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Degradation of gaseous hydrocarbons in aerated stirred bioreactors inoculated with Rhodococcus erythropolis:Effect of the carbon source and SIFT-MS method development

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Journal of Environmental Sciences 2025年第1期147卷 268-281页

作者： Paula Alejandra Lamprea Pineda Kristof Demeestere Allan Augusto Alvarado-Alvarado Frank Devlieghere Nico Boon Herman Van Langenhove Christophe Walgraeve Research group EnVOC Department of Green Chemistry and TechnologyFaculty of Bioscience EngineeringGhent UniversityCoupure Links 6539000Ghent Belgium Research group FMFP Department of Food TechnologySafety and HealthFaculty of Bioscience EngineeringGhent UniversityCoupure Links 6539000Ghent Belgium center for microbial ecology and Technology-CMET Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityCoupure Links 6539000Ghent Belgium

The study of microbial hydrocarbons removal is of great importance for the development of future bioremediation *** this study,we evaluated the removal of a gaseous mixture containing toluene,m-xylene,ethylbenzene,cyclohexane,butane,pentane,hexane and heptane in aerated stirred bioreactors inoculated with Rhodococcus erythropolis and operated under non-sterile *** the real-time measurement of hydrocarbons,a novel systematic approachwas implemented using Selected-Ion Flow TubeMass Spectrometry(SIFTMS).The effect of the carbon source(~9.5 ppmv)on(i)the bioreactors’performance(BR1:dosed with only cyclohexane as a single hydrocarbon versus BR2:dosed with a mixture of the 8 hydrocarbons)and(ii)the evolution of microbial communities over time were *** results showed that cyclohexane reached a maximum removal efficiency(RE)of 53%±4%in *** BR2,almost complete removal of toluene,m-xylene and ethylbenzene,being the most water-soluble and easy-to-degrade carbon sources,was *** below 32%were obtained for the remaining *** exposing the microbial consortium to only the five most recalcitrant hydrocarbons,REs between 45%±5%and 98%±1%were *** addition,we observed that airborne microorganisms populated the bioreactors and that the type of carbon source influenced the microbial communities *** abundance of species belonging to the genus Rhodococcus was below 10%in all bioreactors at the end of the *** work provides fundamental insights to understand the complex behavior of gaseous hydrocarbon mixtures in bioreactors,along with a systematic approach for the development of SIFT-MS methods.

关键词： Hydrocarbons SIFT-MS Rhodococcus erythropolis Biodegradation Bioreactors

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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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Meta-analysis of 21^(st)century studies shows that deforestation induces profound changes in soil characteristics,particularly soil organic carbon accumulation

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Forest Ecosystems 2025年第1期12卷 46-55页

作者： Abubakari Said Mgelwa Mbezele Junior Yannick Ngaba Bin Hu Geshere Abdisa Gurmesa Agnes Godfrey Mwakaje Mateg Pascale Bernadette Nyemeck Feifei Zhu Qingyan Qiu Linlin Song Yingying Wang Yunting Fang Heinz Rennenberg CAS Key Laboratory of Forest ecology and Management Institute of Applied EcologyChinese Academy of SciencesShenyang 110016China Key Laboratory of Stable Isotope Techniques and Applications Shenyang 110016China College of Natural Resources Management&Tourism Mwalimu Julius K.Nyerere University of Agriculture&TechnologyP.O.Box 976MusomaTanzania center of Molecular Ecophysiology(CMEP) College of Resources and EnvironmentSouthwest UniversityChongqing 400715China Higher Technical Teacher’Training College of Ebolowa University of Ebolowa(HTTTC)886EbolowaCameroon Multipolar Consulting Firm 1092Elig EssonoYaoundeCameroon Qingyuan Forest CERN Chinese Academy of SciencesShenyang 110016China Forest ecology&Stable Isotope center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China University of Chinese Academy of Sciences Beijing 100049China

Deforestation is one of the most serious environmental problems facing *** continues to escalate rapidly across many regions of the world,thereby deteriorating the forest soil *** has prompted a large number of field-based studies aimed at understanding the impacts of deforestation on soil ***,the lack of comprehensive meta-analyses that utilized these studies has limited our deeper understanding of how different soil properties,including the soil organic carbon(SOC)pool,respond to *** address this critical knowledge gap,we conducted a meta-analysis of 144 studies to explore the impacts of deforestation on soil chemical,physical,and biological properties,with special emphasis on the long-term changes in SOC,such as concentrations,stocks,and *** results revealed that deforestation significantly decreased soil organic matter,electrical conductivity,and base saturation by 52%,50%,and 98%,*** deforestation increased soil total nitrogen content and decreased available phosphorus content by 51%and 99%,respectively,it resulted in slight decreases in some chemical properties,including soil pH(1%)and base cations(1%–13%).Deforestation significantly increased bulk density by 27%and soil erosion by 47%,but significantly decreased soil aggregate stability by 39%and saturated hydraulic conductivity by 63%.Soil microbial biomass C and N concentrations and enzyme activities were significantly decreased as a consequence of *** biological properties were much more affected by deforestation than soil physical and chemical *** the SOC,the land use conversion from forest to pasture significantly increased SOC concentrations,stocks,and sequestration rates(11%–13%),whereas the land use conversions from forest to both plantation and cropland significantly decreased SOC concentrations,stocks,and sequestration rates(10%–43%).This observed decline in SOC accumulations decreased with inc

关键词： Deforestation Land-use change Soil properties Soil organic carbon

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Genome-wide association analysis reveals regulatory genes for the metabolite synthesis of 2-acetyl-1-pyrroline in aromatic coconut(Cocos nucifera L.)

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Journal of Genetics and genomics 2025年第2期52卷 179-188页

作者： Hao Ding Xiang Lv Guangzhen Zhou Xiaomei Liu Xiwei Sun Jing Li Amjad Iqbal Yaodong Yang Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute Chinese Academy of Tropical Agricultural SciencesWenchangHainan 571339China Hainan Coconut International Joint Research center WenchangHainan 571339China Ministry of Education Key Laboratory for ecology of Tropical Islands Key Laboratory of Tropical Animal and Plant Ecology of Hainan ProvinceCollege of Life SciencesHainan Normal UniversityHaikouHainan 570228China Department of Food Science&Technology Abdul Wali Khan University Mardan23200Pakistan

Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma *** enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of *** this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm *** analysis then pinpoints 22 candidate genes near significant loci involved in 2AP *** encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary *** these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_*** particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype *** variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.

关键词： Aromatic coconut 2AP SNP Genome-wideassociation study(GWAS) Haplotype analysis

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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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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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“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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Nitric Oxide and Brassinosteroids Mediated Fungal Endophyte-Induced Volatile Oil Production Through Protein Phosphorylation Pathways in Atractylodes lancea Plantlets

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Journal of Integrative Plant Biology 2013年第11期55卷 1136-1146页

作者： Cheng-Gang Ren Chuan-Chao Dai Jiangsu Key Laboratory for Microbes and Functional genomics Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources College of Life Sciences in Nanjing Normal University

Fungal endophytes have been isolated from almost every plant, infecting their hosts without causing visible disease symptoms, and yet have still proved to be involved in plant secondary metabolites accumulation. To decipher the possible physiological mechanisms of the endophytic fungus-host interaction, the role of protein phosphorylation and the relationship between endophytic fungus-induced kinase activity and nitric oxide （NO） and brassinolide （BL） in endophyte-enhanced volatile oil accumulation in Atractylodes lancea plantlets were investigated using pharmacological and biochemical approaches. Inoculation with the endophytic fungus Gilmaniella sp. ALl2 enhanced the activities of total protein phosphorylation, Ca2^-dependent protein kinase, and volatile oil accumulation in A. lancea plantlets. The upregulation of protein kinase activity could be blocked by the BL inhibitor brassinazole. Furthermore, pretreatments with the NO-specific scavenger cPTIO significantly reduced the increased activities of protein kinases in A. lancea plantlets inoculated with endophytic fungus. Pretreatments with different protein kinase inhibitors also reduced fungus-induced NO production and volatile oil accumulation, but had barely no effect on the BL level. These data suggest that protein phosphorylation is required for endophyte- induced volatile oil production in A. lancea plantlets, and that crosstalk between protein phosphorylation and the NO pathway may occur and act as a downstream signaling event of the BL pathway.

关键词： Atractylodes lancea endophytic fungus protein phosphorylation signal molecule volatile oi1.

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Synthetic genomes engineered by SCRaMbLEing

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Science China(Life Sciences) 2018年第8期61卷 975-977页

作者： Feng Zhang Daniel F.Voytas Department of Plant and microbial Biology University of Minnesota center for Precision Plant genomics University of Minnesota Department of Genetics Cell Biology and Development University of Minnesota center for Genome Engineering University of Minnesota

The ability to design and synthesize the genome of a living organism marks one of the most significant achievements in synthetic biology. The first synthetic genomes were those of bacteria （Gibson et al., 2010; Hutchison et al., 2016）, but an international consortium of scientists is now undertaking the ambitious task of designing and synthesizing the entire genome of Saccharornayces cerevisiae, a eukaryotic single-celled yeast （Dymond et al., 2011; Kannan and Gibson, 2017）. One feature of the redesigned yeast genome, called Saccharomyces cerevisiae 2.0 or Sc2.0, is the ability to in-duce novel genetic variation.

关键词：合成生物学染色体设计国际协会真核细胞基因变化有机体科学家

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Managing virus diseases in citrus:Leveraging high-throughput sequencing for versatile applications

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Horticultural Plant Journal 2025年第1期11卷 57-68页

作者： Hongming Chen Zhiyou Xuan Lu Yang Song Zhang Mengji Cao Integrative Science center of Germplasm Creation in Western China(Chongqing)Science City Citrus Research InstituteSouthwest UniversityChongqing 400712China National Citrus Engineering Research center Citrus Research InstituteSouthwest UniversityChongqing 400712China

In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future *** the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 *** acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus *** has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free ***,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical *** addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications.

关键词： Deep sequencing Virus epidemics Functional genomics CRISPR/Cas Virus-host interactions

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