三江平原沼泽湿地垦殖及自然恢复对土壤细菌群落多样性的影响
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摘要
为量化垦殖对我国东北沼泽湿地的影响程度,于2015年6月基于Illumina Miseq PE300第二代高通量测序平台,对黑龙江省洪河国家级自然保护区的原始沼泽、耕地、退耕湿地的土壤细菌16S r RNA基因高变区域进行测序,并分析沼泽湿地土壤细菌群落多样性和结构组成与垦殖的关系。结果表明:共获得358737条修剪序列且被划分为36个已知的菌门,在11个主要的土壤细菌门类中(相对丰度>1%),芽单胞菌门(P<0.01)、拟杆菌门(P<0.01)、厚壁菌门(P<0.01)和绿菌门(P<0.01)在不同生境类型样地差异显著,土壤细菌群落alpha多样性由高到低排序依次是:耕地、退耕湿地、原始沼泽。结合相关性分析和冗余分析可以证明,长期的耕作,特别是旱田耕作对沼泽湿地土壤细菌群落组成产生显著的影响,土壤p H、含水量、全碳、有机碳、可溶有机碳、碱解氮、微生物量碳、微生物量氮对土壤细菌的多样性和群落组成产生影响。总之,研究结果发现自然恢复可以显著促进土壤细菌群落多样性的恢复,但是沼泽湿地土壤细菌群落结构一旦被垦殖干扰改变将很难恢复到原始状态,强调了有效地利用土壤细菌群落对维护土壤生态系统平衡具有重要的意义。
Different perturbation regimes,including disturbance caused by cultivation or the process of natural restoration,can have significant effects on the soil bacterial community in marshland. In this study,we investigated the relationship between soil bacterial community composition and perturbation in marshland to quantify the extent of such disturbancerelated changes in northeast China. We assessed the diversity of bacterial communities in twelve samples of marsh soil collected from pristine marsh,neighboring cropland,and a wetland restoration area. High-throughput sequencing of a bacteria-specific genomic sequence,the internal transcribed spacer( 16 S r RNA) region,was used to identify bacterial taxa. We obtained 358,737 sequences that represented 2263 bacterial OTUs across the three types of sampling sites. Of these,1411 OTUs occurred at all three site types,99 were shared between cultivated land and pristine marshland,322were shared between cultivated land and wetland converted from cropland,and 126 were shared between pristine marshland and wetland converted from cropland. All sites also hosted unique fungal OTUs,with 218 OTUs exclusive to cultivated land,52 exclusive to pristine marshland,and 35 exclusive to wetland converted from cropland. Sequences were affiliated to36 different phyla throughout the dataset. Sequence abundance showed that members of the Proteobacteria were more frequently identified in all soil samples than Acidobacteria, and included members of Chloroflexi, Actinobacteria,Bacteroidetes,Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Saccharibacteria, and Chlorobi, which represented an overwhelming proportion of the soil bacterial communities with an average relative abundance of > 1%,and another 25 phyla with an average relative abundance were < 1%. The dominant phyla that showed the greatest variation among habitat types( > 1% of the average relative abundance) were Gemmatimonadetes( P < 0. 01),Bacteroidetes( P <0. 01),Firmicutes( P < 0. 01),and Chlorobi( P < 0. 01). The soil bacterial community diversity decreased from a maximum in cultivated land,through the wetland restoration area,to a minimum in pristine marshland. Redundancy and correlation analyses demonstrated that chronic disturbance through cultivation,especially dry cultivation,significantly altered the bacterial community composition of marsh soil. The α-diversity of the soil bacterial community was most affected by soil moisture,soil p H,total carbon,soil organic carbon,soil dissolved organic carbon,available nitrogen,microbial biomass of carbon, and microbial biomass of nitrogen. Meanwhile, the soil bacterial community composition was significantly affected by soil moisture,soil p H,total carbon,soil organic carbon,and soil dissolved organic carbon.Overall,the results from our study showed that the state of soil carbon and nitrogen is affected by the disturbance by agricultural cultivation,causing long-term accumulated soil nutrients to become available as an energy source that can be rapidly mineralized by soil bacteria. In addition,our results also indicate that cultivation and natural restoration influenced the bacterial community structure and diversity. Natural restoration can significantly enhance the recovery of bacterial diversity; however,once the composition of the marshland bacterial community has been altered by cultivated disturbance,it might be difficult to restore to its original state. These findings highlight the importance of effectively managing the soil bacterial community to maintain a naturally functioning soil ecosystem.
Different perturbation regimes,including disturbance caused by cultivation or the process of natural restoration,can have significant effects on the soil bacterial community in marshland. In this study,we investigated the relationship between soil bacterial community composition and perturbation in marshland to quantify the extent of such disturbancerelated changes in northeast China. We assessed the diversity of bacterial communities in twelve samples of marsh soil collected from pristine marsh,neighboring cropland,and a wetland restoration area. High-throughput sequencing of a bacteria-specific genomic sequence,the internal transcribed spacer( 16 S r RNA) region,was used to identify bacterial taxa. We obtained 358,737 sequences that represented 2263 bacterial OTUs across the three types of sampling sites. Of these,1411 OTUs occurred at all three site types,99 were shared between cultivated land and pristine marshland,322were shared between cultivated land and wetland converted from cropland,and 126 were shared between pristine marshland and wetland converted from cropland. All sites also hosted unique fungal OTUs,with 218 OTUs exclusive to cultivated land,52 exclusive to pristine marshland,and 35 exclusive to wetland converted from cropland. Sequences were affiliated to36 different phyla throughout the dataset. Sequence abundance showed that members of the Proteobacteria were more frequently identified in all soil samples than Acidobacteria, and included members of Chloroflexi, Actinobacteria,Bacteroidetes,Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Saccharibacteria, and Chlorobi, which represented an overwhelming proportion of the soil bacterial communities with an average relative abundance of > 1%,and another 25 phyla with an average relative abundance were < 1%. The dominant phyla that showed the greatest variation among habitat types( > 1% of the average relative abundance) were Gemmatimonadetes( P < 0. 01),Bacteroidetes( P <0. 01),Firmicutes( P < 0. 01),and Chlorobi( P < 0. 01). The soil bacterial community diversity decreased from a maximum in cultivated land,through the wetland restoration area,to a minimum in pristine marshland. Redundancy and correlation analyses demonstrated that chronic disturbance through cultivation,especially dry cultivation,significantly altered the bacterial community composition of marsh soil. The α-diversity of the soil bacterial community was most affected by soil moisture,soil p H,total carbon,soil organic carbon,soil dissolved organic carbon,available nitrogen,microbial biomass of carbon, and microbial biomass of nitrogen. Meanwhile, the soil bacterial community composition was significantly affected by soil moisture,soil p H,total carbon,soil organic carbon,and soil dissolved organic carbon.Overall,the results from our study showed that the state of soil carbon and nitrogen is affected by the disturbance by agricultural cultivation,causing long-term accumulated soil nutrients to become available as an energy source that can be rapidly mineralized by soil bacteria. In addition,our results also indicate that cultivation and natural restoration influenced the bacterial community structure and diversity. Natural restoration can significantly enhance the recovery of bacterial diversity; however,once the composition of the marshland bacterial community has been altered by cultivated disturbance,it might be difficult to restore to its original state. These findings highlight the importance of effectively managing the soil bacterial community to maintain a naturally functioning soil ecosystem.
引文
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[19]朱宝光.三江原始湿地的“缩影”——黑龙江洪河国家级自然保护区.生命世界,2010,(5):16-19.
[20]杨菁,周国英,田媛媛,刘倩丽,刘成锋,杨权,周洁尘.降香黄檀不同混交林土壤细菌多样性差异分析.生态学报,2015,35(24):8117-8217.
[21]孙又宁,保万魁,余梅玲.自动定氮仪碱解蒸馏法测定土壤中水解性氮含量.中国土壤与肥料,2007,(5):64-66.
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[23]李玉洁,王慧,赵建宁,皇甫超河,杨殿林.耕作方式对农田土壤理化因子和生物学特性的影响.应用生态学报,2015,26(3):939-948.
[24]Dennis K L,Wang Y W,Blatner N R,Wang S Y,Saadalla A,Trudeau E,Roers A,Weaver C T,Lee J J,Gilbert J A,Chang E B,Khazaie K.Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10-producing T cells.Cancer Research,2013,73(19):5905-5913.
[25]Schloss P D,Gevers D,Westcott S L.Reducing the effects of PCR amplification and sequencing artifacts on 16S r RNA-Based studies.PLo S ONE,2011,6(12):e27310.
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[27]Yang S Z,Wen X,Jin H J,Wu Q B.Pyrosequencing investigation into the bacterial community in permafrost soils along the China-Russia Crude oil pipeline(CRCOP).PLo S One,2012,7(12):e52730.
[28]Amato K R,Yeoman C J,Kent A,Righini N,Carbonero F,Estrada A,Gaskins H R,Stumpf R M,Yildirim S,Torralba M,Gillis M,Wilson B A,Nelson K E,White B A,Leigh S R.Habitat degradation impacts black howler monkey(Alouatta pigra)gastrointestinal microbiomes.The ISME Journal,2013,7(7):1344-1353.
[29]Fouts D E,Szpakowski S,Purushe J,Torralba M,Waterman R C,Mac Neil M D,Alexander L J,Nelson K E.Next generation sequencing to define prokaryotic and fungal diversity in the Bovine Rumen.PLo S One,2012,7(11):e48289.
[30]Jiang X T,Peng X,Deng G H,Sheng H F,Wang Y,Zhou H W,Tam N F Y.Illumina sequencing of 16S r RNA tag revealed spatial variations of bacterial communities in a Mangrove wetland.Microbial Ecology,2013,66(1):96-104.
[31]Jansson J K,Prosser J I.Microbiology:the life beneath our feet.Nature,2013,494(7435):40-41.
[32]Berg G,Smalla K.Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere.FEMS Microbiology Ecology,2009,68(1):1-13.
[33]苗祯,杜宗军,李会荣,楼妍颖,罗玮.5株北极微藻藻际环境的细菌多样性.生态学报,2015,35(5):1587-1600.
[34]陈波,黄霄,刘小玉,周登博,谭昕,高祝芬,张锡炎,戚春林.不同香蕉枯萎病区土壤细菌群落多样性.应用生态学报,2013,24(8):2281-2286.
[35]张伟,陈一峰.棉花长期连作对新疆土壤细菌群落结构的影响.生态学报,2014,34(16):4682-4689.
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[2]Liu J J,Sui Y Y,Yu Z H,Shi Y,Chu H Y,Jin J,Liu X B,Wang G H.High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China.Soil Biology and Biochemistry,2014,70:113-122.
[3]黄靖宇,宋长春,宋艳宇,刘德燕,万忠梅,廖玉静.湿地垦殖对土壤微生物量及土壤溶解有机碳、氮的影响.环境科学,2008,29(5):1380-1387.
[4]Zhang X M,Zhang G M,Chen Q S,Han X G.Soil bacterial communities respond to climate changes in a temperate steppe.PLo S One.2013,8(11):e78616.
[5]白雪,马克明,杨柳,张洁瑜,张小雷.三江平原湿地保护区内外的生态功能差异.生态学报,2008,28(2):620-626.
[6]霍莉莉,邹元春,郭佳伟,吕宪国.垦殖对湿地土壤有机碳垂直分布及可溶性有机碳截留的影响.环境科学,2013,34(1):283-287.
[7]郭建国,赵龙浩,徐丹,孙野青.人工湿地处理造纸废水后细菌群落结构变化.生态学报,2014,34(8):2095-2101.
[8]张乃莉,郭继勋,王晓宇,马克平.土壤微生物对气候变暖和大气N沉降的响应.植物生态学报,2007,31(2):252-261.
[9]肖烨,黄志刚,武海涛,吕宪国.三江平原4种典型湿地土壤碳氮分布差异和微生物特征.应用生态学报,2014,25(10):2847-2854.
[10]Ribeiro H,Mucha A P,Almeida C M R,Bordalo A A.Bacterial community response to petroleum contamination and nutrient addition in sediments from a temperate salt marsh.Science of the Total Environment,2013,458-460:568-576.
[11]Sura S,Waiser M J,Tumber V,Raina-Fulton R,Cessna A J.Effects of a herbicide mixture on primary and bacterial productivity in four prairie wetlands with varying salinities:an enclosure approach.Science of the Total Environment,2015,512-513:526-539.
[12]Arroyo P,de Miera L E S,Ansola G.Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.Science of the Total Environment,2015,506-507:380-390.
[13]汪仲琼,王为东,祝贵兵,尹澄清.人工和天然湿地芦苇根际土壤细菌群落结构多样性的比较.生态学报,2011,31(16):4489-4498.
[14]Liu J J,Zheng C Y,Song C C,Guo S D,Liu X B,Wang G H.Conversion from natural wetlands to paddy field alters the composition of soil bacterial communities in Sanjiang Plain,Northeast China.Annals of Microbiology,2014,64(3):1395-1403.
[15]Ludwig-Müller J.Bacteria and fungi controlling plant growth by manipulating auxin:balance between development and defense.Journal of Plant Physiology,2015,172:4-12.
[16]王兴春,杨致荣,王敏,李玮,李生才.高通量测序技术及其应用.中国生物工程杂志,2012,32(1):109-114.
[17]刘驰,李家宝,芮俊鹏,安家兴,李香真.16S r RNA基因在微生物生态学中的应用.生态学报,2015,35(9):2769-2788.
[18]袁红朝,吴昊,葛体达,李科林,吴金水,王久荣.长期施肥对稻田土壤细菌、古菌多样性和群落结构的影响.应用生态学报,2015,26(6):1807-1813.
[19]朱宝光.三江原始湿地的“缩影”——黑龙江洪河国家级自然保护区.生命世界,2010,(5):16-19.
[20]杨菁,周国英,田媛媛,刘倩丽,刘成锋,杨权,周洁尘.降香黄檀不同混交林土壤细菌多样性差异分析.生态学报,2015,35(24):8117-8217.
[21]孙又宁,保万魁,余梅玲.自动定氮仪碱解蒸馏法测定土壤中水解性氮含量.中国土壤与肥料,2007,(5):64-66.
[22]鲁如坤.土壤农业化学分析方法.北京:中国农业科技出版社,2000:125-233.
[23]李玉洁,王慧,赵建宁,皇甫超河,杨殿林.耕作方式对农田土壤理化因子和生物学特性的影响.应用生态学报,2015,26(3):939-948.
[24]Dennis K L,Wang Y W,Blatner N R,Wang S Y,Saadalla A,Trudeau E,Roers A,Weaver C T,Lee J J,Gilbert J A,Chang E B,Khazaie K.Adenomatous polyps are driven by microbe-instigated focal inflammation and are controlled by IL-10-producing T cells.Cancer Research,2013,73(19):5905-5913.
[25]Schloss P D,Gevers D,Westcott S L.Reducing the effects of PCR amplification and sequencing artifacts on 16S r RNA-Based studies.PLo S ONE,2011,6(12):e27310.
[26]张芳,林绍艳,徐颖洁.水稻连作对江苏地区稻田土细菌微生物多样性的影响.山东农业大学学报:自然科学版,2014,45(2):161-165.
[27]Yang S Z,Wen X,Jin H J,Wu Q B.Pyrosequencing investigation into the bacterial community in permafrost soils along the China-Russia Crude oil pipeline(CRCOP).PLo S One,2012,7(12):e52730.
[28]Amato K R,Yeoman C J,Kent A,Righini N,Carbonero F,Estrada A,Gaskins H R,Stumpf R M,Yildirim S,Torralba M,Gillis M,Wilson B A,Nelson K E,White B A,Leigh S R.Habitat degradation impacts black howler monkey(Alouatta pigra)gastrointestinal microbiomes.The ISME Journal,2013,7(7):1344-1353.
[29]Fouts D E,Szpakowski S,Purushe J,Torralba M,Waterman R C,Mac Neil M D,Alexander L J,Nelson K E.Next generation sequencing to define prokaryotic and fungal diversity in the Bovine Rumen.PLo S One,2012,7(11):e48289.
[30]Jiang X T,Peng X,Deng G H,Sheng H F,Wang Y,Zhou H W,Tam N F Y.Illumina sequencing of 16S r RNA tag revealed spatial variations of bacterial communities in a Mangrove wetland.Microbial Ecology,2013,66(1):96-104.
[31]Jansson J K,Prosser J I.Microbiology:the life beneath our feet.Nature,2013,494(7435):40-41.
[32]Berg G,Smalla K.Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere.FEMS Microbiology Ecology,2009,68(1):1-13.
[33]苗祯,杜宗军,李会荣,楼妍颖,罗玮.5株北极微藻藻际环境的细菌多样性.生态学报,2015,35(5):1587-1600.
[34]陈波,黄霄,刘小玉,周登博,谭昕,高祝芬,张锡炎,戚春林.不同香蕉枯萎病区土壤细菌群落多样性.应用生态学报,2013,24(8):2281-2286.
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