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Enhancing microbial superoxide generation and conversion to hydroxyl radicals for enhanced bioremediation using iron-binding ligands

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Journal of Environmental Sciences 2025年第1期147卷 597-606页

作者： Yuhan Wang Xue Ning Jinsong Liang Aijie Wang Jiuhui Qu School of Civil and Environmental Engineering Harbin Institute of TechnologyShenzhen 518055China SFI MaREI centre for Energy Climate and MarineEnvironmental Research InstituteUniversity College CorkCorkIreland Center for Water and ecology Tsinghua UniversityBeijing 100084China

Harnessing bacteria for superoxide production in bioremediation holds immense promise,yet its practical application is hindered by slow production rates and the relatively weak redox potential of *** study delves into a cost-effective approach to amplify superoxide production using an Arthrobacter strain,a prevalent soil bacterial *** research reveals that introducing a carbon source along with specific iron-binding ligands,including deferoxamine(DFO),diethylenetriamine pentaacetate(DTPA),citrate,and oxalate,robustly augments microbial superoxide ***,our findings suggest that these iron-binding ligands play a pivotal role in converting superoxide into hydroxyl radicals by modulating the electron transfer rate between Fe(Ⅲ)/Fe(Ⅱ)and ***,among the tested ligands,only DTPA emerges as a potent promoter of this conversion process when complexed with Fe(Ⅲ).We identify an optimal Fe(Ⅲ)to DTPA ratio of approximately 1:1 for enhancing hydroxyl radical production within the Arthrobacter *** research underscores the efficacy of simultaneously introducing carbon sources and DTPA in facilitating superoxide production and its subsequent conversion to hydroxyl radicals,significantly elevating bioremediation ***,our study reveals that DTPA augments superoxide production in cultures of diverse soils,with various soil microorganisms beyond Arthrobacter identified as contributors to superoxide *** emphasizes the universal applicability of DTPA across multiple bacterial *** conclusion,our study introduces a promising methodology for enhancing microbial superoxide production and its conversion into hydroxyl *** findings hold substantial implications for the deployment of microbial reactive oxygen species in bioremediation,offering innovative solutions for addressing environmental contamination challenges.

关键词： Superoxide Hydroxyl radical Iron-binding ligand Bioremediation DTPA

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Cereal-legume intercropping stimulates straw decomposition and promotes soil organic carbon stability

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Science China Life Sciences 2025年

作者： Wei Wang Meng-Ying Li Qing-Hui Wen Yue Ma Zhi-Ming Zhang Muhammad Maqsood Ur Rehman Fei Mo Hong-Yan Tao Bao-Luo Ma Joann K.Whalen You-Cai Xiong State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems College of Ecology Lanzhou University School of ecology and Environmental Science Yunnan University College of Agronomy Northwest A&F University Ottawa Research and Development centre Agriculture and Agri-Food Canada Department of Natural Resource Sciences McGill University

Increasing carbon（C） sequestration and stability in agricultural soils is a key strategy to mitigate climate change towards C neutrality. Crop diversification is an initiative to increase C sequestration in fields, but it is unclear how legume-based crop diversification impacts the functional components of soil organic carbon（SOC） in dryland, including the formation and transformation of particulate organic carbon（POC） and mineral-associated organic carbon（MAOC）. We investigated the decomposition of straw residues, the fate of photosynthesized C,as well as the formation of MAOC and POC fractions using an in situ13C labeling technique in the soybean-wheat intercropping, soybeanmaize intercropping and their respective monocropping systems, with and without cover crops. After 4-year treatments, the total SOC content in bulk soil remained unchanged, while MAOC content increased significantly by 5.6% with intercropping. Moreover, the in situ13C labeling results confirmed that more photosynthesized C was transferred to MAOC, and less was retained in the POC fraction. Intercropping significantly increased total soil N and mineral N content by 15.3% and 13.4%, respectively, and decreased soil and microbial C/N ratio by11.3% and 17.4%, respectively. This outcome, therefore, relieved microbial N limitation and accelerated straw residue ***, the potential of MAOC formation was strengthened for better SOC persistence. Our study suggests that legume-based crop diversification can effectively enrich N and support POC transformation to MAOC, accordingly contributing to the persistent SOC pool and thus potentially achieving C neutrality under climate change in dryland agroecosystems.

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“Winter Is Coming” : How did Polyploid Plants Survive?

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Molecular Plant 2020年第1期13卷 4-5页

作者： Zhen Li Yves Van de Peer Department of Plant Biotechnology and Bioinformatics Ghent University9052 GhentBelgium VIB Center for Plant Systems Biology 9052 GhentBelgium centre for microbial ecology and genomics Department of BiochemistryGenetics and MicrobiologyUniversity of PretoriaPretoria 0028South Africa.

Cold and dark periods have descended on Earth several times in geological history. One such period characterized the Cretaceous-Paleogene (K-Pg) boundary, following a meteor impact near Chicxulub in Mexico, about 66 million years ago, which caused dust, sulfate aerosols, and soot particles to be ejected into the atmosphere. This in turn led to a so-called “impact winter,” inhibiting photosynthesis and causing a global collapse of terrestrial and marine food webs, leading to the extinction of 60%–70% of plants and animals ( Alvarez et al., 1980 ). Different from animals that might still be able to find shelter and detritus food in a harsh environment, plants are sessile and require (lots of) light for photosynthesis. How did they survive in a time of prolonged darkness and decreasing temperatures ( Vellekoop et al., 2016 )?

关键词： winter Cretaceous terrestrial

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A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

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Science Bulletin 2016年第13期61卷 1052-1060页

作者： Yong-Guan Zhu Jian-Qiang Su Zhihong Cao Kai Xue John Quensen Guang-Xia Guo Yun-Feng Yang Jizhong Zhou Hai-Yan Chu James M.Tiedje Key Laboratory of Urban Environment and Health Institute of Urban Environment Chinese Academy of Sciences State Key Laboratory of Urban and Regional ecology Research Center for Eco-environmental Sciences Chinese Academy of Sciences Institute of Soil Science Chinese Academy of Sciences Institute for Environmental genomics University of Oklahoma Center for microbial ecology Department of Plant Soil and Microbial Sciences Michigan State University State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment Tsinghua University

It has been documented that human activities are causing the rapid loss of taxonomic, phylogenetic, genetic and functional diversity in soils. However, it remains unclear how modern intensive rice cultivation impacts the soil microbiome and its functionality. Here we examined the microbial composition and function differences between a buried Neolithic paddy soil and an adjacent, currently-cultivated paddy soil using high throughput metagenomics technologies. Our results showed that the currently cultivated soil contained about 10-fold more microbial biomass than the buried one. Analyses based on both 16S rRNA genes and functional gene array showed that the currently cultivated soil had significantly higher phylogenetic diversity, but less functional diversity than the buried Neolithic one. The community structures were significantly different between modern and ancient soils, with functional structure shifting towards accelerated organic carbon （C） degradation and nitrogen （N） transfor- mation in the modem soils. This study implies that, modern intensive rice cultivation has substantially altered soil microbial functional structure, leading to functional homogenization and the promotion of soil ecological functions related to the acceleration of nutrient cycling which is necessary for high crop yields.

关键词： Neolithic paddy soil Long-term ricecultivation 16S rRNA gene pyrosequencing -Bacterial community - Functional gene diversityGeoChip

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Multispecies hybridization in birds

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Avian Research 2019年第3期10卷 239-249页

作者： Jente Ottenburghs Resource ecology Group Wageningen University Department of ecology and Genetics Evolutionary Biology Centre Uppsala University

Hybridization is not always limited to two species;often multiple species are interbreeding. In birds, there are numerous examples of species that hybridize with multiple other species. The advent of genomic data provides the oppotunity to investigate the ecological and evolutionary consequences of multispecies hybridization. The interactions between several hybridizing species can be depicted as a network in which the interacting species are connected by edges. Such hybrid networks can be used to identify ‘hub-species’ that interbreed with multiple other species. Avian examples of such ‘hub-species’ are Common Pheasant (Phasianus colchicus), Mallard (Anas platyrhynchos) and European Herring Gull (Larus argentatus). These networks might lead to the formulation of hypotheses, such as which connections are most likely conducive to interspecific gene flow (i.e. introgression). Hybridization does not necessarily result in introgression. Numerous statistical tests are available to infer interspecific gene flow from genetic data and the majority of these tests can be applied in a multispecies setting. Specifically, model-based approaches and phylogenetic networks are promising in the detection and characterization of multispecies introgression. It remains to be determined how common multispecies introgression in birds is and how often this process fuels adaptive changes. Moreover, the impact of multispecies hybridization on the build-up of reproductive isolation and the architecture of genomic landscapes remains elusive. For example, introgression between certain species might contribute to increased divergence and reproductive isolation between those species and other related species. In the end, a multispecies perspective on hybridization in combination with network approaches will lead to important insights into the history of life on this planet.

关键词： Adaptation Admixture genomics Introgression Network analysis Phylogenetics Speciation

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Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales

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mLife 2024年第1期3卷 21-41页

作者： Vadakattu V.S.R.Gupta James M.Tiedje CSIRO Agriculture&Food UrrbraeSouth AustraliaAustralia centre for microbial ecology Michigan State UniversityEast LansingMichiganUSA

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures *** community structure is mainly a result of the inoculum(dispersal),the selective advantages of those organisms under the habitat-based environmental attributes,and the ability of those colonizers to sustain themselves over *** soil is protective,and its microbial inhabitants have long adapted to varied soil conditions,significant portions of the soil microbial community structure are likely ***,a substantial portion of the community will not correlate to often measured soil *** suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes:(i)those that supply energy,i.e.,organic carbon and electron acceptors;(i)environmental effectors or stressors,i.e.,pH,salt,drought,and toxic chemicals;(ii)macro-organism associations,i.e.,plants and their seasonality,animals and their fecal matter,and soil fauna;and(iv)nutrients,in order,N,P,and probably of lesser importance,other micronutrients,and *** relevance of drivers also varies with spatial and time scales,for example,aggregate to field to regional,and persistent to dynamic populations to transcripts,and with the extent of phylogenetic difference,hence phenotypic differences in organismal *** present a summary matrix to provide guidance on which drivers are important for particular studies,with special emphasis on a wide range of spatial and temporal scales,and illustrate this with genomic and population(rRNA gene)data from selected studies.

关键词： abundance community structure diversity functional microbiome microorganisms

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Finding Evidenee for Whole Genome Duplications: A Reappraisal

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Molecular Plant 2019年第2期12卷 133-136页

作者： Arthur Zwaenepoel Zhen Li Rolf Lohaus Yves Van de Peer Department of Plant Biotechnology and Bioinformatics Ghent University 9052 Ghent Belgium Center for Plant Systems Biology VIB 9052 Ghent Belgium Center for microbial ecology and genomics Department of Biochemistry Genetics and Microbiology University of Pretoria Pretoria South Africa

Dear Editor, Recently, Ren et al. reported an extensive analysis of the incidence of whole genome duplications (WGDs) throughout the evolutionary history of extant angiosperms (Ren et al., 2018). Examining a wealth of genomic data (36 complete genomes and 69 transcriptomic datasets) using commonly applied methods, they detected and located 55 WGDs throughout the an giosperm phylogeny.

关键词： Finding Evidenee Whole Genome Duplications Reappraisal

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Vallisneria spiralis L. adaptive capacity improves pore water chemistry and increasespotential nitrification in organic polluted sediments

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Ecological Processes 2024年第2期13卷 72-89页

作者： Leonardo Morini Claudio Ferrari Marco Bartoli Mindaugas Zilius Elias Broman Giovanna Visioli Department of Chemistry Life Science and Environmental Sustainability University of Parma Department of Environmental and Prevention Sciences University of Ferrara Department of Integrative Marine ecology (EMI) Genoa Marine Centre Stazione Zoologica Anton Dohrn-National Institute of Marine BiologyEcology and Biotechnology Marine Research Institute Klaipeda University Department of ecology Environment and Plant Sciences Stockholm University Baltic Sea centre Stockholm University

Background Macrophytes may modify benthic biodiversity and biogeochemistry via radial oxygen loss from roots. This condition contrasts sediments anoxia, allows roots respiration, and facilitates aerobic microbial communities and processes in the rhizosphere. Simultaneously, the rhizosphere can stimulate anaerobic microorganisms and processes via exudates or by favoring the build-up of electron acceptors as nitrate. As eutrophication often results in organic enrichment in sediments and large internal nutrients recycling, an interesting research question is to investigate whether plants maintain the capacity to stimulate aerobic or anaerobic microbial communities and processes also under elevated organic *** A manipulative experiment was carried out under laboratory-controlled conditions. Microcosms containing bare sediments and sediments transplanted with the macrophyte Vallisneria spiralis L. were created. The effect of the plant was investigated on sediments with moderate(8%) and elevated(21%) organic matter content, after an acclimatization period of 30 days. Chemical and physical parameters, microbial community composition and the potential rates of nitrification, denitrification and nitrate ammonification were measured at two different depths(0–1 and 1–5 cm) after the acclimatization period to evaluate the role of *** Vallisneria spiralis grew and assimilated pore water nutrients at the two organic matter levels and vegetated sediments had always nutrient-depleted porewaters as compared to bare sediments. Nitrifying microbes had a lower relative abundance and diversity compared to denitrifying bacteria. However, regardless of the organic content, in vegetated sediments nitrifiers were detected in deeper horizons as compared to bare sediments, where nitrification was confined near the surface. In contrast, potential denitrification rates were not affected by the presence of roots, but probably regulated by the presence of nitrate and by ro

关键词： Ammonium oxidation Macrophyte microbial functional group Nature-based solution Nitrate reduction Rhizosphere

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Genomic analysis of Tibetan ground tits identifies molecular adaptations associated with cooperative breeding

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Current Zoology 2023年第5期69卷 620-630页

作者： Yi Wang Chen Wang Wei Hong Shilin Tian Qin Lu Bing-Jun Wang Huaiming Jin Nima Zhuoma Xin Lu Huabin Zhao Department of ecology Tibetan Centre for Ecology and Conservation at Wuhan University—Tibet UniversityHubei Key Laboratory of Cell HomeostasisCollege of Life SciencesWuhan UniversityWuhan 430072China Research Center for ecology College of ScienceTibet UniversityLhasa 850000China

Cooperative breeding is a sophisticated altruistic social behavior that helps social animals to adapt to harsh *** Tibetan ground tit,Pseudopodoces humilis,is a high-altitude bird endemic to the Tibetan ***,it has become an exciting system for studying the evolution of facultative cooperative *** test for molecular adaptations associated with cooperative breeding,we resequenced the whole genome of ground tits from 6 wild populations that display remarkable variation in the frequency of cooperative *** structure analyses showed that the 6 populations were divided into 4 lineages,which is congruent with the major geographical distribution of the sampling *** genome-wide selective sweep analysis,we identified putative positively selected genes(PSGs)in groups of tits that displayed high and low cooperative breeding *** total number of PSGs varied from 146 to 722 in high cooperative breeding rate populations,and from 272 to 752 in low cooperative breeding rate *** enrichment analysis of these PSGs identified several significantly enriched ontologies related to oxytocin signaling,estrogen signaling,and insulin *** involved in these functional ontologies suggest that molecular adaptations in hormonal regulation may have played important roles in shaping the evolution of cooperative breeding in the ground *** together,our study provides candidate genes and functional ontologies involved in molecular adaptations associated with cooperative breeding in Tibetan ground tits,and calls for a better understanding of the genetic roles in the evolution of cooperative breeding.

关键词： cooperative breeding ground tit population genomics social behavior

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NGSmirPlant： comprehensive characterization of the small RNA transcriptomes of plants

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Protein & Cell 2015年第6期6卷 397-402页

作者： Jie Bai Chen Dan Yi Zhang Guoping Zhao Xiaoming Ding Department of Microbiology and microbial Engineering School of Life Sciences Fudan University Shanghai 200433 China Key Laboratory of Synthetic Biology Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Shanghai-MOST Key Laboratory of Health and Disease genomics Chinese National Human Genome Center at Shanghai Shanghai 201203 China

MicroRNAs （miRNAs） are short, endogenously expressed RNAs （-21-22 nt） processed from stem-loop regions of longer RNA precursors by a Dicer-like enzyme （Jones- Rhoades et al., 2006）. In plants, microRNAs play an essential role in regulating many fundamental molecular in- teractions, including plant growth, development and re- sponse to environmental stress （Rogers and Chen, 2013）. In comparison with the roles of microRNAs in animals, bio- genesis and function of microRNAs in plants appears to be drastically different （Llave et al., 2002; Zhang et al., 2007）.

关键词： NGSmirPlant comprehensive characterization RNA

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