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Direct evidence of microbiological water quality changes on bacterial quantity and community caused by plumbing system

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Journal of Environmental Sciences 2022年第6期34卷 175-183页

作者： Jun Li Anran Ren Ed van der Mark Gang Liu Key Laboratory of Drinking Water Science and Technology Research Centre for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of Sciences Beijing 100049China Dunea Water Company Plaza of the United Nations 11-15Zoetermeer 2700 ATthe Netherlands Sanitary engineering Department of Water managementFaculty of Civil Engineering and GeosciencesDelft University of TechnologyDelft 2600 GAthe Netherlands

Drinking water quality deteriorates from treatment plant to customer taps, especially in the plumbing system. There is no direct evidence about what the differences are contributed by plumbing system. This study compared the water quality in the water main and at customer tap by preparing a sampling tap on the water main. The biomass was quantified by adenosine triphosphate(ATP) and the microbial community was profiled by 454 pyrosequencing.The results showed that in distribution pipes, biofilm contributed >94% of the total biomass,while loose deposits showed little contribution(< 2%) because of the low amount of loose deposits. The distribution of biological stable water had minor effects on the microbiocidal water quality regarding both quantity(ATP 1 ng/L vs. 1.7 ng/L) and community of the bacteria. Whereas the plumbing system has significant contribution to the increase of active biomass(1.7 ng/L vs. 2.9 ng/L) and the changes of bacterial community. The relative abundance of Sphingomonas spp. at tap(22%) was higher than that at water main(2%), while the relative abundance of Pseudomonas spp. in tap water(15%) was lower than that in the water from street water main(29%). Though only one location was prepared and studied, the present study showed that the protocol of making sampling tap on water main offered directly evidences about the impacts of plumbing system on tap water quality, which makes it possible to distinguish and study the processes in distribution system and plumbing system separately.

关键词： Drinking water distribution system Plumbing system Microbiological water quality Sampling program 454 pyrosequencing

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Comparison of the Bacterial Microbiota in a Bale of Collected Cardboard Determined by 454 pyrosequencing and Clone Library

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Advances in Microbiology 2014年第12期4卷 754-760页

作者： Valérie Lalande Simon Barnabé Jean-Charles Coté Département de Biologie Médicale Université du Québec à Trois-RivièresTrois-RivièresCanada Agriculture and Agri-Food Canada Research and Development CentreSaint-Jean-sur-RichelieuCanada Département de Chimie Biochimie et PhysiqueUniversité du Québec à Trois-RivièresTrois-RivièresCanada

Biofouling, the accumulation of microorganisms, is a major problem in paper mills processing paper and cardboard. This leads to the production of lower quality recycled products. Several studies have focused on the microbial content in the paper mill and the final products. Our aim was to determine the microbial biota in a bale of collected cardboard prior to entering the paper mill. Total genomic DNA was isolated and analyzed using two different methods for comparison purposes: 454 pyrosequencing and clone library. A total of 3268 V6-V8 454 pyrosequencing reads and 322 cloned V6-V8 16S rRNA nucleotide sequences were obtained. Both methods showed the presence of three major bacterial genera: Bacillus, Solibacillus and Paenibacillus, all members of the spore-forming phylum Firmicutes. pyrosequencing, however, revealed a richer and more diverse bacterial community than clone library. It showed the presence of additional minor Firmicute genera and of a small number of Proteobacteria. The sorting at the recycling plant, the storing, and the processing at the paper mill, the end uses, will all contribute to the bacterial microbiota present in a bale of collected cardboard as revealed here.

关键词： 454 pyrosequencing Bacterial Microbiota Cardboard Clone Library Paper Mill

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Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system

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Journal of Environmental Sciences 2017年第11期29卷 110-117页

作者： Lingwei Meng Xiangkun Li Xinran Wang Kaili Ma Gaige Liu Jie Zhang School of Municipal and Environmental Engineering State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology Harbin 150090 China

This study aimed to reveal how amoxicillin（AMX） affected the microbial community and the spread mechanism of antibiotic resistance genes（ARGs） in the AMX manufacture wastewater treatment system. For this purpose, a 1.47 L expanded granular sludge bed（EGSB） reactor was designed and run for 241 days treating artificial AMX manufacture wastewater. 454 pyrosequencing was applied to analyze functional microorganisms in the system. The antibiotic genes OXA_（-1）, OXA_（-2）, OXA_（-10）, TEM_（-1）, CTX-M_（-1）, class I integrons（intI1） and 16 SrRNA genes were also examined in sludge samples. The results showed that the genera Ignavibacterium, Phocoenobacter,Spirochaeta, Aminobacterium and Cloacibacillus contributed to the degradation of different organic compounds（such as various sugars and amines）. And the relative quantification of eachβ-lactam resistance gene in the study was changed with the increasing of AMX concentration.Furthermore the vertical gene transfer was the main driver for the spread of ARGs rather than horizontal transfer pathways in the system.

关键词： Amoxicillin（AMX） Expanded granular sludge bed（EGSB） 454 pyrosequencing Antibiotic resistance genes（ARGs）

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The Nitrogen-Cycling Network of Bacterial Symbionts in the Sponge Spheciospongia vesparium

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Journal of Ocean University of China 2021年第4期20卷 999-1012页

作者： HE Liming KARLEP Liisi LI Zhiyong Marine Biotechnology Laboratory State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Joint International Research Laboratory of Metabolic&Developmental Sciences Shanghai Jiao Tong UniversityShanghai 200240China Department of Chemistry and Biotechnology Division of Gene TechnologyTallinn University of TechnologyEstonia

The microbes associated with sponges play important roles in the nitrogen cycle of the coral reefs ecosystem,e.g.,nitrification,denitrification,and nitrogen fixation.However,the whole nitrogen-cycling network has remained incomplete in any individual sponge holobiont.In this study,454 pyrosequencing of the 16S rRNA genes revealed that the sponge Spheciospongia vesparium from the South China Sea has a unique bacterial community(including 12 bacterial phyla),dominated particularly by the genus Shewanella(order Alteromonadales).A total of 10 functional genes,nifH,amoA,narG,napA,nirK,norB,nosZ,ureC,nrfA,and gltB,were detected in the microbiome of the sponge S.vesparium by gene-targeted analysis,revealing an almost complete nitrogen-cycling network in this sponge.Particularly,bacterial urea utilization and the whole denitrification pathway were highlighted.MEGAN analysis suggests that Proteobacteria(e.g.,Shewanella)and Bacteroidetes(e.g.,Bizionia)are probably involved in the nitrogen cycle in the sponge S.vesparium.

关键词： Spheciospongia vesparium bacterial symbionts 454 pyrosequencing functional gene analysis nitrogen-cycling net-work

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Shifts in soil bacterial communities induced by the controlled-release fertilizer coatings

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Journal of Integrative Agriculture 2016年第12期15卷 2855-2864页

作者： PAN Pan JIANG Hui-min ZHANG Jian-feng YANG Jun-cheng LI Shu-shan LIU Lian ZHANG Shui-qin LEI Mei Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Institute of Agricultural Resources and Regional Planning Chinese Academy of Agricultural Sciences

Coated controlled-release fertilizers （CRFs） have been widely applied in agriculture due to their increased efficiency. However, the widespread and a lot of coated CRFs application may leave undesired coating residues in the soil due to their slow degradation. Limited information is available on the effects of substantial residual coatings on the soil bacterial community. By adding 0, 5, 10, 20, and 50 times quantities of residual coating from conventional application amount of resin and water-soluble coated CRFs, we studied the responses of soil properties and bacterial community composition to these two residual coatings in black soil. The results showed that the resin and water-soluble coatings did not essentially alter the properties of black soil or cause dramatic changes to bacterial diversity within the test concentration range. The residual resin and water-soluble coatings also did not distinctly alter the relative abundance of the top ten bacteria at phylum level. Heatmap results suggested that the treatments were basically clustered into two groups by concentration rather than types of coating material. Pearson correlation analysis showed that the Simpson＇s diversity index of the bacterial community was significantly correlated with microbial biomass carbon （MBC, r=0.394, P〈0.05）, and the richness index abundance-based coverage estimator （ACE） of the bacterial community was significantly correlated with microbial biomass nitrogen （MBN, t=0.407, P〈0.05）. Overall, results of this study suggested that substantial residual resin and water-soluble coatings with 0-50 times quantities of residual coating from conventional application amount of coated CRFs did not generate obviously negative impacts on the bacterial community in black soil.

关键词： soil bacterial community controlled-release fertilizer residual coatings 454 pyrosequencing

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A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes

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Fungal Diversity 2016年第2期77卷 317-333页

作者： Carolina Senés-Guerrero Arthur Schüßler Department of Biology GeneticsLudwig-Maximilians UniversityGrosshaderner Str.482152 PlaneggMartinsriedGermany

Plant-symbiotic arbuscular mycorrhizal fungi(AMF)are of high global ecological and economic importance,but describing environmental communities of AMF at the species level remains a challenge,despite the need to understand AMF-plant preferences and to apply AMF in sustainable agriculture.Here,the potato-associated AMF species community composition was assessed for three Andean countries along an altitudinal gradient and at different plant stages,by using 454 GS-FLX+sequencing of a 760 bp LSU rRNA gene PCR amplicon.Two methods were compared:defining OTUs based on a simple sequence similarity threshold,or affiliating reference sequences to species based on a high throughput phylogenetic annotation approach using an evolutionary placement algorithm(EPA).The EPA-based approach was not only more precise,but also fundamental to robustly unveil the AMF species community composition.The principal advantage of this approach was also demonstrated by using artificially constructed datasets based on validated public database sequences.The affiliation of sequence reads to species using phylogenetic annotation revealed a surprisingly conserved AMF core-species community structure in Andean potatoes,regardless of different plant stages and environmental factors.In total,41 species were detected and in some cases more than 25 species were found colonizing an individual root system.Acaulospora species were identified as dominant colonizers,co-occurring with Cetraspora nodosa and certain Claroideoglomus and Rhizophagus species in most potato root samples.

关键词： 454 pyrosequencing Andean ecosystems Arbuscular mycorrhizal fungi species communities DNA based species identification Evolutionary placement algorithm Solanum tuberosum(potato)

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Contrasting soil fungal communities in Mediterranean pine forests subjected to different wildfire frequencies

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Fungal Diversity 2015年第1期70卷 85-99页

作者： Erika Buscardo Susana Rodríguez-Echeverría Helena Freitas Paolo De Angelis João Santos Pereira Ludo A.H.Muller Centro de Ecologia Funcional(CEF) Departamento de Ciências da VidaUniversidade de CoimbraCalçada Martim de Freitas3000-456 CoimbraPortugal Department for Innovation in Biological Agro-Food and Forest Systems(DIBAF)University of TusciaVia S.Camillo de Lellis snc01100 ViterboItaly Escritório Central do LBA Instituto Nacional de Pesquisa da Amazônia(INPA)Av.AndréAraújo2936Campus IIAleixo69060-001 ManausAmazonasBrazil Departamento de Engenharia Florestal Instituto Superior de AgronomiaUniversidade Técnica de LisboaTapada da Ajuda1349-018 LisbonPortugal Institut für Biologie—Botanik Freie Universität BerlinAltensteinstrasse 614195 BerlinGermany

Mediterranean forest ecosystems are characterized by various vascular plant groups with their associated mycor-rhizae and free living soil fungi with various ecological functions.Fire plays a major role in Mediterranean ecosystem dynamics and impacts both above-and below-ground community structure and functioning.However,studies on the effects induced by altered disturbance regimes(associated with recent land use and climate extremes)on fire ecology and especially on its below-ground impacts are few.The objectives of this study were to evaluate the effects of different wildfire regimes on soil fungal community structure using two different molecular methods.We investigated the long-term effects of wildfire on soil fungal communities associated with Pinus pinaster forests in central Portugal,by comparing the results of denaturing gradient gel electrophoresis(DGGE)-based profiling with those obtained with 454 pyrosequencing.Four forest stands with differing fire history and fire return interval,and vegetation cover(mature forest,early successional stage of pine regeneration,and forest converted to scrubland)were sampled 6 years after the last fire event.The pyrosequencing-based approach indicated ca.eight-fold higher numbers of taxa than DGGE.However,fungal community fingerprinting data obtained for the different study stands with DGGE were congruent with those obtained with pyrosequencing.Both short(7.6 years)and long(24 years)fire return intervals(indicated by the presence of ericaceous shrubs in the understorey)induced a decrease in the abun-dance ratio between basidiomycetes and ascomycetes and appeared to reduce the frequency of ectomycorrhizal fungal species and saprophytes.Wildfire significantly reduced the frequency of late stage successional taxa(e.g.Atheliaceae and Cantharellales)and known or putative saprophytes belonging to the Clavulinaceae and the Archaeorhizomycetaceae.Conversely,early successional fungal species belonging to the Thelephoraceae were favoured by both fire return inter-vals,while the a

关键词： 454 pyrosequencing DGGE Wildfire frequency Soil fungal community Maritime pine

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Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession

Community assembly of ectomycorrhizal fungi along a subtropi...

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中国菌物学会2015年学术年会

作者： Gao Cheng Zhang Yu Shi Nan-Nan Zheng Yong Chen Liang Wubet Tesfaye Bruelheide Helge Both Sabine Buscot Francois Ding Qiong Erfmeier Alexander Kuhn Peter Nadrowski Karin Scholten Thomas Guo Liang-Dong State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences College of Life Science and Engineering Qiqihar University University of Chinese Academy of Sciences Department of Soil Ecology UFZ-Helmholtz Centre for Environmental Research Institute of Biology Martin Luther University Institute of Biology Leipzig University Department of Geoscieneces Research Area GeographyUniversity of Tubingen

Environmental selection and dispersal limitation are two of the primary processes structuring biotic communities in ecosystems, but little is known about these processes in shaping soil microbial communities during secondary forest succession. We examined the communities of ectomycorrhizal（EM） fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing. The EM fungal community consisted of 393 operational taxonomic units（OTUs）, belonging to 21 EM fungal lineages, in which three EM fungal lineages and 11 EM fungal OTUs showed significantly biased occurrence among the young, intermediate and old forests. The EM fungal community was structured by environmental selection and dispersal limitation in old forest, but only by environmental selection in young, intermediate, and whole forests. Furthermore, the EM fungal community was affected by different factors in the different forest successional stages, and the importance of these factors in structuring EM fungal community dramatically decreased along the secondary forest succession series. This study suggests that different assembly mechanisms operate on the EM fungal community at different stages in secondary subtropical forest succession.

关键词： 454 pyrosequencing dispersal limitation ectomycorrhizal（EM） fungal community ITS2 plant community subtropical secondary forest succession

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Characterization and experimental analysis of microsatellites in the genome of crape myrtle

Characterization and experimental analysis of microsatellite...

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江苏省遗传学会2014年学术研讨会

作者： Jing Wang Xiaogang Dai Yingnan Chen Yanling Yang Xinye Zhang Shuxian Li Tongming Yin The Southern Modern Forestry Collaborative Innovation Centre Nanjing Forestry University

Crape myrtle is an important ornamental plant because of its long florescence.In contrast to their highly ornamental value,there are only limited genetic and genomic resources available for this species.In this study,we characterized the microsatellites in crape myrtle by using 454 pyrosequencing.Totally,over 1.2 million high quality reads in a total length of 837.4 Mb were generated,with an average read length of 679 bp.Of which,779,744（63.2%） were assembled into 65,129 contigs covering a physical length of 93.6 Mb,with N50 contig size of 1,648 bp.The assembled contigs were used to recover microsatellite repeats by tapping with repeat motif in lengths of 1 to 6 bp.A total of 33,026 microsatellites were detected from the assembled genomic sequences.Subsequently,a SSR primer database was established referring to the flanking sequences of the detected microsatellites.Tested with 48 randomly selected SSR primer pairs,experimental analysis revealed that 89.5% of them succeeded in PCR amplification,and 66.7% of them amplified polymorphic loci.For the polymorphic SSRs,their polymorphic information contents ranged from 0.08 to 0.79,with an average value of 0.44.Further examination revealed that around 78% of the developed primer pairs were moderately to highly informative.This study provided valuable marker resources for different aspects of genetic study on this important ornamental plant.

关键词： Crape myrtle genome 454 pyrosequencing microsatellite

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Responses of AM fungal community to fertilization and plant identity in an alpine meadow on the Qinghai–Tibet Plateau

Responses of AM fungal community to fertilization and plant ...

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中国菌物学会2016年学术年会

作者： Yong Zheng Liang Chen Cheng Gao Liang-Dong Guo State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences

Arbuscular mycorrhizal（AM） fungi form symbiotic associations with the majority of land plants and play crucial roles in ecosystems.Understanding the responses of belowground AM fungi in alpine meadow ecosystem facing environmental variation and anthropogenic manipulation may aid sustainable grassland management.Here we studied AM fungal responses to fertilization and plant identity in a natural alpine meadow and a sown pasture on the Qinghai–Tibet Plateau.AM fungal extraradical hyphal（ERH） density was significantly decreased by ammonium nitrogen（NH4+-N） only in May,but was significantly increased by urea and manure under Avena sativa and by manure only under Elymus nutans plantation.AM fungal spore density was not significantly affected by plant identity or fertilizer form,whereas was potentially decreased by higher rate（7.5 g N m-2 yr-1） compared with lower rate（1.5 g N m-2 yr-1） of N addition.Using high-throughput（454） sequencing of 18 S r RNA gene,we observed that AM fungal diversity was significantly higher under E.nutans than Vicia sativa cultivation condition,but AM fungal diversity was not significantly affected by fertilizer urea or sheep manure regardless of plant species.Structural equation model results showed that AM fungal community composition was significantly structured directly by plant identity rather than fertilization,but N rate could strongly affect soil characteristics which subsequently directly influenced community compositions of plants and AM fungi.Taken together,our findings highlight that AM fungal community was influenced by NH4+-N and/or nitrate N（NO3--N） fertilization via mainly altered soil characteristics in the natural alpine meadow,and that plant identity exerts stronger effect than fertilization on soil-dwelling AM fungi in the converted pastureland from the similar alpine meadow.

关键词： 454 pyrosequencing AM fungi community composition fertilization manure nitrogen plant identity sown pasture

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