Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake
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摘要
Agricultural activities, including stock-farming, planting industry, and fish aquaculture,can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear.Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO_3~--N, and NO_2~--N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.
Agricultural activities, including stock-farming, planting industry, and fish aquaculture,can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear.Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO_3~--N, and NO_2~--N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.
Agricultural activities, including stock-farming, planting industry, and fish aquaculture,can affect the physicochemical and biological characters of freshwater lakes. However, the effects of pollution producing by agricultural activities on microbial ecosystem of lakes remain unclear.Hence, in this work, we selected Honghu Lake as a typical lake that is influenced by agriculture activities. We collected water and sediment samples from 18 sites, which span a wide range of areas from impacted and less-impacted areas. We performed a geospatial analysis on the composition of microbial communities associated with physicochemical properties and antibiotic pollution of samples. The co-occurrence networks of water and sediment were also built and analyzed. Our results showed that the microbial communities of impacted and less-impacted samples of water were largely driven by the concentrations of TN, TP, NO_3~--N, and NO_2~--N, while those of sediment were affected by the concentrations of Sed-OM and Sed-TN. Antibiotics have also played important roles in shaping these microbial communities: the concentrations of oxytetracycline and tetracycline clearly reflected the variance in taxonomic diversity and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Furthermore, for samples from both water and sediment, large differences of network topology structures between impacted and less-impacted were also observed. Our results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu Lake.
引文
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[6]Baquero F,Mart?′nez JL,Canto′n R.Antibiotics and antibiotic resistance in water environments.Curr Opin Biotechnol2008;19:260-5.
[7]Bowles TM,Acosta Martinez V,Calderon F,Jackson LE.Soil enzyme activities,microbial communities,and carbon and nitrogen availability in organic agroecosystems across an intensivelymanaged agricultural landscape.Soil Biol Biochem2014;68:252-62.
[8]Xu H,Paerl HW,Qin B,Zhu G,Gao G.Nitrogen and phosphorus inputs control phytoplankton growth in eutrophic Lake Taihu,China.Limnol Oceanogr 2010;55:420.
[9]Lindstro¨m ES.Kamst Van Agterveld MP,Zwart G.Distribution of typical freshwater bacterial groups is associated with pH,temperature,and lake water retention time.Appl Environ Microbiol 2005;71:8201-6.
[10]Lee LS,Carmosini N,Sassman SA,Dion HM,Sepulveda MS.Agricultural contributions of antimicrobials and hormones on soil and water quality.Adv Agron 2007;93:1-68.
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[13]Wang H,Sangwan N,Li HY,Su JQ,Oyang WY,Zhang ZJ,et al.The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome.ISME J 2017;11:100-11.
[14]Pei R,Kim SC,Carlson KH,Pruden A.Effect of river landscape on the sediment concentrations of antibiotics and corresponding antibiotic resistance genes(ARG).Water Res 2006;40:2427-35.
[15]Zhang X.On the estimation of biomass of submerged vegetation using Landsat thematic mapper(TM)imagery:a case study of the Honghu Lake,PR China.Int J Remote Sens 1998;19:11-20.
[16]Ban X,Wu Q,Pan B,Du Y,Feng Q.Application of Composite Water Quality Identification Index on the water quality evaluation in spatial and temporal variations:a case study in Honghu Lake.China.Environ Monit Assess 2014;186:4237-47.
[17]Zhang T,Ban X,Wang X,Cai X,Li E,Wang Z,et al.Analysis of nutrient transport and ecological response in Honghu Lake,China by using a mathematical model.Sci Total Environ2017;575:418-28.
[18]Beck DA,Kalyuzhnaya MG,Malfatti S,Tringe SG,del Rio TG,Ivanova N,et al.A metagenomic insight into freshwater methaneutilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae.PeerJ 2013;1:e23.
[19]Cha′vez Romero Y,Navarro Noya YE,Reynoso Mart?′nez SC,Sarria Guzma′n Y,Govaerts B,Verhulst N,et al.16S metagenomics reveals changes in the soil bacterial community driven by soil organic C,N-fertilizer and tillage-crop residue management.Soil Tillage Res 2016;159:1-8.
[20]Chen M,Chen J,Sun F.Agricultural phosphorus flow and its environmental impacts in China.Sci Total Environ2008;405:140-52.
[21]Sand jensen K..Influence of submerged macrophytes on sediment composition and near-bed flow in lowland streams.Freshw Biol1998;39:663-79.
[22]Horppila J,Nurminen L.Effects of submerged macrophytes on sediment resuspension and internal phosphorus loading in Lake Hiidenvesi(southern Finland).Water Res 2003;37:4468-74.
[23]Takamura N,Kadono Y,Fukushima M,Nakagawa M,Kim BH.Effects of aquatic macrophytes on water quality and phytoplankton communities in shallow lakes.Ecol Res 2003;18:381-95.
[24]Han M,Gong Y,Zhou C,Zhang J,Wang Z,Ning K.Comparison and interpretation of taxonomical structure of bacterial communities in two types of lakes on Yun-Gui plateau of China.Sci Rep 2016;6:30616.
[25]Guo D,Guan L,Zhang C,Wang X,Shan L.UV mutagenesis breeding of bacillus flexus highly degrading organic nitrogen.Guizhou Agric Sci 2013;41:106-8.
[26]Divyashree MS,Rastogi NK,Shamala TR.A simple kinetic model for growth and biosynthesis of polyhydroxyalkanoate in Bacillus flexus.Nat Biotechnol 2009;26:92-8.
[27]Wang X,Zhao H.Isolation and characterization of a Bacillus flexus strain used in alkaline wastewater treatment.Adv Mat Res2013;750:1381-4.
[28]Gechemba OR,Budambula N,Makonde HM,Julius M,Matiru VN.Potentially beneficial rhizobacteria associated with banana plants in Juja,Kenya.J Biodivers Environ Sci 2015;7:181-8.
[29]Sundaramanickam A,Kumar PS,Kumaresan S,Balasubramanian T.Isolation and molecular characterization of multidrugresistant halophilic bacteria from shrimp farm effluents of Parangipettai coastal waters.Environ Sci Pollut Res Int2015;22:11700-7.
[30]Babujia LC,Silva AP,Nakatani AS,Canta?o ME,Vasconcelos ATR,Visentainer JV,et al.Impact of long-term cropping of glyphosate-resistant transgenic soybean[Glycine max(L.)Merr.]on soil microbiome.Transgenic Res 2016;25:425-40.
[31]Pesaro M,Widmer F.Identification and specific detection of a novel Pseudomonadaceae cluster associated with soils from winter wheat plots of a long-term agricultural field experiment.Appl Environ Microbiol 2006;72:37-43.
[32]Nielsen PH,Kragelund C,Seviour RJ,Nielsen JL.Identity and ecophysiology of filamentous bacteria in activated sludge.FEMSMicrobiol Rev 2009;33:969-98.
[33]Shao K,Gao G,Wang Y,Tang X,Qin B.Vertical diversity of sediment bacterial communities in two different trophic states of the eutrophic Lake Taihu,China.J Environ Sci(China)2013;25:1186-94.
[34]Ye W,Liu X,Lin S,Tan J,Pan J,Li D,et al.The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu.FEMS Microbiol Ecol2009;70:263-76.
[35]O’neil J,Davis TW,Burford MA,Gobler C.The rise of harmful cyanobacteria blooms:the potential roles of eutrophication and climate change.Harmful Algae 2012;14:313-34.
[36]Wood SA,Maier MY,Puddick J,Pochon X,Zaiko A,Dietrich DR,et al.Trophic state and geographic gradients influence planktonic cyanobacterial diversity and distribution in New Zealand lakes.FEMS Microbiol Ecol 2017;93:fiw234.
[37]Dennis PG,Seymour J,Kumbun K,Tyson GW.Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients.ISME J 2013;7:1661-4.
[38]Wang Z,Du Y,Yang C,Liu X,Zhang J,Li E,et al.Occurrence and ecological hazard assessment of selected antibiotics in the surface waters in and around Lake Honghu,China.Sci Total Environ 2017;609:1423-32.
[39]Federation WE,Association APH.Standard methods for the examination of water and wastewater.Washington,DC,USA:American Public Health Association(APHA);2005.
[40]Bao S.Agricultural and chemistry analysis of soil.Beijing,China:Agric.Press;2005.
[41]Yang Y,Cao X,Lin H,Wang J.Antibiotics and antibiotic resistance genes in sediment of Honghu Lake and East Dongting Lake.China.Microb Ecol 2016;72:791-801.
[42]Cheng X,Chen X,Su X,Zhao H,Han M,Bo C,et al.DNAextraction protocol for biological ingredient analysis of LiuWei DiHuang Wan.Genomics Proteomics Bioinformatics2014;12:137-43.
[43]Cheng X,Su X,Chen X,Zhao H,Bo C,Xu J,et al.Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing:the story for Liuwei Dihuang Wan.Sci Rep 2014;4:5147.
[44]Porebski S,Bailey LG,Baum BR.Modification of a CTAB DNAextraction protocol for plants containing high polysaccharide and polyphenol components.Plant Mol Biol Report 1997;15:8-15.
[45]Schloss PD,Westcott SL,Ryabin T,Hall JR,Hartmann M,Hollister EB,et al.Introducing mothur:open-source,platformindependent,community-supported software for describing and comparing microbial communities.Appl Environ Microbiol2009;75:7537-41.
[46]Quast C,Pruesse E,Yilmaz P,Gerken J,Schweer T,Yarza P,et al.The SILVA ribosomal RNA gene database project:improved data processing and web-based tools.Nucleic Acids Res 2013;41:D590-6.
[47]Caporaso JG,Bittinger K,Bushman FD,DeSantis TZ,Andersen GL,Knight R.PyNAST:a flexible tool for aligning sequences to a template alignment.Bioinformatics 2010;26:266-7.
[48]Caporaso JG,Kuczynski J,Stombaugh J,Bittinger K,Bushman FD,Costello EK,et al.QIIME allows analysis of high-throughput community sequencing data.Nat Methods 2010;7:335-6.
[49]DeSantis TZ,Hugenholtz P,Larsen N,Rojas M,Brodie EL,Keller K,et al.Greengenes,a chimera-checked 16S rRNA gene database and workbench compatible with ARB.Appl Environ Microbiol 2006;72:5069-72.
[50]Li J,Zhang J,Liu L,Fan Y,Li L,Yang Y,et al.Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu.Sci Rep 2015;5:15488.
[51]He Y,Zhou BJ,Deng GH,Jiang XT,Zhang H,Zhou HW.Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons.BMC Microbiol 2013;13:208.
[52]Lozupone C,Knight R.UniFrac:a new phylogenetic method for comparing microbial communities.Appl Environ Microbiol2005;71:8228-35.
[53]Va′zquez Baeza Y,Pirrung M,Gonzalez A,Knight R.EMPeror:a tool for visualizing high-throughput microbial community data.GigaScience 2013;2:1.
[54]Anderson MJ.A new method for non-parametric multivariate analysis of variance.Austral Ecol 2001;26:32-46.
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