from stool and sequenced using the Illumina technique.nnRESULTS: Twenty-two IBD patients and 17 healthy controls were included in the study. Baseline diversity was higher in healthy controls. Bowel preparation longitudinally decreased alpha diversity and altered beta diversity and taxonomic composition in both groups. Alterations were more pronounced in healthy controls, and the microbial composition converged between the 2 groups. Bowel preparation resulted in an increased relative abundance of Anaerostipes and Coprococcus in both groups and in decreased relative abundance of Bifidobacterium and Clostridium sensu stricto in IBD patients and of Eubacterium hallii group and Ruminococcus in healthy controls. Changes largely restored to baseline composition within 1 week in both groups and remained stable thereafter.nnCONCLUSIONS: Bowel preparation induced reversible short-term microbial perturbations which were less pronounced in IBD patients than in healthy comparators suggesting that a single external disruptive factor may have less impact on an already altered fecal microbiome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40511921,

title = {Mimivirus transcription and translation occur at well-defined locations within amoeba host cells},

author = {Lotte Mayer and Georgi Nikolov and Martin Kunert and Matthias Horn and Anouk Willemsen},

doi = {10.1128/jvi.00554-25},

issn = {1098-5514},

year  = {2025},

date = {2025-07-01},

journal = {J Virol},

volume = {99},

number = {7},

pages = {e0055425},

abstract = {Many giant viruses replicate in the cytoplasm in viral factories. How exactly these viral factories are established and where the different steps of the replication cycle occur remain largely obscure. We have developed a single-molecule messenger RNA fluorescence  hybridization (smFISH) protocol for giant viruses in an  host. Combined with other labeling techniques (FUNCAT, DiD, rRNA FISH, and DAPI), we show the Mimivirus transcription and translation sites during an infection cycle in the amoeba host cell. Although viral mRNA localization changes depend on the infection stage, transcription occurs at well-defined spots within the viral factory. The original viral cores released within the cytoplasm most likely define these spots. When transported outside of the viral factory, the translation of viral mRNA takes place in a well-defined ring surrounding it. With this study, we obtained novel insights into giant virus replication, of which the methods are widely applicable to other viruses for the visualization and quantification of RNA molecules.IMPORTANCEGiant viruses have massive particle and genome sizes, which are known to infect unicellular eukaryotes. Although most viruses replicate in the host cell's nucleus, the giant Mimivirus replicates in viral factories established in the host cell's cytoplasm. Before this study, the location of the various steps in the Mimivirus replication cycle was largely unknown. By developing new protocols to label giant virus mRNA, protein synthesis, host cell membranes and rRNA, we demonstrate that Mimivirus transcription occurs at well-defined sites within the viral factory. In contrast, translation takes place directly outside of it. This is different from other viruses known to have a cytoplasmic life cycle. These results bring us a step closer to understanding how the genome complexity of viruses influences the virus-host interactions and viral replication strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}