Fermentation-based antibiotic production results in abundant nutrient-rich fermentation residue with high potential for recycling,but the high antibiotic residual concentration restricts its usefulness(e.g.,in land ap...Fermentation-based antibiotic production results in abundant nutrient-rich fermentation residue with high potential for recycling,but the high antibiotic residual concentration restricts its usefulness(e.g.,in land application as organic fertilizer).In this study,an industrial-scale hydrothermal facility for the treatment of erythromycin fermentation residue(EFR)was investigated,and the potential risk of the long-term soil application of treated EFR promoting environmental antibiotic resistance development was evaluated.The treatment effectively removed bacteria and their DNA,and an erythromycin removal ratio of up to approximately 98%was achieved.The treated EFR was utilized as organic fertilizer for consecutive field applications from 2018 to 2020,with dosages ranging from 3750 to 15000 kg·hm^(-2),resulting in subinhibitory levels of erythromycin(ranging from 0.83-76.00μg·kg^(-1))in soils.Metagenomic shotgun sequencing was then used to characterize the antibiotic resistance genes(ARGs),mobile genetic elements(MGEs),and bacterial community composition of the soils.The soil ARG abundance and diversity did not respond to the treated EFR application in the first year,but gradually changed in the second and third year of application.The highest fold change in relative abundance of macrolide-lincosamide-streptogramin(MLS)and total ARGs were 12.59 and 2.75 times,compared with the control(CK;without application),respectively.The soil MGEs and taxonomic composition showed similar temporal trends to those of the ARGs,and appeared to assist in driving increasing ARG proliferation,as revealed by correlation analysis and structural equation models(SEMs).The relative abundance of particular erm resistance genes(RNA methyltransferase genes)increased significantly in the third year of treated EFR application.The close association of erm with MGEs suggested that horizontal gene transfer played a critical role in the observed erm gene enrichment.Metagenomic binning results demonstrated that the proliferation of mac genecarrying hosts was responsible for the increased abundance of mac genes(efflux pump genes).This study shows that sub-inhibitory levels of erythromycin in soils had a cumulative effect on soil ARGs over time and emphasizes the importance of long-term monitoring for assessing the risk of soil amendment with treated industrial waste.展开更多
A great deal of oil contaminated the shoreline by the Qingdao oil pipeline explosion in 2013. The four oildegrading consortia were enriched from sediment samples with crude oil as sole carbon and energy sources. The b...A great deal of oil contaminated the shoreline by the Qingdao oil pipeline explosion in 2013. The four oildegrading consortia were enriched from sediment samples with crude oil as sole carbon and energy sources. The biodiversity and community analysis showed that the Luteibacter, Parvibaculum and a genus belonging to Alcanivoracaceae were found predominant bacteria in the four consortia, which belonged to Proteobacteria. Nine strains exhibiting distinct 16S rRNA gene sequences were isolated from the consortia. These strains were identified to eight genera based on 16S rRNA gene sequences. Five of the nine strains degraded more than 30% of the crude oil in two weeks by gravimetric method. From the analysis of GC-MS, most of the isolated strains tended to degrade n-alkanes rather than PAHs. Five strains showed high degrading ability of the total n-alkanes. Only Strain D2 showed great PAHs degrading ability and the degrading rates ranged from 34.9% to 77.5%. The sequencing analysis of the oil-degrading consortia confirmed that the genus of Alcanivorax was one of the dominant bacteria in Consortia A and E and Strain E4 might be one of the dominant bacteria. The strains obtained in this study demonstrated the potential for oil bioremediation in oil-contaminated beach ecosystems.展开更多
Although the microbial diversity of the Indian Ocean has been extensively investigated,little is known about the community composition of microbes in the Southern Indian Ocean.In the present study,we divided 60 water ...Although the microbial diversity of the Indian Ocean has been extensively investigated,little is known about the community composition of microbes in the Southern Indian Ocean.In the present study,we divided 60 water column samples on the Ninety-East Ridge(NER)into fi ve water masses according to the temperature-salinity curves.We presented,for the fi rst time,a full description of the microbial biodiversity on NER through high-throughput amplicon sequencing approach,including bacteria,archaea,and fungi.We found that bacteria exhibited higher richness and diversity than archaea and fungi across the water masses on NER.More importantly,each water mass on NER featured distinct prokaryotic microbial communities,as indicated by the results of non-metric multidimensional scaling.In contrast,fungi were eurybathic across the water masses.Redundancy analysis results demonstrated that environmental factors might play a pivotal role in the formation and stability of prokaryotic communities in each water mass,especially that of archaea.In addition,indicator species might be used as fi ngerprints to identify corresponding water masses on NER.These results provide new insights into the vertical distribution,structure,and diversity of microorganisms on NER from the perspective of water mass.展开更多
Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils.However,little is known about the effects of plant-derived fertilizer on soil antibiotic resistome.Herein,metagenomic sequen...Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils.However,little is known about the effects of plant-derived fertilizer on soil antibiotic resistome.Herein,metagenomic sequencing was used to investigate the effects of a plantderived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes(ARGs)in a soybean field along crop growth stages.ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure.The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly(P<0.05)elevated at the sprout stage,to a level comparable to that in the manured soils.Whereas,unlike chicken manure mainly introducing manure-borne ARGs to soil,the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria.ARGs with abundances in amended soils significantly(P<0.05)higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs.Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest.Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer,while in manured soils were Firmicutes and Actinobacteria.As revealed by multivariate statistical analyses,variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients,which was different from the failed establishment of manure-borne bacteria in the manured soils.Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome,and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.展开更多
Antibiotic fermentation residue(AFR)is nutrient-rich solid waste generated from fermentative antibiotic production process.It is demonstrated that AFR contains high-concentration of remaining antibiotics,and thus may ...Antibiotic fermentation residue(AFR)is nutrient-rich solid waste generated from fermentative antibiotic production process.It is demonstrated that AFR contains high-concentration of remaining antibiotics,and thus may promote antibiotic resistance development in receiving environment or feeding farmed animals.However,the dominate microorganisms and antibiotic resistance genes(ARGs)in AFRs have not been adequately explored,hampering understanding on the potential antibiotic resistance risk development caused by AFRs.Herein,seven kinds of representative AFRs along their production,storage,and treatment processes were collected,and multiple methods including amplicon sequencing,metagenomic sequencing,and bioinformatic approaches were adopted to explore the biological characteristics of AFRs.As expected,antibiotic fermentation producer was found as the predominant species in raw AFRs,which were collected at the outlet of fermentation tanks.However,except for producer species,more environment-derived species persisted in stored AFRs,which were temporarily stored at a semi-open space.Lactobacillus genus,classified as Firmicutes phylum and Bacilli class,became predominant bacterial taxa in stored AFRs,which might attribute to its tolerance to high concentration of antibiotics.Results from metagenomic sequencing together with assembly and binning approaches showed that these newly-colonizing species(e.g.,Lactobacillus genus)tended to carry ARGs conferring resistance to the remaining antibiotic.However,after thermal treatment,remaining antibiotic could be efficiently removed from AFRs,and microorganisms together with DNA could be strongly destroyed.In sum,the main risk from the AFRs was the remaining antibiotic,while environment-derived bacteria which tolerate extreme environment,survived in ARFs with high content antibiotics,and may carry ARGs.Thus,hydrothermal or other harmless treatment technologies are recommended to remove antibiotic content and inactivate bacteria before recycling of AFRs in pharmaceutical industry.展开更多
基金obtained from National Natural Science Foundation of China(32141002 and 22076203)。
文摘Fermentation-based antibiotic production results in abundant nutrient-rich fermentation residue with high potential for recycling,but the high antibiotic residual concentration restricts its usefulness(e.g.,in land application as organic fertilizer).In this study,an industrial-scale hydrothermal facility for the treatment of erythromycin fermentation residue(EFR)was investigated,and the potential risk of the long-term soil application of treated EFR promoting environmental antibiotic resistance development was evaluated.The treatment effectively removed bacteria and their DNA,and an erythromycin removal ratio of up to approximately 98%was achieved.The treated EFR was utilized as organic fertilizer for consecutive field applications from 2018 to 2020,with dosages ranging from 3750 to 15000 kg·hm^(-2),resulting in subinhibitory levels of erythromycin(ranging from 0.83-76.00μg·kg^(-1))in soils.Metagenomic shotgun sequencing was then used to characterize the antibiotic resistance genes(ARGs),mobile genetic elements(MGEs),and bacterial community composition of the soils.The soil ARG abundance and diversity did not respond to the treated EFR application in the first year,but gradually changed in the second and third year of application.The highest fold change in relative abundance of macrolide-lincosamide-streptogramin(MLS)and total ARGs were 12.59 and 2.75 times,compared with the control(CK;without application),respectively.The soil MGEs and taxonomic composition showed similar temporal trends to those of the ARGs,and appeared to assist in driving increasing ARG proliferation,as revealed by correlation analysis and structural equation models(SEMs).The relative abundance of particular erm resistance genes(RNA methyltransferase genes)increased significantly in the third year of treated EFR application.The close association of erm with MGEs suggested that horizontal gene transfer played a critical role in the observed erm gene enrichment.Metagenomic binning results demonstrated that the proliferation of mac genecarrying hosts was responsible for the increased abundance of mac genes(efflux pump genes).This study shows that sub-inhibitory levels of erythromycin in soils had a cumulative effect on soil ARGs over time and emphasizes the importance of long-term monitoring for assessing the risk of soil amendment with treated industrial waste.
基金The National Natural Science Foundation of China under contract Nos 41406127 and 41476103the Basic Scientific Fund for National Public Research Institutes of China under contract No.2015T05+2 种基金the National Natural Science Foundation of ChinaShandong Joint Funded Project under contract No.U1406403the Marine Science and Technology Project of Huangdao District under contract No.2014-4-20the 2012 Taishan Scholar Award and China-ASEAN Maritime Cooperation Fund East Asia Marine Cooperation Platform
文摘A great deal of oil contaminated the shoreline by the Qingdao oil pipeline explosion in 2013. The four oildegrading consortia were enriched from sediment samples with crude oil as sole carbon and energy sources. The biodiversity and community analysis showed that the Luteibacter, Parvibaculum and a genus belonging to Alcanivoracaceae were found predominant bacteria in the four consortia, which belonged to Proteobacteria. Nine strains exhibiting distinct 16S rRNA gene sequences were isolated from the consortia. These strains were identified to eight genera based on 16S rRNA gene sequences. Five of the nine strains degraded more than 30% of the crude oil in two weeks by gravimetric method. From the analysis of GC-MS, most of the isolated strains tended to degrade n-alkanes rather than PAHs. Five strains showed high degrading ability of the total n-alkanes. Only Strain D2 showed great PAHs degrading ability and the degrading rates ranged from 34.9% to 77.5%. The sequencing analysis of the oil-degrading consortia confirmed that the genus of Alcanivorax was one of the dominant bacteria in Consortia A and E and Strain E4 might be one of the dominant bacteria. The strains obtained in this study demonstrated the potential for oil bioremediation in oil-contaminated beach ecosystems.
基金Supported by the China Ocean Mineral Resources R&D Association(Nos.DY135-B2-11,DY135-E2-4)the National Natural Science Foundation of China(No.42076165)+2 种基金the Natural Science Foundation of Shandong Province(No.ZR2018MD017)the National Key Research and Development Program(No.2016YFC1402301)the Fundamental Research Funds for the Central Universities(No.201822009)。
文摘Although the microbial diversity of the Indian Ocean has been extensively investigated,little is known about the community composition of microbes in the Southern Indian Ocean.In the present study,we divided 60 water column samples on the Ninety-East Ridge(NER)into fi ve water masses according to the temperature-salinity curves.We presented,for the fi rst time,a full description of the microbial biodiversity on NER through high-throughput amplicon sequencing approach,including bacteria,archaea,and fungi.We found that bacteria exhibited higher richness and diversity than archaea and fungi across the water masses on NER.More importantly,each water mass on NER featured distinct prokaryotic microbial communities,as indicated by the results of non-metric multidimensional scaling.In contrast,fungi were eurybathic across the water masses.Redundancy analysis results demonstrated that environmental factors might play a pivotal role in the formation and stability of prokaryotic communities in each water mass,especially that of archaea.In addition,indicator species might be used as fi ngerprints to identify corresponding water masses on NER.These results provide new insights into the vertical distribution,structure,and diversity of microorganisms on NER from the perspective of water mass.
基金supported by the National Natural Science Foundation of China (Nos.32141002 and 22076203)。
文摘Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils.However,little is known about the effects of plant-derived fertilizer on soil antibiotic resistome.Herein,metagenomic sequencing was used to investigate the effects of a plantderived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes(ARGs)in a soybean field along crop growth stages.ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure.The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly(P<0.05)elevated at the sprout stage,to a level comparable to that in the manured soils.Whereas,unlike chicken manure mainly introducing manure-borne ARGs to soil,the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria.ARGs with abundances in amended soils significantly(P<0.05)higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs.Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest.Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer,while in manured soils were Firmicutes and Actinobacteria.As revealed by multivariate statistical analyses,variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients,which was different from the failed establishment of manure-borne bacteria in the manured soils.Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome,and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.
基金supported by the National Natural Science Foundation of China (No.32141002)。
文摘Antibiotic fermentation residue(AFR)is nutrient-rich solid waste generated from fermentative antibiotic production process.It is demonstrated that AFR contains high-concentration of remaining antibiotics,and thus may promote antibiotic resistance development in receiving environment or feeding farmed animals.However,the dominate microorganisms and antibiotic resistance genes(ARGs)in AFRs have not been adequately explored,hampering understanding on the potential antibiotic resistance risk development caused by AFRs.Herein,seven kinds of representative AFRs along their production,storage,and treatment processes were collected,and multiple methods including amplicon sequencing,metagenomic sequencing,and bioinformatic approaches were adopted to explore the biological characteristics of AFRs.As expected,antibiotic fermentation producer was found as the predominant species in raw AFRs,which were collected at the outlet of fermentation tanks.However,except for producer species,more environment-derived species persisted in stored AFRs,which were temporarily stored at a semi-open space.Lactobacillus genus,classified as Firmicutes phylum and Bacilli class,became predominant bacterial taxa in stored AFRs,which might attribute to its tolerance to high concentration of antibiotics.Results from metagenomic sequencing together with assembly and binning approaches showed that these newly-colonizing species(e.g.,Lactobacillus genus)tended to carry ARGs conferring resistance to the remaining antibiotic.However,after thermal treatment,remaining antibiotic could be efficiently removed from AFRs,and microorganisms together with DNA could be strongly destroyed.In sum,the main risk from the AFRs was the remaining antibiotic,while environment-derived bacteria which tolerate extreme environment,survived in ARFs with high content antibiotics,and may carry ARGs.Thus,hydrothermal or other harmless treatment technologies are recommended to remove antibiotic content and inactivate bacteria before recycling of AFRs in pharmaceutical industry.
