Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2025
Authors
Igor A. Yakovlev Thiago Inagaki Junbin Zhao Pierre-Adrien Rivier Hege Særvold Steen Inger Heldal Daniel Rasse Jihong Liu Clarke Nicholas ClarkeAbstract
No abstract has been registered
Authors
Teresa Gómez de la Bárcena Tatiana Francischinelli Rittl Eva Farkas Daniel Rasse Cédric Plessis Helge Meissner Christophe Moni Trond Henriksen Randi Berland FrøsethAbstract
No abstract has been registered
Abstract
Research Highlights The microbial community applied with the digestate accelerated methane formation. CO2 emission was higher under waterlogging than at field capacity in soil with low organic content. Waterlogging decreased methane emission in unamended soil. Only digestate where some methane potential was left induced high methane emission. Methanogens and methanotrophs abundances dynamics partly explain emission patterns.
Authors
Qiang Liu Mahmoud Mazarji Yeqing Li Lu Feng Hongjun Zhou Quan Xu Alastair James Ward Yajing Wang Jianping Su Chunming Xu Junting PanAbstract
Humic acid (HA) is an inhibitor that can diminish bioconversion during anaerobic digestion (AD). In this study, a non-metallic nanomaterial, N-doped carbon quantum dots (NCQD), was synthesized to alleviate the HA inhibition, followed by exploring its mechanism. Adding 500 mg/L NCQD prevented HA inhibition by binding to HA or microorganism surfaces, thus avoiding contact between them. This phenomenon, known as shielding inhibition, involves the formation of hydrogen bonds and chemical bonds. The intermolecular force and dissociation constant (KD) between NCQD and HA were determined to be 112.83 ±3.98 nN and 1.0 ±0.07 ×10 7 M, respectively. NCQD could promote electron transfer in AD systems. According to the in-depth microbial analysis, NCQD significantly enhanced the metabolic pathways of methanogenesis and biosynthesis of coenzyme F420. This groundbreaking research demonstrates the dual functionality of NCQD by effectively shielding against HA inhibition and promoting electron transfer. The study also unravels the mechanism of interface interaction, electron transfer, and metabolic pathways, leading to significant breakthroughs in addressing HA inhibition.
Authors
Getachew Birhanu Abera Aryan Bhusal Thea Os Andersen Shuai Wang Nabin Aryal Svein Jarle Horn Lu FengAbstract
In-situ biomethanation is an efficient process for converting carbon dioxide (CO2) to methane (CH4) using hydrogen (H2) alongside anaerobic digestion (AD) process. However, AD of protein rich substrate often leads to the accumulation of ammonia nitrogen at high concentration. As a major inhibitor, this accumulation affects not only the AD process but also in-situ biomethanation. This study investigated the impact of ammonia nitrogen (0.5–5 g/L) on biomethanation performance using anaerobic moving-bed biofilm reactors (AnMBBRs). Without biofilm/biocarrier support, methane production was significantly inhibited above 3 g/L of ammonia nitrogen. In contrast, AnMBBR maintained high methane yields of 156.5 NmL/Lreactor at 2.5 g/L and 151.3 NmL/Lreactor at 5 g/L ammonia nitrogen, representing increases of 49 % and 76 %, respectively, compared to reactors without biofilm. Microbial analysis via 16S rRNA sequencing showed that Methanothermobacter, a thermophilic hydrogenotrophic methanogen, increased in relative abundance under ammonia nitrogen stress, which was further supported by carbon isotope analysis. Overall, these results highlighted the potential of AnMBBR to overcome ammonia nitrogen stress in in-situ biomethanation.
Authors
Ya-Lan Hong Wei-Ming Xi Ya-Ting Wang Yi Yuan Zong-Zhuan Shen Ming Tian Jihong Liu Clarke Wang-Ying Xie Fang-jie ZhaoAbstract
Environmental transmission of antibiotic resistance poses a significant threat to human health by undermining the efficacy of therapeutic interventions against bacterial infections. Agricultural practices, particularly the application of organic fertilizers derived from animal manure, are major contributors to the spread of antibiotic resistance determinants (ARDs) in soil ecosystems. However, the fates of ARDs and their bacterial hosts in soil following organic fertilization as well as the impact of water management regimes remain poorly understood. We investigated the attenuation and persistence of ARDs in soil following organic fertilization under water management practices of upland, continuous flooding, and intermittent flooding. Most ARDs introduced via the organic fertilizer exhibited significant attenuation, with half-lives ranging from 19 to 50 days, primarily due to the decline of fertilizer-derived bacterial hosts. Specific ARDs, such as aph(3’)-IIIa and tetO, persisted across all treatments. Upland conditions accelerated the attenuation of ARDs and their pathogenic hosts compared to f looding conditions, which prolonged their survival and promoted horizontal gene transfer. The divergent responses of ARD composition and soil bacterial communities to the environmental variables revealed a unique dissemination pattern, wherein the soil co-occurring bacterial communities served as critical hubs for the dissemination of ARDs and their bacterial hosts from organic fertilizers. The soil co-occurring bacterial communities exhibited strong interspecies interactions and high sensitivity to environmental changes. Targeted strategies to disrupt these assembly hubs may provide an effective way to mitigate the spread of antibiotic resistance from organic fertilizers to soil ecosystems.
Authors
Ana-Maria Pantazica Alexander Hammel Iuliana Caras Irina Ionescu Catalin Tucureanu Adrian Onu Maria Murace Jihong Liu Clarke Crina Stavaru Norica Branza-Nichita Ralph BockAbstract
Microalgae represent promising production factories for the light-driven, cost-effective production of recombinant proteins. The red microalga Porphyridium purpureum displays particularly favourable transgene expression properties due to the episomal maintenance of transformation vectors at high copy numbers in the nucleus. In this work, we explored the potential of Porphyridium purpureum to synthesise a candidate vaccine against Hepatitis B virus (HBV). We show high-yield expression of an HBV chimeric surface antigen and efficient assembly of virus-like particles (VLPs) in algal cells. We established a purification protocol for the VLPs and conducted vaccination studies in experimental animals. The results demonstrate that the alga-produced HBV antigen elicits superior humoral and cellular immune responses compared to a commercial HBV vaccine produced in yeast. The antigen triggers virus-neutralising antibodies against different HBV variants, including vaccine-escape mutations that evade the immune response to current vaccines in humans. Our work establishes Porphyridium as a highly promising production platform for vaccines and other proteinaceous biopharmaceuticals.
Abstract
Syngas biomethanation represents a promising pathway to convert recalcitrant feedstocks into biomethane. However, the hydrogen (H2) content in syngas is often insufficient or fluctuates, which affects the overall performance. This study evaluated the effect of H2 addition on syngas conversion efficiency and microbial community dynamics using two trickle bed reactors (TBRs). One TBR was fed with syngas, while another received syngas supplemented with H2. Both TBRs demonstrated the feasibility of converting CO from syngas to methane, with the H2 supplemented TBR outperforming the syngas-only TBR. The H2 supplemented TBR achieved over 90 % conversion rate at a gas loading rate of 15 NL/Lreactor/d and reached peak methane production at a gas loading rate at 20 NL/Lreactor/d. Microbial community structure analysis revealed a dominance of Methanobacterium, a known thermophilic hydrogenotrophic methanogen. Although H2 addition enhanced performance, a decline in conversion efficiency at higher gas loading rates highlights the need for further optimization.
Authors
Xiaoge Fan Xiang Cao Min Zhang Jianwu Jiang Caihua Li Ou Fang Wenbing Wang Jin Zhang Nicholas Clarke Wenbo Liu Shengdao ShanAbstract
Although biochar application is regarded as a promising agronomic strategy to enhance soil functions, research employing quantitative techniques to evaluate its influence on microbial functional genes specifically in paddy soils is still scarce. The objective of this study was to quantify the abundance of microbial functional genes associated with carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling over a 2-year paddy field experiment after biochar application, employing a quantitative metagenomic sequencing with the spike-in method. An increase in rice yield of 7.0% and 12.5% relative to the control was observed following biochar amendment over the 2 study years. The majority of soil microbial functional genes related to C, N, P, and S cycling exhibited higher abundances in soils amended with biochar. Notably, genes associated with the Wood-Ljungdahl pathway, Calvin-Benson-Bassham cycle, and denitrification increased by 18.5%–197.4%, 25.9%–116.0%, and 5.1%–405.3% over 2 years. Gene responsible for P regulators increased approximately 10.5%–109.6%, while the assimilatory sulfate reduction process exhibited an increase of 12.7%–246.0%. Random forest highlighted key biogeochemical processes (e.g., C degradation, tricarboxylic acid cycle, and dissimilatory N reduction) as potential contributors to improving rice yields. Biochar amendment led to the formation of a more complex gene co-occurrence network, as exposed by network analysis. Collectively, these findings underscore that biochar application may consequently enhance microbial functional capacity in paddy soils, fostering improved agroecosystem functions.
Abstract
Environmental observation networks, such as AmeriFlux, are foundational for monitoring ecosystem response to climate change, management practices, and natural disturbances; however, their effectiveness depends on their representativeness for the regions or continents. We proposed an empirical, time series approach to quantify the similarity of ecosystem fluxes across AmeriFlux sites. We extracted the diel and seasonal characteristics (i.e., amplitudes, phases) from carbon dioxide, water vapor, energy, and momentum fluxes, which reflect the effects of climate, plant phenology, and ecophysiology on the observations, and explored the potential aggregations of AmeriFlux sites through hierarchical clustering. While net radiation and temperature showed latitudinal clustering as expected, flux variables revealed a more uneven clustering with many small (number of sites < 5), unique groups and a few large (> 100) to intermediate (15–70) groups, highlighting the significant ecological regulations of ecosystem fluxes. Many identified unique groups were from under-sampled ecoregions and biome types of the International Geosphere-Biosphere Programme (IGBP), with distinct flux dynamics compared to the rest of the network. At the finer spatial scale, local topography, disturbance, management, edaphic, and hydrological regimes further enlarge the difference in flux dynamics within the groups. Nonetheless, our clustering approach is a data-driven method to interpret the AmeriFlux network, informing future cross-site syntheses, upscaling, and model-data benchmarking research. Finally, we highlighted the unique and underrepresented sites in the AmeriFlux network, which were found mainly in Hawaii and Latin America, mountains, and at under- sampled IGBP types (e.g., urban, open water), motivating the incorporation of new/unregistered sites from these groups.