盐碱地和近海沉积物中真核微生物多样性及与环境的关系
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摘要
真核微生物主要指原生生物，广义上还包括真菌和线虫等小型动物。土壤及沉积物中真核微生物具有高度的形态和功能多样性，可通过改变细菌群落结构及自身代谢途径影响生态系统中物质循环和能量流动。其多样性分布特征是“微型生物地理分布”这一国际热点问题争论焦点。但是限于技术手段的局限及研究力量的不足，有关土壤和沉积物中真核微生物的研究仍然匮乏，其多样性、分布特征及与环境关系仍不明了。
本研究首先构建土壤原生生物研究体系。将Ludox-QPS方法稍作改良用于评价土壤纤毛虫群落结构，结果表明该法在定量分析上可以检获比直接计数法更多的纤毛虫，定性分析上检获的纤毛虫物种数也高于DGGE技术获得的条带数。同时，结合密度梯度离心技术和经典DNA直接提取法，提出一种适用于土壤真核微生物的DNA间接提取法。与经典直接提取法和试剂盒法相比，该法可获得纯度较高的DNA产物，有助于后续PCR及真核微生物分子多样性研究。
构建方法学体系基础上，结合分子手段和形态学方法研究了不同类型盐碱土壤纤毛虫多样性及其环境驱动因子。基于形态学手段结果显示，滨海土壤纤毛虫活动虫体物种数及丰度随盐度增高呈下降趋势，在盐度接近5‰时，未发现纤毛虫活动虫。而分子指纹图谱则显示随着盐度增高纤毛虫多样性并未降低，甚至略有升高，直至盐度高于30‰时纤毛虫分子多样性水平才呈下降趋势。且纤毛虫分子指纹图谱的相似度随着地理距离的增大而降低，表明纤毛虫多样性分布呈现出地理限定性，与其分布最相关的环境因子是土壤盐度。多样性构成来看，不同类型盐碱土壤中均存在肾形纲、旋唇纲、裂口纲和寡膜纲纤毛虫，在纲级水平上多样性差异不明显，但物种水平上则差异明显。滨海土壤中存在与海洋种相似的纤毛虫序列，而内陆土壤中仅检获与土壤及淡水种相似的序列。
以黄河三角洲自然保护区及昌邑海洋生态特别保护区为例，研究了滨海土壤中微型生物分子多样性及时空变化，尤其是对滨海土壤盐渍化的响应。真核及原核微生物分子多样性随土壤盐渍化程度加深发生明显变化，但其在时间尺度上的变化不显著。滨海土壤中微型生物分子多样性与环境密切相关，其中盐碱度及有机物含量为影响滨海微型生物多样性的主要因子。
黄海沉积物中真核微生物分子多样性呈由北向南递增的趋势，此分布模式与水深、沉积物中叶绿素a含量和底栖桡足类丰度相关性最高。克隆文库结果表明冷水团中存在丰富的真核微生物多样性。长江口海域沉积物中真核微生物分子多样性高于黄海，其分子指纹图谱模式与水深和有机质含量相关性最高，且空间变化的影响大于时间尺度的影响。克隆文库结果表明长江口海域夏季多样性高于春季，春季至夏季原生生物比例下降，小型动物比例增加，硅藻仅出现在春季，甲藻一直存在，真菌在不同季节优势类群变化。纤毛虫多样性较高，其活动虫丰度及生物量可维持在较高的水平，一些浮游寡毛类及舞毛类纤毛虫在环境条件恶化时，可形成包囊储存于沉积物中。
总体来讲，本研究发现大部分真核微生物分布具有地理限定性，但一些物种对特定环境条件适应后，可分布于生境类似的不同区域。盐碱土壤中盐度为影响其分布的重要环境因子，近海沉积物中水深、沉积物中有机质和叶绿素a为重要的限制因子。真核微生物多样性分布基本呈现：近海沉积物>滨海盐碱土壤>内陆盐碱土壤。阐明不同生境下真核微生物的多样性分布及与环境因子关系仍需大量数据的积累，结合分子手段和形态学手段有助于从不同角度探讨并理解自然生境中真核微生物的多样性与变动特点。
Microbial eukaryotes including protists, algae, fungi and meiofauna areubiquitous in soil and marine sediment and probably play key roles in maintainingecosystem function. Moreover, microeukaryotic diversity and their geographicdistribution have controversially debated in recent years. The study on themicroeukaryotic diversity is limited by the availability of appropriate method, and thusthe knowledge on the diversity and distribution of microbial eukaryotes as well as theirrelationships with environments is far from being fully discovered, especially in someextreme microhabitats.
Here, we utilized the improved Ludox-Quantitative Protargol Stain (Ludox-QPS)method which was originally developed for marine sediment to assess ciliate diversityin soil. The method was tested with three soil samples and compared with a ciliate-specific Denaturing Gradient Gel Electrophoresis (DGGE) and direct count method.The Ludox-QPS method obtained significantly higher number of ciliates with highertaxonomic resolution than the direct count, and revealed higher diversity than theDGGE as well as subsequent gene sequencing. Besides, we developed a new indirectDNA extraction method for investigating the molecular diversity of soil microbialeukaryotes which combined the silica sol Ludox density centrifugation and thetraditional Sodium Dodecyl Sulfate (SDS)-based DNA extraction method. Its efficiencywas evaluated and compared with the direct lysis methods (the SDS-based method and commercial DNA extraction kit). The indirect method could obtain a high purity ofintracellular DNA and had high efficiency in estimation of molecular diversity of soilmicrobial eukaryotes.
We investigated the ciliate diversity and their relationships with theenvironments in the different type of saline-alkali soil using both the moleculartechniques and morphological methods. The species richness and abundance of activeciliate were decreased with increasing the salt content, and even no active ciliates wereobserved from soil when the salinity was close to5‰by the Ludox-QPS method. Incontrast, the results based on the ciliate-specific DGGE indicated that if the soil salinitywas under30‰, high diversity of ciliates could be maintained in spite of salinityincrease. Moreover, the similarity in saline soil ciliate genetic diversity generallyexhibited a decreasing trend as distance increased and soil salinity might be the mostsignificant factor affecting the distribution of ciliates. Colpodea, Spirotrichea,Litostomatea and Oligohymenophorea were commonly found in different type of saline-alkali soil. The ciliate community in saline-alkali soil was similar at class level, while itwas significant different at species level. The coastal soil near the sea hosted a ciliatecommunity of both marine and soil taxa.
We investigate the response of microeukaryotic and prokaryotic moleculardiversity to the change of environment in particular salinization in coastal soil of theLaizhou Bay and Yellow River Delta, China by the DGGE as well as sequencing. Theobvious shifts of DGGE patterns were detected along an environmental gradient amongsites, while statistically indistinguishable among seasons. Soil salinity and pH as well asorganic matters might be the main factor affecting the distribution of microeukaryotesand prokaryotes in the coastal soil.
An increasing trend of the microeukaryotic diversity was detected from north tosouth in the sediments of the Yellow Sea. Water depth, Chl a and the abundance of Copepod might be the most significant factor regulating the distribution of microbialeukaryotes. Moreover, a higher diversity was found in the sediments of the ChangjiangRiver estuary than that in the Yellow Sea. Location rather than seasonal change wasimportant in regulating the community composition of microeukaryotes in sediments.Water depth and TOC might be the main factor affecting the distribution of soilmicroeukaryotes in the Changjiang River estuary. The results based on the clone libraryrevealed that the summer samples of each sites were with higher diversity than that ofspring samples. The protozoan diversity decreased from spring to summer, while thediversity of meiofauna increased. Bacillariophyta was only detected in spring anddisappeared in summer, while Dinoflagellata were present in both seasons. Thedominant group of fungi was changed between different seasons. High diversity andabundance of ciliates existed in the sediments, and the planktonic Choreotrichia andOligotrichia could encyst and reserve in the sediments as environmental deterioration.
In sum, our study indicated that the distribution of most microbial eukaryotes wasgeographically restricted, while some species adapted to the special environment couldexist in different locations with similar environmental conditions. Soil salinity might bethe main factors regulating the distribution of microeukaryotes in the saline soil, andwater depth, Chl a and organic matter were important restricting factors in marinesediments. The diversity of microbial eukaryotes was higher in the marine sedimentsthan that in the coastal saline-alkali soil, and the lowest in the inland saline-alkali soil.The data indicate that both molecular and microscopy-based methods have particularshortcomings, and it was difficult to identify all species by a single method. Thus,combined approaches will provide more information than either alone.
本研究首先构建土壤原生生物研究体系。将Ludox-QPS方法稍作改良用于评价土壤纤毛虫群落结构，结果表明该法在定量分析上可以检获比直接计数法更多的纤毛虫，定性分析上检获的纤毛虫物种数也高于DGGE技术获得的条带数。同时，结合密度梯度离心技术和经典DNA直接提取法，提出一种适用于土壤真核微生物的DNA间接提取法。与经典直接提取法和试剂盒法相比，该法可获得纯度较高的DNA产物，有助于后续PCR及真核微生物分子多样性研究。
构建方法学体系基础上，结合分子手段和形态学方法研究了不同类型盐碱土壤纤毛虫多样性及其环境驱动因子。基于形态学手段结果显示，滨海土壤纤毛虫活动虫体物种数及丰度随盐度增高呈下降趋势，在盐度接近5‰时，未发现纤毛虫活动虫。而分子指纹图谱则显示随着盐度增高纤毛虫多样性并未降低，甚至略有升高，直至盐度高于30‰时纤毛虫分子多样性水平才呈下降趋势。且纤毛虫分子指纹图谱的相似度随着地理距离的增大而降低，表明纤毛虫多样性分布呈现出地理限定性，与其分布最相关的环境因子是土壤盐度。多样性构成来看，不同类型盐碱土壤中均存在肾形纲、旋唇纲、裂口纲和寡膜纲纤毛虫，在纲级水平上多样性差异不明显，但物种水平上则差异明显。滨海土壤中存在与海洋种相似的纤毛虫序列，而内陆土壤中仅检获与土壤及淡水种相似的序列。
以黄河三角洲自然保护区及昌邑海洋生态特别保护区为例，研究了滨海土壤中微型生物分子多样性及时空变化，尤其是对滨海土壤盐渍化的响应。真核及原核微生物分子多样性随土壤盐渍化程度加深发生明显变化，但其在时间尺度上的变化不显著。滨海土壤中微型生物分子多样性与环境密切相关，其中盐碱度及有机物含量为影响滨海微型生物多样性的主要因子。
黄海沉积物中真核微生物分子多样性呈由北向南递增的趋势，此分布模式与水深、沉积物中叶绿素a含量和底栖桡足类丰度相关性最高。克隆文库结果表明冷水团中存在丰富的真核微生物多样性。长江口海域沉积物中真核微生物分子多样性高于黄海，其分子指纹图谱模式与水深和有机质含量相关性最高，且空间变化的影响大于时间尺度的影响。克隆文库结果表明长江口海域夏季多样性高于春季，春季至夏季原生生物比例下降，小型动物比例增加，硅藻仅出现在春季，甲藻一直存在，真菌在不同季节优势类群变化。纤毛虫多样性较高，其活动虫丰度及生物量可维持在较高的水平，一些浮游寡毛类及舞毛类纤毛虫在环境条件恶化时，可形成包囊储存于沉积物中。
总体来讲，本研究发现大部分真核微生物分布具有地理限定性，但一些物种对特定环境条件适应后，可分布于生境类似的不同区域。盐碱土壤中盐度为影响其分布的重要环境因子，近海沉积物中水深、沉积物中有机质和叶绿素a为重要的限制因子。真核微生物多样性分布基本呈现：近海沉积物>滨海盐碱土壤>内陆盐碱土壤。阐明不同生境下真核微生物的多样性分布及与环境因子关系仍需大量数据的积累，结合分子手段和形态学手段有助于从不同角度探讨并理解自然生境中真核微生物的多样性与变动特点。
Microbial eukaryotes including protists, algae, fungi and meiofauna areubiquitous in soil and marine sediment and probably play key roles in maintainingecosystem function. Moreover, microeukaryotic diversity and their geographicdistribution have controversially debated in recent years. The study on themicroeukaryotic diversity is limited by the availability of appropriate method, and thusthe knowledge on the diversity and distribution of microbial eukaryotes as well as theirrelationships with environments is far from being fully discovered, especially in someextreme microhabitats.
Here, we utilized the improved Ludox-Quantitative Protargol Stain (Ludox-QPS)method which was originally developed for marine sediment to assess ciliate diversityin soil. The method was tested with three soil samples and compared with a ciliate-specific Denaturing Gradient Gel Electrophoresis (DGGE) and direct count method.The Ludox-QPS method obtained significantly higher number of ciliates with highertaxonomic resolution than the direct count, and revealed higher diversity than theDGGE as well as subsequent gene sequencing. Besides, we developed a new indirectDNA extraction method for investigating the molecular diversity of soil microbialeukaryotes which combined the silica sol Ludox density centrifugation and thetraditional Sodium Dodecyl Sulfate (SDS)-based DNA extraction method. Its efficiencywas evaluated and compared with the direct lysis methods (the SDS-based method and commercial DNA extraction kit). The indirect method could obtain a high purity ofintracellular DNA and had high efficiency in estimation of molecular diversity of soilmicrobial eukaryotes.
We investigated the ciliate diversity and their relationships with theenvironments in the different type of saline-alkali soil using both the moleculartechniques and morphological methods. The species richness and abundance of activeciliate were decreased with increasing the salt content, and even no active ciliates wereobserved from soil when the salinity was close to5‰by the Ludox-QPS method. Incontrast, the results based on the ciliate-specific DGGE indicated that if the soil salinitywas under30‰, high diversity of ciliates could be maintained in spite of salinityincrease. Moreover, the similarity in saline soil ciliate genetic diversity generallyexhibited a decreasing trend as distance increased and soil salinity might be the mostsignificant factor affecting the distribution of ciliates. Colpodea, Spirotrichea,Litostomatea and Oligohymenophorea were commonly found in different type of saline-alkali soil. The ciliate community in saline-alkali soil was similar at class level, while itwas significant different at species level. The coastal soil near the sea hosted a ciliatecommunity of both marine and soil taxa.
We investigate the response of microeukaryotic and prokaryotic moleculardiversity to the change of environment in particular salinization in coastal soil of theLaizhou Bay and Yellow River Delta, China by the DGGE as well as sequencing. Theobvious shifts of DGGE patterns were detected along an environmental gradient amongsites, while statistically indistinguishable among seasons. Soil salinity and pH as well asorganic matters might be the main factor affecting the distribution of microeukaryotesand prokaryotes in the coastal soil.
An increasing trend of the microeukaryotic diversity was detected from north tosouth in the sediments of the Yellow Sea. Water depth, Chl a and the abundance of Copepod might be the most significant factor regulating the distribution of microbialeukaryotes. Moreover, a higher diversity was found in the sediments of the ChangjiangRiver estuary than that in the Yellow Sea. Location rather than seasonal change wasimportant in regulating the community composition of microeukaryotes in sediments.Water depth and TOC might be the main factor affecting the distribution of soilmicroeukaryotes in the Changjiang River estuary. The results based on the clone libraryrevealed that the summer samples of each sites were with higher diversity than that ofspring samples. The protozoan diversity decreased from spring to summer, while thediversity of meiofauna increased. Bacillariophyta was only detected in spring anddisappeared in summer, while Dinoflagellata were present in both seasons. Thedominant group of fungi was changed between different seasons. High diversity andabundance of ciliates existed in the sediments, and the planktonic Choreotrichia andOligotrichia could encyst and reserve in the sediments as environmental deterioration.
In sum, our study indicated that the distribution of most microbial eukaryotes wasgeographically restricted, while some species adapted to the special environment couldexist in different locations with similar environmental conditions. Soil salinity might bethe main factors regulating the distribution of microeukaryotes in the saline soil, andwater depth, Chl a and organic matter were important restricting factors in marinesediments. The diversity of microbial eukaryotes was higher in the marine sedimentsthan that in the coastal saline-alkali soil, and the lowest in the inland saline-alkali soil.The data indicate that both molecular and microscopy-based methods have particularshortcomings, and it was difficult to identify all species by a single method. Thus,combined approaches will provide more information than either alone.
引文
Acosta-Mercado D, Lynn DH.2002. A preliminary assessment of spatial patterns of soil ciliatediversity in two subtropical forests in Puerto Rico and its implications for designing anappropriate sampling approach. Soil Biology&Biochemistry,34:1517-1520.
Acosta-Mercado D, Lynn DH.2003. The edaphic quantitative protargol stain: A sampling protocolfor assessing soil ciliate abundance and diversity. Journal of Microbiological Methods,53:365-375.
Acosta-Mercado D, Lynn DH.2004. Soil ciliate species richness and abundance associated with therhizosphere of different subtropical plant species. Journal of Eukaryotic Microbiology,51:582-588.
Acosta-Mercado D, Lynn DH.2006. Contrasting soil ciliate species richness and abundance betweentwo tropical plant species: A test of the plant effect. Microbial Ecology,51:453-459.
Adl SM, Coleman DC.2005. Dynamics of soil protozoa using a direct count method. Biology andFertility of Soils,42:168-171.
Adl SM.2007. Motility and migration rate of protozoa in soil columns. Soil Biology&Biochemistry,39:700-703.
Aguilera A, Gomez F, Lospitao E, Amils R.2006. A molecular approach to the characterization ofthe eukaryotic communities of an extreme acidic environment: Methods for DNA extractionand denaturing gradient gel electrophoresis analysis. Systematic and Applied Microbiology,29:593-605.
Amann R, Fuchs BM, Behrens S.2001. The identification of microorganisms by fluorescence in situhybridization. Current Opinion in Biotechnology,12:231-236.
Anderson IC, Cairney JWG.2004. Diversity and ecology of soil fungal communities: Increasedunderstanding through the application of molecular techniques. Environmental Microbiology,6:769-779.
Angel R, Soares MIM, Ungar ED, Gillor O.2010. Biogeography of soil archaea and bacteria along asteep precipitation gradient. ISME Journal,4:553-563.
Ansorge WJ.2009. Next-generation DNA sequencing techniques. New Biotechnology,25:195-203.
Ascher J, Ceccherini MT, Pantani OL, Agnelli A, Borgogni F, Guerri G, Nannipieri P, PietramellaraG.2009. Sequential extraction and genetic fingerprinting of a forest soil metagenome. AppliedSoil Ecology,42:176-181.
Azam F, Fenchel T, Field JG, Gray JS, Meyerreil LA, Thingstad F.1983. The ecological role ofwater-column microbes in the sea. Marine Ecology Progress Series,10:257-263.
Bamforth SS.1991. Enumeration of soil ciliate active forms and cysts by a direct count method.Agriculture Ecosystems&Environment,34:209-212.
Bamforth SS.1995. Interpreting soil ciliate biodiversity. Plant Soil,170:159-164.
Bamforth SS.2001. Proportions of active ciliate taxa in soils. Biology and Fertility of Soils,33:197-203.
Bare J, Sabbe K, Van Wichelen J, D'Hondt S, Houf K.2009. Diversity and habitat specificity offree-living protozoa in commercial poultry houses. Applied and Environmental Microbiology,75:1417-1426.
Barrios E.2007. Soil biota, ecosystem services and land productivity. Ecological Economics,64:269-285.
Bass D, Cavalier-Smith T.2004. Phylum-specific environmental DNA analysis reveals remarkablyhigh global biodiversity of Cercozoa (Protozoa). International Journal of Systematic andEvolutionary Microbiology,54:2393-2404.
Bass D, Howe AT, Mylnikov AP, Vickerman K, Chao EE, Smallbone JE, Snell J, Cabral C, Cavalier-Smith T.2009. Phylogeny and classification of Cercomonadida (Protozoa, Cercozoa):Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. nov. Protist,160:483-521.
Benlloch S, López-López A, Casamayor EO, Ovreas L, Goddard V, Daae FL, Smerdon G, MassanaR, Joint I, Thingstad F, Pedros-Alio C, Rodriguez-Valera F.2002. Prokaryotic genetic diversitythroughout the salinity gradient of a coastal solar saltern. Environmental Microbiology,4:349-360.
Berney C, Fahrni J, Pawlowski J.2004. How many novel eukaryotic “kingdoms”? Pitfalls andlimitations of environmental DNA surveys. BMC Biology,2:13.
Bernhard JM, Bowser SS.1999. Benthic foraminifera of dysoxic sediments: chloroplastsequestration and functional morphology. Earth-Science Reviews,46:149-165.
Bernhard D, Stechmann A, Foissner W, Ammermann, D, Hehn M, Schlegel M.2001. Phylogeneticrelationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA genesequences. Molecular Phylogenetics and Evolution,21:86-92.
Berthold A, Bruckner A, Kampichler C.1999. Improved quantification of active soil microfauna bya “counting crew”. Biology and Fertility of Soils,28:352-355.
Berthold A, Palzenberger M.1995. Comparison between direct counts of active soil ciliates(protozoa) and most probable number estimates obtained by Singh’s dilution culture method.Biology and Fertility of Soils,19:348-356.
Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK.2012a.Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns indeep-sea and shallow water sediments. Molecular Ecology,21:1048-1059.
Bik HM, Halanych KM, Sharma J, Thomas WK.2012b. Dramatic shifts in benthic microbialeukaryote communities following the deepwater horizon oil spill. PLoS One,7.
Billen G, Lancelot C.1988. Modeling benthic nitrogen cycling in temperate coastal ecosystems. In:Nitrogen Cycling in the Coastal Marine Environment (eds Blackburn TH, Sorensen J), pp.341–378. Wiley and Sons, New York.
Bird E.2008. Coastal geomorphology: an introduction.2nd ed. John Wiley&Sons Ltd, the Atrium,Southern Gate, Chichester.
Bongers T, Ferris H.1999. Nematode community structure as a bioindicator in environmentalmonitoring. Trends in Ecology&Evolution,14:224-248.
Boon N, Marle C, Top EM, Verstraete W.2000. Comparison of the spatial homogeneity of physico-chemical parameters and bacterial16S rRNA genes in sediment samples from a dumping sitefor dredging sludge. Applied and Environmental Microbiology,53:742-747.
Breitburg DL, Crump BC, Dabiri JO, Gallegos CL.2010. Ecosystem engineers in the pelagic realm:alteration of habitat by species ranging from microbes to jellyfish. Integrative and ComparativeBiology,50:188-200.
Bremner JM, Mulvaney CS.1982. Nitrogen-total. In Page AL, Miller RH, Keeney DK.(Ed.),Methods of soil analysis. Part2. Chemical and microbiological properties. American Society ofAgronomy, Madison WI. USA.
Bridge P, Spooner B.2001. Soil fungi: diversity and detection. Plant Soil,232:147-154.
Brussaard L, de Ruiter PC, Brown GG.2007. Soil biodiversity for agricultural sustainability.Agriculture, Ecosystems&Environment,121:233-244.
Burgess R.2001. An improved protocol for separating meiofauna from sediments using colloidalsilica sols. Marine Ecology Progress Series,214:161-165.
Cabrol L, Malhautier L, Poly F, Lepeuple AS, Fanlo JL.2010. Assessing the bias linked to DNArecovery from biofiltration woodchips for microbial community investigation by fingerprinting.Applied Microbiology and Biotechnology,85:779-790.
Cao D, Shi F, Ruan W, Lu Z, Chai M.2011. Seasonal changes in and relationship between soilmicrobial and microfaunal communities in a Tamarix chinensis community in the Yellow RiverDelta. African Journal of Biotechnology,10:18425-18432.
Caron DA.2009. New accomplishments and approaches for assessing protistan diversity andecology in natural ecosystems. Bioscience,59:287-299.
Caron DA, Worden AZ, Countway PD, Demir E, Heidelberg KB.2009. Protists are microbes too: aperspective. ISME Journal,3:4-12.
Carrigg C, Rice O, Kavanagh S, Collins G, O'Flaherty V.2007. DNA extraction method affectsmicrobial community profiles from soils and sediment. Applied Microbiology andBiotechnology,77:955-964.
Casamayor EO, Massana R, Benlloch S, vre s L, Díez B, Goddard VJ, Gasol JM, Joint I,Rodriguez-Valera F, Pedrós-Alió C.2002. Changes in archaeal, bacterial and eukaryalassemblages along a salinity gradient by comparison of genetic fingerprinting methods in amultipond solar saltern. Environmental Microbiology,4:338-348.
Chandler DP.1998. Redefining relativity: quantitative PCR at low template concentrations forindustrial and environmental microbiology. Journal of Industrial Microbiology&Biotechnology,21:128-140.
Chao A, Li PC, Agatha S, Foissner W.2006. A statistical approach to estimate soil ciliate diversityand distribution based on data from five continents. Oikos,114:479-493.
Chen M, Li X, Yang Q, Chi X, Pan L, Chen N, Yang Z, Wang T, Wang M, Yu S.2012. Soileukaryotic microorganism succession as affected by continuous cropping of peanut-pathogenic and beneficial fungi were selected. PLoS One,7.
Chen X, Daniell TJ, Neilson R, O'Flaherty V, Griffiths BS.2010. A comparison of molecularmethods for monitoring soil nematodes and their use as biological indicators. European Journalof Soil Biology,46:319-324.
Choi JW, Stoecker DK.1989. Effects of fixation on cell-volume of marine planktonic protozoa.Applied and Environmental Microbiology,55:1761-1765.
Clarholm M.2005. Soil protozoa: an under-researched microbial group gaining momentum. SoilBiology&Biochemistry,37:811-817.
Clarke KR.1993. Non-parametric multivariate analyses of changes in community structure.Australian Journal of Ecology,18:117-143.
Coats WD, Heinbokel JF.1982. A study of reproduction and other life cycle phenomena inplanktonic protists using an acridine orange fluorescence technique. Marine Biology,67:71-79.
Coesel PFM, Krienitz L.2008. Diversity and geographic distribution of desmids and other coccoidgreen algae. Biodiversity and Conservation,17:381-392.
Condon RH, Decker MB, Purcell JE.2001. Effects of low dissolved oxygen on survival and asexualreproduction of scyphozoan polyps (Chrysaora quinquecirrha). Hydrobiologia,451:89-95.
Courtois S, Frostegard A, Goransson P, Depret G, Jeannin P, Simonet P.2001. Quantification ofbacterial subgroups in soil: comparison of DNA extracted directly from soil or from cellspreviously released by density gradient centrifugation. Environmental Microbiology,3:431-439.
Countway PD, Gast RJ, Savai P, Caron DA.2005. Protistan diversity estimates based on18S rDNAfrom seawater incubations in the western North Atlantic. Journal of Eukaryotic Microbiology,52:95-106.
Co teaux MM, Palka L.1988. A direct counting method for soil ciliates. Soil Biology&Biochemistry,20:7-10.
Co teaux MM, Darbyshire JF.1998a. Functional diversity amongst soil protozoa. Applied SoilEcology,10:229-237.
Co teaux MM, Raubuch M, Berg M.1998b. Response of protozoan and microbial communities invarious coniferous forest soils after transfer to forests with different levels of atmosphericpollution. Biology and Fertility of Soils,27:179-188.
Cytryn E, Minz D, Oremland RS, Cohen Y.2000. Distribution and diversity of archaeacorresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai,Egypt). Applied and Environmental Microbiology,66:3269-3276.
Daniel R.2005. The metagenomics of soil. Nature Reviews Microbiology,3:470-478.
Dang H, Zhang X, Sun J, Li T, Zhang Z, Yang G.2008. Diversity and spatial distribution ofsediment ammonia-oxidizing crenarchaeota in response to estuarine and environmentalgradients in the Changjiang Estuary and East China Sea. Microbiology,154:2084-2095.
Darby BJ, Housman DC, Zaki AM, Shamout, Y., Adl, S. M., Belnap, J., Neher, D. A.2006. Effectsof altered temperature and precipitation on desert protozoa associated with biological soil crusts.Journal of Eukaryotic Microbiology,53:507-514.
De Lipthay JR, Enzinger C, Johnsen K, Aamand J, Sorensen SJ.2004. Impact of DNA extractionmethod on bacterial community composition measured by denaturing gradient gelelectrophoresis. Soil Biology&Biochemistry,36:1607-1614.
Díez B, Pedrós-Alió C, Marsh TL, Massana R.2001. Application of denaturing gradient gelelectrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages andcomparison of DGGE with other molecular techniques. Applied and EnvironmentalMicrobiology,67:2942-2951.
Doherty M, Tamura M, Vriezen JAC, McManus GB, Katz LA.2010. Diversity of Oligotrichia andChoreotrichia ciliates in coastal marine sediments and in overlying plankton. Applied andEnvironmental Microbiology,76:3924-3935.
Dong D, Yan A, Liu H, Zhang X, Xu Y.2006. Removal of humic substances from soil DNA usingaluminium sulfate. Journal of Microbiological Methods,66:217-222.
Dopheide A, Lear G, Stott R, Lewis G.2009. Relative diversity and community structure of ciliatesin stream biofilms according to molecular and microscopy methods. Applied andEnvironmental Microbiology,75:5261-5272.
Du Y, Xu K, Lei Y.2009. Simultaneous enumeration of diatom, protozoa and meiobenthos frommarine sediments using Ludox-QPS method. Chinese Journal of Oceanology and Limnology,27:775-783.
Du Y, Xu K, Warren A, Lei Y, Dai R.2012. Benthic ciliate and meiofaunal communities in twocontrasting habitats of an intertidal estuarine wetland. Journal of Sea Research,70:50-63.
Edgcomb VP, Kysela DT, Teske A, Gomez AD, Sogin ML.2002. Benthic eukaryotic diversity inthe Guaymas Basin hydrothermal vent environment. Proceedings of the National Academy ofSciences of the United States of America,99:7658-7662.
Edgcomb V, Orsi W, Bunge J, Jeon S, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, VarelaR, Epstein S.2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. I.Pyrosequencing vs Sanger insights into species richness. ISME Journal,5:1344-1356.
Edmonds JW, Weston NB, Joye SB, Mou X, Moran MA.2009. Microbial community response toseawater amendment in low-salinity tidal sediments. Microbial Ecology,58:558-68.
Emmerling C, Schloter M, Hartmann A, Kandeler, E.2002. Functional diversity of soil organisms-a review of recent research activities in Germany. Journal of Plant Nutrition and Soil Science,165:408-420.
Epstein S, López-García P.2008."Missing" protists: a molecular prospective. Biodiversity andConservation,17:261-276.
Fawley MJ, Fawley KP, Buchheim MA.2004. Molecular diversity among communities offreshwater microchlorophytes. Microbial Ecology,48:489-499.
Fenchel T, Finlay BJ.2004. The ubiquity of small species: Patterns of local and global diversity.Bioscience,54:777-784.
Feng BW, Li XR, Wang JH, Hu ZY, Meng H, Xiang LY, Quan ZX.2009. Bacterial diversity ofwater and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMSMicrobiology Ecology,70:236-248.
Fierer N, Jackson RB.2006. The diversity and biogeography of soil bacterial communities.Proceedings of the National Academy of Sciences of the United States of America,103:626-631.
Finlay BJ.2002. Global dispersal of free-living microbial eukaryote species. Science,296:1061-1063.
Finlay BJ, Black HIJ, Brown S, Clarke KJ, Esteban GF, Hindle RM, Olmo JL, Rollett A, VickermanK.2000. Estimating the growth potential of the soil protozoan community. Protist,151:69-80.
Finlay BJ, Clarke KJ.1999. Ubiquitous dispersal of microbial species. Nature,400:828-828.
Finlay BJ, Esteban GF, Fenchel T.1996. Global diversity and body size. Nature,383:132-133.
First MR.2008. Benthic microbial food webs: apatial and temporal variations and the role ofheterotrophic protists in salt marsh sediments. The University of Georgia, USA.
Foissner W.1987. Soil protozoa: fundamental problems, ecological significance, adaptations inciliates and testaceans, bioindicators, and guide to the literature. Progress in Protistology,2:69-212.
Foissner W.1991. Basic light and scanning electron microscopic methods for taxonomic studies ofciliated protozoa. European Journal of Protistology,27:313-330.
Foissner W.1993. Colpodea (Ciliophora), Gustav Fischer Verlag, New York.
Foissner W.1997. Protozoa as bioindicators in agroecosystems, with emphasis on farming practices,biocides, and biodiversity. Agriculture Ecosystems&Environment,62:93-103.
Foissner W.1999a. Soil protozoa as bioindicators: Pros and cons, methods, diversity, representativeexamples. Agriculture Ecosystems&Environment,74:95-112.
Foissner W.1999b. Protist diversity: Estimates of the near-imponderable. Protist,150:363-368.
Foissner W.2008. Protist diversity and distribution: some basic considerations. Biodiversity andConservation,17:235-242.
Foissner W, Agatha S, Berger H.2002. Soil ciliates (Protozoa, Ciliophora) from Namibia(Southwest Africa), with emphasis on two contrasting environments, the Etosha Region and theNamib Desert. Denisia5:1-1459.
Foissner W, Chao A, Katz LA.2008. Diversity and geographic distribution of ciliates (Protista:Ciliophora). Biodiversity and Conservation,17:345-363.
Fontaine M, Guillot E.2002. Development of a TaqMan quantitative PCR assay specific forCryptosporidium parvum. FEMS Microbiology Letters,214:13-17.
Frahm JP.2008. Diversity, dispersal and biogeography of bryophytes (mosses). Biodiversity andConservation,17:277-284.
Freeman KR, Martin AP, Karki D, Lynch RC, Mitter MS, Meyer AF, Longcore JE, Simmons DR,Schmidt SK.2009. Evidence that chytrids dominate fungal communities in high-elevation soils.Proceedings of the National Academy of Sciences of the United States of America,106(43):18315-18320.
Fredslund L, Ekelund F, Jacobsen CS, Johnsen K.2001. Development and application of a most-probable-number-PCR assay to quantify flagellate populations in soil samples. Applied andEnvironmental Microbiology,67:1613-1618.
Fortin N, Beaumier D, Lee K, Greer CW.2004. Soil washing improves the recovery of totalcommunity DNA from polluted and high organic content sediments. Journal of MicrobiologicalMethods,56:181-191.
Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S,Gillet F, Aragno M, Rossi P.2002. Statistical analysis of denaturing gel electrophoresis (DGE)fingerprinting patterns. Environmental Microbiology,4:634-643.
Gabor EM, de Vries EJ, Janssen DB.2003. Efficient recovery of environmental DNA for expressioncloning by indirect extraction methods. FEMS Microbiology Ecology,44:153-163.
Gafan GP, Spratt DA.2005. Denaturing gradient gel electrophoresis gel expansion (DGGEGE)-Anattempt to resolve the limitations of co-migration in the DGGE of complex polymicrobialcommunities. FEMS Microbiology Letters,253:303-307.
Gao XL, Song JM.2005. Phytoplankton distributions and their relationship with the environment inthe Changjiang Estuary, China. Marine Pollution Bulletin,50:327-335.
Garstecki T, Verhoeven R, Wickham SA, Arndt H.2000. Benthic-pelagic coupling: a comparison ofthe community structure of benthic and planktonic heterotrophic protists in shallow inlets of thesouthern Baltic. Freshwater Biology,45:147-167.
Griffiths, B.S., Ritz, K.,1988. A technique to extract, enumerate and measure protozoa from mineralsoils. Soil Biology&Biochemistry,20:163-173.
Gomes NC, Fagbola O, Costa R, Rumjanek NG, Buchner A, Mendona-Hagler L, Smalla K.2003.Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Applied andEnvironmental Microbiology,69:3758-3766.
Guidot A, Debaud JC, Marmeisse R.2002. Spatial distribution of the below-ground mycelia of anectomycorrhizal fungus inferred from specific quantification of its DNA in soil samples. FEMSMicrobiology Ecology,42:477-486.
Hall TA.1999. BioEdit: a user-friendly biological sequence alignment editor and analysis programfor Windows95/98/NT. Nucleic Acids Symposium Series,41:95-98.
Hamels I, Sabbe K, Muylaert K, Vyverman W.2004. Quantitative importance, composition, andseasonal dynamics of protozoan communities in polyhaline versus freshwater intertidalsediments. Microbial Ecology,47:18-29.
Hamilton HC, Strickland MS, Wickings K, Bradford MA, Fierer N.2009. Surveying soil faunalcommunities using a direct molecular approach. Soil Biology&Biochemistry,41:1311-1314.
Hatamoto M, Tanahashi T, Murase J, Hayashi M, Kimura M, Asakawa S.2008. Eukaryoticcommunities associated with the decomposition of rice straw compost in a Japanese rice paddyfield estimated by DGGE analysis. Biology and Fertility of Soils,44:527-532.
Hausmann K, Huelsmann N, Radek R.2003. Protistology. Schweizernart’sche Verlagsbuchhandlung,Stuttgart.
Hausmann K, Hülsmann N, Polianski I, Schade S, Weitere M.2002. Composition of benthicprotozoan communities along a depth transect in the eastern Mediterranean Sea. Deep-SeaResearch Part I-Oceanographic Research Papers,49:1959-1970.
He J, Xu Z, Hughes J.2005a. Pre-lysis washing improves DNA extraction from a forest soil. SoilBiology&Biochemistry,37:2337-2341.
He J, Xu Z, Hughes J.2005b. Analyses of soil fungal communities in adjacent natural forest andhoop pine plantation ecosystems of subtropical Australia using molecular approaches based on18S rRNA genes. FEMS Microbiology Letters,247:91-100.
He J.2008. Molecular biological studies of soil microbial communities under different managementpractices in forest ecosystems of Queensland. Germany: VDM Verlag.
He Y, Xu K.2011. Morphology and small subunit rDNA phylogeny of a new soil ciliate, Bistichellavariabilis n. sp.(Ciliophora, Stichotrichia). Journal of Eukaryotic Microbiology,58:332–338.
Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR., Jurkonie DD, Ficke A, Maldonado-RamirezS, Lynch ST, Nelson EB.2000. Methods for assessing the composition and diversity of soilmicrobial communities. Applied Soil Ecology,15:25-36.
Hirsch PR, Mauchline TH, Clark IM.2010. Culture-independent molecular techniques for soilmicrobial ecology. Soil Biology&Biochemistry,42:878-887.
Hollister EB, Engledow AS, Hammett AJM, Provin TL, Wilkinson HH, Gentry TJ.2010. Shifts inmicrobial community structure along an ecological gradient of hypersaline soils and sediments.ISME Journal,4:829-838.
Hunt HW, Coleman DC, Ingham ER, Ingham RE, Elliott ET, Moore JC, Rose SL, Reid CPP, MorleyCR.1987. The detrital food web in a shortgrass prairie. Biology and Fertility of Soils,3:57-68.
Hurt RA, Qiu X, Wu L, Roh Y, Palumbo AV, Tiedje JM, Zhou JH.2001. Simultaneous recovery ofRNA and DNA from soils and sediments. Applied and Environmental Microbiology,67:4495-4503.
Huws SA, McBain AJ, Gilbert P.2005. Protozoan grazing and its impact upon population dynamicsin biofilm communities. Journal of Applied Microbiology,98:238-244.
Ikenaga M, Guevara R, Dean AL, Pisani C, Boyer JN.2010. Changes in community structure ofsediment bacteria along the Florida coastal everglades marsh-mangrove-seagrass salinitygradient. Microbial Ecology,59:284-295.
Inceoglu O, Salles JF, van Overbeek L, van Elsas JD.2010. Effects of plant genotype and growthstage on the Betaproteobacterial communities associated with different potato cultivars in twofields. Applied and Environmental Microbiology,76:3675-3684.
Ishii H, Katsukoshi K.2010. Seasonal and vertical distribution of Aurelia aurita polyps on a pylon inthe innermost part of Tokyo bay. Journal of Oceanography,66:329-336.
Ishii H, Ohba T, Kobayasi T.2008. Effects of low dissolved oxygen on planula settlement, polypgrowth and asexual reproduction of Aurelia aurita. Plankton&Benthos Research,3:107-113.
Jackson CR, Langner HW, Donahoe-Christiansen J, Inskeep WP, McDermott TR.2001. Molecularanalysis of microbial community structure in an arsenite-oxidizing acidic thermal spring.Environmental Microbiology,3:532-542.
Jerome CA, Montagnes DJS, Taylor FJR.1993. The effect of the quantitative protargol stain andLugol’s and Bouin’s fixatives on cell size: a more accurate estimate of ciliate species biomass.Journal of Eukaryotic Microbiology,40:254-259.
Jiao N, Zhang Y, Zeng Y, Gardner W, Mishonov A, Richardson MJ, Hong N, Pan D, Yan X, Jo Y,Chen C, Wang P, Chen Y, Hong H, Bai Y, Chen X, Huang B, Deng H, Shi Y, Yang D.2007.Ecological anomalies in the East China Sea: Impacts of the three gorges dam? Water Research,41:1287-1293.
Jousset A, Lara E, Nikolausz M, Harms H, Chatzinotas A.2010. Application of the denaturinggradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliatecommunities in soil. Science of the Total Environment,408:1221-1225.
Kamiyama T.2011. Planktonic ciliates as a food source for the scyphozoan Aurelia aurita (s.l.):Feeding activity and assimilation of the polyp stage. Journal of Experimental Marine Biologyand Ecology,407:207-215.
Kang S, Mills AL.2006. The effect of sample size in studies of soil microbial community structure.Journal of Microbiological Methods,66:242-250.
Kellogg CA, Griffin DW.2006. Aerobiology and the global transport of desert dust. Trends inEcology&Evolution,21:638-644.
Klammer S, Mondini C, Insam H.2005. Microbial community fingerprints of composts stored underdifferent conditions. Annals of Microbiology,55:299-305.
Kleinsteuber S, Riis V, Fetzer I, Harms H, Müller S.2006. Population dynamics within a microbialconsortium during growth on diesel fuel in saline environments. Applied and EnvironmentalMicrobiology,72:3531-3542.
Lakay FM, Botha A, Prior BA.2007. Comparative analysis of environmental DNA extraction andpurification methods from different humic acid-rich soils. Journal of Applied Microbiology,102:265-273.
Lakhdar A, Rabhi M, Ghnaya T, Montemurro F, Jedidi N, Abdelly C.2009. Effectiveness ofcompost use in salt-affected soil. Journal of Hazardous Materials,171:29-37.
Lara E, Berney C, Harms H, Chatzinotas A.2007a. Cultivation-independent analysis reveals a shiftin ciliate18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil. FEMSMicrobiology Ecology,62:365-373.
Lara E, Berney C, Ekelund F, Harms H, Chatzinotas A.2007b. Molecular comparison of cultivableprotozoa from a pristine and a polycyclic aromatic hydrocarbon polluted site. Soil Biology&Biochemistry,39:139-148.
Lara E, Mitchell EAD, Moreira D, López-García P.2011. Highly diverse and seasonally dynamicprotist community in a pristine peat bog. Protist,162:14-32.
Lara E, Acosta-Mercado D.2012. A molecular perspective on ciliates as soil bioindicators.European Journal of Soil Biology,49:107-111.
Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N.2010. Effect of storage conditions on theassessment of bacterial community structure in soil and human-associated samples. FEMSMicrobiology Letters,307:80-86.
Lawley B, Ripley S, Bridge P, Convey P.2004. Molecular analysis of geographic patterns ofeukaryotic diversity in Antarctic soils. Applied and Environmental Microbiology,70:5963-5972.
Levin LA, Ekau W, Gooday AJ, Jorissen F, Middelburg JJ, Naqvi SWA, Neira C, Rabalais NN,Zhang J.2009. Effects of natural and human-induced hypoxia on coastal benthos.Biogeosciences,6:2063-2098.
Levin LA, Gutiérrez D, Rathburn AE, Neira C, Sellanes J, Munoz P, Gallardo VA, Salamanca MA.2002. Benthic processes on the Peru margin: A transect across the oxygen minimum zoneduring the1997–98El Nino. Progress in Oceanography,53:1-27.
Lim EL, Caron DA, Delong EF.1996. Development and field application of a quantitative methodfor examining natural assemblages of protists with oligonucleotide probes. Applied andEnvironmental Microbiology,62:1416-1423.
Liu L, Yang J, Zhang Y.2011. Genetic diversity patterns of microbial communities in a subtropicalriverine ecosystem (Jiulong River, southeast China). Hydrobiologia,678:113-125.
Liu L, Zhang D, Lv H, Yu X, Yang J.2012. Plankton communities along a subtropical urban river(Houxi River, southeast China) as revealed by morphological and molecular methods. Journalof Freshwater Ecology,28:99-112.
Long LK, Yao Q, Guo J, Yang RH, Huang YH, Zhu HH.2010. Molecular community analysis ofarbuscular mycorrhizal fungi associated with five selected plant species from heavy metalpolluted soils. European Journal of Soil Biology,46:288-294.
López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D.2001. Unexpected diversity ofsmall eukaryotes in deep-sea Antarctic plankton. Nature,409:603-607.
López-García P, Philippe H, Gail F, Moreira D.2003. Autochthonous eukaryotic diversity inhydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge.Proceedings of the National Academy of Sciences of the United States of America,100:697-702.
Lozupone CA, Knight R.2007. Global patterns in bacterial diversity. Proceedings of the NationalAcademy of Sciences of the United States of America,104:11436-11440.
Lueders T, Wagner B, Claus P, Friedrich MW.2004. Stable isotope probing of rRNA and DNAreveals a dynamic methylotroph community and trophic interactions with fungi and protozoa inoxic rice field soil. Environmental Microbiology,6:60-72.
Lüftenegger G, Petz W, Foissner W, Adam H.1988. The efficiency of a direct counting method inestimating the numbers of microscopic soil organisms. Pedobiologia,31:95-101.
Lynn DH, Small EB.2002. Phylum Ciliophora, in: Lee JJ, Bradbury PC, Leedale GF.(ed.), AnIllustrated Guide to the Protozoa, Society of Protozoologists, Lawrence, Kansas.
Magurran AE.1988. Ecological diversity and its measurement. Princeton University Press,Princeton, New Jersey.
Mardis ER.2008. The impact of next-generation sequencing technology on genetics. Trends inGenetics,24:133-141
Maron PA, Schimann H, Ranjard L, Brothier E, Domenach AM, Lensi R, Nazaret S.2006.Evaluation of quantitative and qualitative recovery of bacterial communities from different soiltypes by density gradient centrifugation. European Journal of Soil Biology,42:65-73.
Mayzlish E, Steinberger Y.2004. Effects of chemical inhibitors on soil protozoan dynamics in adesert ecosystem. Biology and Fertility of Soils,39:415-421.
McGrath CL, Katz LA.2004. Genome diversity in microbial eukaryotes. Trends in Ecology&Evolution,19:32-38.
Medinger R, Nolte V, Pandey RV, Jost S, Ottenwaelder B, Schloetterer C, Boenigk J.2010.Diversity in a hidden world: potential and limitation of next-generation sequencing for surveysof molecular diversity of eukaryotic microorganisms. Molecular Ecology,19:32-40.
Meng Z, Xu K, Lei Y.2011. Community composition, distribution, and contribution ofmicrobenthos in offshore sediments from the Yellow Sea. Continental Shelf Research,31:1437-1446.
Meng Z, Xu K, Dai R, Lei Y.2012. Ciliate community structure, diversity and trophic role inoffshore sediments from the Yellow Sea. European Journal of Protistology,48:73-84.
Miller DN.2001. Evaluation of gel filtration resins for the removal of PCR-inhibitory substancesfrom soils and sediments. Journal of Microbiological Methods,44:49-58.
Mitchell KR, Takacs-Vesbach CD.2008. A comparison of methods for total community DNApreservation and extraction from various thermal environments. Journal of IndustrialMicrobiology&Biotechnology,35:1139-1147.
Monroy F, van der Putten WH, Yergeau E, Mortimer SR, Duyts H, Bezemer TM.2012. Communitypatterns of soil bacteria and nematodes in relation to geographic distance. Soil Biology&Biochemistry,45:1-7.
Montagnes DJS, Lynn DH.1987. A quantitative protargol stain (QPS) for ciliates: Methoddescription and test of its quantitative nature. Marine Microbial Food Webs,2:83-93.
Moon-van der Staay SY, Tzeneva VA, van der Staay GWM, de Vos WM, Smidt H, Hackstein JHP.2006. Eukaryotic diversity in historical soil samples. FEMS Microbiology Ecology,57:420-428.
Moreira D, López-García P.2002. The molecular ecology of microbial eukaryotes unveils a hiddenworld. Trends in Microbiology,10:31-38.
Murray SA, Patterson DJ, Thessen AE.2012. Transcriptomics and microbial eukaryote diversity: away forward. Trends in Ecology&Evolution,27:651-652.
Muyzer G, Dewaal EC, Uitterlinden AG.1993. Profiling of complex microbial-populations bydenaturing gradient gel-electrophoresis analysis of polymerase chain reaction-coding for16Sribosomal-RNA. Applied and Environmental Microbiology,59:695-700.
Mylnikov AP, Karpov SA.2004. Review of the diversity and taxonomy of cercomonads.Protistology,3:201-217.
Neira C, Sellanes J, Levin LA, Arntz WE.2001. Meiofaunal distributions on the Peru margin:relationship to oxygen and organic matter availability. Deep-Sea Research Part I,48:2453-2472.
Nekola JC, White PS.1999. The distance decay of similarity in biogeography and ecology. Journalof Biogeography,26:867-878
Ning J, Liebich J, Kastner M, Zhou J, Schaffer A, Burauel P.2009. Different influences of DNApurity indices and quantity on PCR-based DGGE and functional gene microarray in soilmicrobial community study. Applied Microbiology and Biotechnology,82:983-993.
Oren A.2008. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. SalineSystems,4:2.
O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R.2005. Fungal community analysisby large-scale sequencing of environmental samples. Applied and Environmental Microbiology,71:5544-5550.
Oros-Sichler M, Gomes NCM, Neuber G, Smalla, K.2006. A new semi-nested PCR protocol toamplify large18S rRNA gene fragments for PCR-DGGE analysis of soil fungal communities.Journal of Microbiological Methods,65:63-75.
Orsi W, Song Y, Hallam S, Edgcomb V.2012. Effect of oxygen minimum zone formation oncommunities of marine protists. ISME Journal,6:1586-1601.
Pawlowski J, Holzmann M.2008. Diversity and geographic distribution of benthic foraminifera: amolecular perspective. Biodiversity and Conservation,17;317-328.
Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, Guillou L.2011.Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One,6.
Persoh D, Theuerl S, Buscot F, Rambold, G.2008. Towards a universally adaptable method forquantitative extraction of high-purity nucleic acids from soil. Journal of MicrobiologicalMethods,75:19-24.
Petz W, Foissner W.1989. The effects of mancozeb and lindane on the soil microfauna of a spruceforest: a field study using a completely randomized block design. Biology and Fertility of Soils,7:225-231.
Pfister G, Sonntag B, Posch T.1999. Comparison of a direct live count and an improved quantitativeprotargol stain (QPS) in determining abundance and cell volumes of pelagic freshwaterprotozoa. Aquatic Microbial Ecology,18:95-103.
Pokarzhevskii AD, van Straalen NM, Zaboev DP, Zaitsev AS.2003. Microbial links and elementflows in nested detrital food-webs. Pedobiologia,47:213-224.
Porteous LA, Seidler RJ, Watrud LS.1997. An improved method for purifying DNA from soil forpolymerase chain reaction amplification and molecular ecology applications. MolecularEcology,6:787-791.
Puitika T, Kasahara Y, Miyoshi N, Rambold G.2007. A taxon-specific oligonucleotide primer setfor PCR-based detection of soil ciliate. Microbes and Environments,22:78-81.
Putt M, Stoecker DK.1989. An experimentally determined carbon-volume ratio for marineoligotrichous ciliates from estuarine and coastal waters. Limnology and Oceanography,34:1097-1103
Rajendhran J, Gunasekaran P.2008. Strategies for accessing soil metagenome for desiredapplications. Biotechnology Advances,26:576-590.
Ranjard L, Lejon DPH, Mougel C, Schehrer, L., Merdinoglu, D., Chaussod, R.2003. Samplingstrategy in molecular microbial ecology: Influence of soil sample size on DNA fingerprintinganalysis of fungal and bacterial communities. Environmental Microbiology,5:1111-1120.
Richards TA, Bass D.2005. Molecular screening of free-living microbial eukaryotes: diversity anddistribution using a meta-analysis. Current Opinion in Microbiology,8:240-252.
Roose-Amsaleg CL, Garnier-Sillam E, Harry M.2001. Extraction and purification of microbialDNA from soil and sediment samples. Applied Soil Ecology,18:47-60.
Sardinha M, Muller T, Schmeisky H, Joergensen RG.2003. Microbial performance in soils along asalinity gradient under acidic conditions. Applied Soil Ecology,23:237-244.
Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J.2008. Innovativemethods for soil DNA purification tested in soils with widely differing characteristics. Appliedand Environmental Microbiology,74:2902-2907.
SAS Institute Inc.1989. SAS/STAT Users Guide. Version6,4th ed, vol.2. SAS Institute Inc, Cary,NC.
Schwarz MVJ, Frenzel P.2003. Population dynamics and ecology of ciliates (Protozoa, Ciliophora)in an anoxic rice field soil. Biology and Fertility of Soils,38:245-252.
Segers H, De Smet WH.2008. Diversity and endemism in Rotifera: a review, and Keratella Bory deSt Vincent. Biodiversity and Conservation,17:303-316.
Sherr EB, Sherr BF.1993. Preservation and storage of samples for enumeration of heterotrophicprotists, in: Kemp PF, Sherr BF, Sherr EB, Cole JJ.(Eds.), Handbook of Methods in AquaticMicrobial Ecology, Lewis Publishers.
Shoji J, Kudoh T, Takatsuji H, Kawaguchi O, Kasai A.2010. Distribution of moon jellyfish Aureliaaurita in relation to summer hypoxia in Hiroshima Bay, Seto Inland Sea. Estuarine Coastal andShelf Science,86:485-490.
Shoji J, Masuda R, Yamashita Y, Tanaka M.2005. Effect of low dissolved oxygen concentrations onbehavior and predation rates on red sea bream Pagrus major larvae by the jellyfish Aureliaaurita and by juvenile Spanish mackerel Scomberomorus niphonius. Marine Biology,147:863-868.
Sime-Ngando T, Hartmann HJ, Grolière CA.1990. Rapid quantification of planktonic ciliates:comparison of improved live counting with other methods. Applied and EnvironmentalMicrobiology,56:2234-2242.
Sime-Ngando TS, Grolière CA.1991. Quantitative effects of fixatives on the storage of freshwaterplanktonic ciliates. Archiv Für Protistenkunde,140:109-120.
Simon N, Lebot N, Marie D, Partensky F, Vaulot D.1995. Fluorescent in-situ hybridization withribosomal-RNA-targeted oligonucleotide probes to identify small phytoplankton by flow-cytometry. Applied and Environmental Microbiology,61:2506-2513.
Skibbe O.1994. An improved quantitative protargol stain for ciliates and other planktonic protists.Archiv Für Hydrobiologie,130:339-347.
Skillman LC, Toovey AF, Williams AJ, Wright, ADG.2006. Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability betweenEntodinium populations in sheep offered a hay-based diet. Applied and EnvironmentalMicrobiology,72:200-206.
Smalla K, Cresswell N, Mendoncahagler LC, Wolters A, Vanelsas JD.1993. Rapid DNA extractionprotocol from soil for polymerase chain reaction-mediated amplification. Journal of AppliedBacteriology,74:78-85.
Smith HG, Bobrov A, Lara E.2008. Diversity and biogeography of testate amoebae. Biodiversityand Conservation,17:329-343.
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ.2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedingsof the National Academy of Sciences of the United States of America,103:12115-12120.
Starink M, B r-Gilissen MJ, Bak RPM, Cappenberg TE.1994. Quantitative centrifugation to extractbenthic protozoa from freshwater sediments. Applied and Environmental Microbiology,60:167–173.
Stephenson SL, Schnittler M, Novozhilov YK.2008. Myxomycete diversity and distribution fromthe fossil record to the present. Biodiversity and Conservation,17:285-301.
Stewart FJ, Ulloa O, Delong EF.2012. Microbial metatranscriptomics in a permanent marineoxygen minimum zone. Environmental Microbiology,14:23-40.
Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner HW, Richards TA.2010. Multiplemarker parallel tag environmental DNA sequencing reveals a highly complex eukaryoticcommunity in marine anoxic water. Molecular Ecology,19:21-31.
Stoeck T, Taylor GT, Epstein SS.2003. Novel eukaryotes from the permanently anoxic CariacoBasin (Caribbean sea). Applied and Environmental Microbiology,69:5656-5663.
Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S.2007. Protistan diversity in the Arctic: acase of paleoclimate shaping modern biodiversity? PLoS One,2.
Strüder-Kypke MC, Wright ADG, Fokin SI, Lynn DH.2000. Phylogenetic relationships of thegenus Paramecium inferred from small subunit rRNA gene sequences. Molecular Phylogeneticsand Evolution,14:122-130.
Sugano A, Tsuchimoto H, Tun CC, Asakawa S, Kimura M.2007. Succession and phylogeneticprofile of eukaryotic communities in rice straw incorporated into a rice field: Estimation byPCR-DGGE and sequence analyses. Soil Science and Plant Nutrition,53:585-594.
Swofford DL.2002. Paup*. Phylogenetic analysis using parsimony (*and other methods). Version4.Sinauer Associates, Sunderland, MA.
Takishita K, Miyake H, Kawato M, Maruyama T.2005. Genetic diversity of microbial eukaryotes inanoxic sediment around fumaroles on a submarine caldera floor based on the small-subunitrDNA phylogeny. Extremophiles,9:185-196.
Taylor FJR, Hoppenrath M, Saldarriaga JF.2008. Dinoflagellate diversity and distribution.Biodiversity and Conservation,17:407-418.
ter Braak CJF, milauer P.2002. CANOCO reference manual and CanoDraw for windows user'sguide: software for canonical community ordination (version4.5). Microcomputer Power,Ithaca, New York.
Terrado R, Vincent WF, Lovejoy C.2009. Mesopelagic protists: diversity and succession in acoastal Arctic ecosystem. Aquatic Microbial Ecology,56:25-39.
Torsvik VL, Goksoyr J.1978. Determination of bacterial DNA in soil. Soil Biology&Biochemistry,10:7-12.
Tripathi S, Chakraborty A, Chakrabarti K, Bandyopadhyay BK.2007. Enzyme activities andmicrobial biomass in coastal soils of India. Soil Biology&Biochemistry,39:2840-2848.
Tsai YL, Olson BH.1991. Rapid method for direct extraction of DNA from soil and sediments.Applied and Environmental Microbiology,57:1070-1074.
Usher MB, Sier ARJ, Hornung M, Millard P.2006. Understanding biological diversity in soil: theUK's soil biodiversity research programme. Applied Soil Ecology,33:101-113.
Vaerewijck MJM, Sabbe K, Bare J, Houf K.2008. Microscopic and molecular studies of thediversity of free-living protozoa in meat-cutting plants. Applied and EnvironmentalMicrobiology,74:5741-5749.
Valenzuela-Encinas C, Neria-González I, Alcántara-Hernández RJ, Estrada-Alvarado I, Zavala-Díazde la Serna FJ, Dendooven L, Marsch R.2009. Changes in the bacterial populations of thehighly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.Extremophiles,13:609-621.
Vanormelingen P, Verleyen E, Vyverman W.2008. The diversity and distribution of diatoms: fromcosmopolitanism to narrow endemism. Biodiversity and Conservation,17:393-405.
Verhoeven R.2002. Ciliates in coastal dune soils of different stages of development. EuropeanJournal of Soil Biology,38:187-191.
Vigil P, Countway PD, Rose J, Lonsdale DJ, Gobler CJ, Caron DA.2009. Rapid shifts in dominanttaxa among microbial eukaryotes in estuarine ecosystems. Aquatic Microbial Ecology,54:83-100.
Wang J, Yang D, Zhang Y, Shen J, van der Gast C, Hahn MW, Wu Q.2011. Do patterns of bacterialdiversity along salinity gradients differ from those observed for macroorganisms? PLoS ONE,6.
Wang S, Li Q, Liang W, Jiang Y, Jiang S.2008. PCR-DGGE analysis of nematode diversity in Cu-contaminated soil. Pedosphere,18:621--627.
Weston NB, Porubsky WP, Samarkin VA, Erickson M, Macavoy SE, Joye SB.2006. Porewaterstoichiometry of terminal metabolic products, sulfate, and dissolved organic carbon andnitrogen in estuarine intertidal creek-bank sediments. Biogeochemistry,77:375-408.
Wickham S, Gieseke A, Berninger UG.2000. Benthic ciliate identification and enumeration: animproved methodology and its application. Aquatic Microbial Ecology,22:79-91.
Worden AZ, Allen AE.2010. The voyage of the microbial eukaryote. Current Opinion inMicrobiology,13:652-660.
Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP, Hahn MW.2006. Bacterioplanktoncommunity composition along a salinity gradient of sixteen high-mountain lakes located on theTibetan Plateau, China. Applied and Environmental Microbiology,72:5478-5485.
Wu Q, Chatzinotas A, Wang J, Boenigk J.2009. Genetic diversity of eukaryotic planktonassemblages in eastern Tibetan lakes differing by their salinity and altitude. Microbial Ecology,58:569-581.
Wu RSS.2002. Hypoxia: from molecular responses to ecosystem responses. Marine PollutionBulletin,45:35-45.
Wu T, Ayres E, Li G, Bardgett RD, Wall DH, Garey JR.2009. Molecular profiling of soil animaldiversity in natural ecosystems: incongruence of molecular and morphological results. SoilBiology&Biochemistry,41:849-857.
Xu K, Du Y, Lei Y, Dai R.2010. A practical method of Ludox density gradient centrifugationcombined with protargol staining for extracting and estimating ciliates in marine sediments.European Journal of Protistology,46:263-270.
Xu X, Lin H, Fu Z.2004. Probe into the method of regional ecological risk assessment-a case studyof wetland in the Yellow River delta in China. Journal of Environmental Management,70:253-262.
Yan Q, Yu Y, Feng W, Deng W, Song X.2007. Genetic diversity of plankton community asdepicted by PCR-DGGE fingerprinting and its relation to morphological composition andenvironmental factors in lake Donghu. Microbial Ecology,54:290-297.
Yu Y, Yan Q, Feng W.2008. Spatiotemporal heterogeneity of plankton communities in LakeDonghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation tobiotic and abiotic factors. FEMS Microbiology Ecology,63:328-337.
Zahran HH.1997. Diversity, adaptation and activity of the bacterial flora in saline environments.Biology and Fertility of Soils,25:211-223.
Zeng Y, Chen X, Jiao N.2007. Contrasting diversity pattern of Cytophaga-Flavobacteria in theestuarine and open ocean regions of the East China Sea. Marine Biology Research,3:428-437.
Zhang J, Zhang Z, Liu S, Wu Y, Xiong H, Chen H.1999. Human impacts on the large world rivers:Would the Changjiang (Yangtze River) be an illustration? Global Biogeochemical Cycles,13(4):1099-1106.
Zhang J, Su J.2006. Nutrient dynamics of the Chinese Seas: The Bohai, Yellow Sea, East China Seaand South China Sea, in:The Sea, Robinson AR, Brink KH (eds). Harvard University Press,Cambridge MA.
Zhang J, Liu SM, Ren JL, Wu Y, Zhang GL.2007. Nutrient gradients from the eutrophic Changjiang(Yangtze River) Estuary to the oligotrophic Kuroshio waters and re-evaluation of budgets forthe East China Sea Shelf. Progress in Oceanography,74:449–478.
Zhang L, Xu Z, Patel BKC.2009. An improved method for purifying genomic DNA from forest leaflitters and soil suitable for PCR. Journal of Soils and Sediments,9:261-266.
Zhao B, Chen M, Sun Y, Yang J, Chen F.2011. Genetic diversity of picoeukaryotes in eight lakesdiffering in trophic status. Canadian Journal of Microbiology,57:115-26.
Zhao F, Xu K.2012. Efficiency of DNA extraction methods on the evaluation of soilmicroeukaryotic diversity. Acta Ecologica Sinica,32:209-214.
Zhao F, Xu K, He Y.2012. Application of the Ludox-QPS method for estimating ciliate diversity insoil and comparison with direct count and DNA fingerprinting, European Journal of SoilBiology,49:112-118.
Zhao F, Xu K.2013. Microbial genetic diversity and ciliate community structure along anenvironmental gradient in coastal soil. European Journal of Protistology,doi:10.1016/j.ejop.2013.01.002.
Zhao F, Xu K, Zhang D.2013. Spatio-temporal variations in the molecular diversity ofmicroeukaryotes in particular ciliates in soil of the Yellow River Delta, China. Journal ofEukaryotic Microbiology, doi:10.1111/jeu.12035.
Zhou J, Bruns MA, Tiedje JM.1996. DNA recovery from soils of diverse composition. Applied andEnvironmental Microbiology,62:316-322.
曹志平,陈国康,张凯等.2005.不同土壤培肥措施对华北高产农田原生动物丰度的影响.生态学报,25(11):2992-2996.
陈春辉,王春生,许学伟等,2009.河口缺氧生物效应研究进展.生态学报,29(5):2595-2602.
陈素芳,徐润林.2003.土壤原生动物的研究进展.中山大学学报(自然科学版),42(增刊):187-194.
代仁海,2012.黄东海底栖纤毛虫多样性及微型底栖生物群落结构特点.中国科学院研究生院博士学位论文.
杜萍,刘晶晶,曾江宁等,2011.长江口低氧区异养细菌及氮磷细菌分布.应用生态学报,22(5):1316-1324.
冯伟松,余育和.2000.南极菲尔德斯半岛地区土壤原生动物生态学研究.水生生物学报,24(6):610-615.
冯旭文,于晓果,陈建芳等,2006.河口季节性缺氧在沉积物中记录的研究进展.海洋学研究,24(1):50-61.
高云超,朱文珊,陈文新.2000.土壤原生动物群落及其生态功能.生态学杂志,19(1):59-65.
顾宏堪,1980.黄海溶解氧垂直分布中的最大值.海洋学报,2:70-79.
郭非凡,史雅娟,孟凡乔等.2006.典型POPs物质对土壤原生动物丰度的影响.生态学报,26(1):70-74.
类彦立,徐奎栋.2007.海洋底栖原生动物生态学研究方法综述.海洋科学,31(5):49-57.
类彦立,徐奎栋.2008.底栖纤毛虫原生动物的生态学研究进展.水生生物学报,32:155-160.
类彦立,徐奎栋.2011.海洋微型底栖生物调查方法与操作规范.海洋与湖沼,42(1):157-164.
李洪波,肖天,丁涛等.2006.浮游细菌在黄海冷水团中的分布.生态学报,26(4):1012-1020.
李琦路,宁应之.2008.土壤生态环境中纤毛虫的研究与应用.西北师范大学学报(自然科学版),44(3):82-87.
李新正.2011.我国海洋大型底栖生物多样性研究及展望:以黄海为例.生物多样性,19(6):676–684.
廖庆玉,章金鸿,李玫等.2008.海南东寨港红树林土壤原生动物的群落结构特征.生态环境,17(3):1077-1081.
刘瑞玉等.2008.中国海洋生物名录.科学出版社,北京.
马正学,康瑞琴,孙宏飞等.2007.焦化废水污染土壤中原生动物的群落特征.西北师范大学学报(自然科学版),43(5):90-93.
孟昭翠,2011.黄海夏季微型底栖生物群落结构与生态特点.中国科学院研究生院博士学位论文.
宁应之,沈韫芬.1996.路咖山森林土壤原生动物生态学研究及土壤原生动物定量方法探讨.动物学研究,17(3):225-232.
屈佩,张学雷,王宗灵等.2010.南黄海夏季微微型浮游植物丰度的分布.海洋学报,32(4):155-167.
单秀娟,庄志猛,金显仕等.2011.长江口及其邻近水域大型水母资源量动态变化对渔业资源结构的影响.应用生态学报,22(12):3321-3328.
沈蕴芬等.2000.原生动物学.科学出版社,北京
宋微波等.1999.原生动物学专论.青岛海洋大学出版社,青岛
宋雪英,宋玉芳,孙铁珩等.2004.土壤原生动物对环境污染的生物指示作用.应用生态学报,15(10):1979-1982.
孙宏飞,马正学,宁应之等.2007.皮革废水污染的土壤原生动物生态效应.甘肃科学学报,19(1):82-84.
孙金凤,刘清志.2010.黄河三角洲风能资源评价及开发利用研究.资源与产业,12(4):107-112.
孙松,王荣,张光涛等.2002.黄海中华哲水蚤度夏机制,海洋与湖沼,浮游动物研究专辑,92-100.
唐启生.2006.中国专属经济区海洋生物资源与栖息环境.科学出版社,北京
王冬,宁应之,马正学等.2007.新疆石河子市蘑菇湖混合污水污染土壤中原生动物的群落特征.西北师范大学学报(自然科学版),43(1):83-86.
王家栋,类彦立,徐奎栋等.2011.黄海冷水团及周边海域夏初小型底栖动物现存量及空间分布研究.海洋与湖沼,42(3):359-366.
王丹,孙军,周锋等.2008.2006年6月长江口低氧区及邻近水域浮游植物.海洋与湖沼,39(6):619-627.
王延明,李道季,方涛等.2008.长江口及邻近海域底栖生物分布及与低氧区的关系研究.海洋环境科学,27(2):139-164.
韦钦胜,战闰,魏修华等.2010.夏季长江口东北部海域DO的分布及低氧特征.海洋科学进展,28(1):32-40.
杨庆霄,董娅婕,蒋岳文等.2001.黄海和东海海域溶解氧的分布特征.海洋环境科学,20(3):9-13.
尹文英等.2000.中国土壤动物.科学出版社,北京
徐奎栋.2011.海洋微型底栖生物的多样性和地理分布.生物多样性,19(6):661-675.
徐润林,孙逸湘.2000.大鹏半岛土壤纤毛虫的群落特点.应用生态学报,11(3):428-430.
赵延茂,宋朝枢.1994.黄河三角洲自然保护区科学考察集.中国林业出版社,北京.
张翠霞.2011.我国海区浮游纤毛虫的生态学研究.中国科学院研究生院博士学位论文.
张芳,孙松,李超伦.2009.海洋水母类生态学研究进展.自然科学进展,19(2):121-130.
张莹莹,张经,吴莹等.2007.长江口溶解氧的分布特征及影响因素研究.环境科学,28(8):1649-1654.
张竹琦. l990.黄海和东海北部夏季底层溶解氧最大值和最小值特征分析.海洋通报,9(4):22-26.
赵峰,徐奎栋,孟昭翠.2012.长江口低氧区沉积物表层纤毛虫多样性及其时空变化研究.应用生态学报,23(12):3441-3448.
郑元甲等.2003.东海大陆架生物资源与环境.上海科学技术出版社,上海.
周锋,黄大吉,倪晓波等.2010.影响长江口毗邻海域低氧区多种时间尺度变化的水文因素.生态学报,30(17):4728-4740.
周可新,许木启,曹宏等.2003.土壤原生动物在环境监测中的应用.动物学杂志,38(1):80-84.
Acosta-Mercado D, Lynn DH.2003. The edaphic quantitative protargol stain: A sampling protocolfor assessing soil ciliate abundance and diversity. Journal of Microbiological Methods,53:365-375.
Acosta-Mercado D, Lynn DH.2004. Soil ciliate species richness and abundance associated with therhizosphere of different subtropical plant species. Journal of Eukaryotic Microbiology,51:582-588.
Acosta-Mercado D, Lynn DH.2006. Contrasting soil ciliate species richness and abundance betweentwo tropical plant species: A test of the plant effect. Microbial Ecology,51:453-459.
Adl SM, Coleman DC.2005. Dynamics of soil protozoa using a direct count method. Biology andFertility of Soils,42:168-171.
Adl SM.2007. Motility and migration rate of protozoa in soil columns. Soil Biology&Biochemistry,39:700-703.
Aguilera A, Gomez F, Lospitao E, Amils R.2006. A molecular approach to the characterization ofthe eukaryotic communities of an extreme acidic environment: Methods for DNA extractionand denaturing gradient gel electrophoresis analysis. Systematic and Applied Microbiology,29:593-605.
Amann R, Fuchs BM, Behrens S.2001. The identification of microorganisms by fluorescence in situhybridization. Current Opinion in Biotechnology,12:231-236.
Anderson IC, Cairney JWG.2004. Diversity and ecology of soil fungal communities: Increasedunderstanding through the application of molecular techniques. Environmental Microbiology,6:769-779.
Angel R, Soares MIM, Ungar ED, Gillor O.2010. Biogeography of soil archaea and bacteria along asteep precipitation gradient. ISME Journal,4:553-563.
Ansorge WJ.2009. Next-generation DNA sequencing techniques. New Biotechnology,25:195-203.
Ascher J, Ceccherini MT, Pantani OL, Agnelli A, Borgogni F, Guerri G, Nannipieri P, PietramellaraG.2009. Sequential extraction and genetic fingerprinting of a forest soil metagenome. AppliedSoil Ecology,42:176-181.
Azam F, Fenchel T, Field JG, Gray JS, Meyerreil LA, Thingstad F.1983. The ecological role ofwater-column microbes in the sea. Marine Ecology Progress Series,10:257-263.
Bamforth SS.1991. Enumeration of soil ciliate active forms and cysts by a direct count method.Agriculture Ecosystems&Environment,34:209-212.
Bamforth SS.1995. Interpreting soil ciliate biodiversity. Plant Soil,170:159-164.
Bamforth SS.2001. Proportions of active ciliate taxa in soils. Biology and Fertility of Soils,33:197-203.
Bare J, Sabbe K, Van Wichelen J, D'Hondt S, Houf K.2009. Diversity and habitat specificity offree-living protozoa in commercial poultry houses. Applied and Environmental Microbiology,75:1417-1426.
Barrios E.2007. Soil biota, ecosystem services and land productivity. Ecological Economics,64:269-285.
Bass D, Cavalier-Smith T.2004. Phylum-specific environmental DNA analysis reveals remarkablyhigh global biodiversity of Cercozoa (Protozoa). International Journal of Systematic andEvolutionary Microbiology,54:2393-2404.
Bass D, Howe AT, Mylnikov AP, Vickerman K, Chao EE, Smallbone JE, Snell J, Cabral C, Cavalier-Smith T.2009. Phylogeny and classification of Cercomonadida (Protozoa, Cercozoa):Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. nov. Protist,160:483-521.
Benlloch S, López-López A, Casamayor EO, Ovreas L, Goddard V, Daae FL, Smerdon G, MassanaR, Joint I, Thingstad F, Pedros-Alio C, Rodriguez-Valera F.2002. Prokaryotic genetic diversitythroughout the salinity gradient of a coastal solar saltern. Environmental Microbiology,4:349-360.
Berney C, Fahrni J, Pawlowski J.2004. How many novel eukaryotic “kingdoms”? Pitfalls andlimitations of environmental DNA surveys. BMC Biology,2:13.
Bernhard JM, Bowser SS.1999. Benthic foraminifera of dysoxic sediments: chloroplastsequestration and functional morphology. Earth-Science Reviews,46:149-165.
Bernhard D, Stechmann A, Foissner W, Ammermann, D, Hehn M, Schlegel M.2001. Phylogeneticrelationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA genesequences. Molecular Phylogenetics and Evolution,21:86-92.
Berthold A, Bruckner A, Kampichler C.1999. Improved quantification of active soil microfauna bya “counting crew”. Biology and Fertility of Soils,28:352-355.
Berthold A, Palzenberger M.1995. Comparison between direct counts of active soil ciliates(protozoa) and most probable number estimates obtained by Singh’s dilution culture method.Biology and Fertility of Soils,19:348-356.
Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK.2012a.Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns indeep-sea and shallow water sediments. Molecular Ecology,21:1048-1059.
Bik HM, Halanych KM, Sharma J, Thomas WK.2012b. Dramatic shifts in benthic microbialeukaryote communities following the deepwater horizon oil spill. PLoS One,7.
Billen G, Lancelot C.1988. Modeling benthic nitrogen cycling in temperate coastal ecosystems. In:Nitrogen Cycling in the Coastal Marine Environment (eds Blackburn TH, Sorensen J), pp.341–378. Wiley and Sons, New York.
Bird E.2008. Coastal geomorphology: an introduction.2nd ed. John Wiley&Sons Ltd, the Atrium,Southern Gate, Chichester.
Bongers T, Ferris H.1999. Nematode community structure as a bioindicator in environmentalmonitoring. Trends in Ecology&Evolution,14:224-248.
Boon N, Marle C, Top EM, Verstraete W.2000. Comparison of the spatial homogeneity of physico-chemical parameters and bacterial16S rRNA genes in sediment samples from a dumping sitefor dredging sludge. Applied and Environmental Microbiology,53:742-747.
Breitburg DL, Crump BC, Dabiri JO, Gallegos CL.2010. Ecosystem engineers in the pelagic realm:alteration of habitat by species ranging from microbes to jellyfish. Integrative and ComparativeBiology,50:188-200.
Bremner JM, Mulvaney CS.1982. Nitrogen-total. In Page AL, Miller RH, Keeney DK.(Ed.),Methods of soil analysis. Part2. Chemical and microbiological properties. American Society ofAgronomy, Madison WI. USA.
Bridge P, Spooner B.2001. Soil fungi: diversity and detection. Plant Soil,232:147-154.
Brussaard L, de Ruiter PC, Brown GG.2007. Soil biodiversity for agricultural sustainability.Agriculture, Ecosystems&Environment,121:233-244.
Burgess R.2001. An improved protocol for separating meiofauna from sediments using colloidalsilica sols. Marine Ecology Progress Series,214:161-165.
Cabrol L, Malhautier L, Poly F, Lepeuple AS, Fanlo JL.2010. Assessing the bias linked to DNArecovery from biofiltration woodchips for microbial community investigation by fingerprinting.Applied Microbiology and Biotechnology,85:779-790.
Cao D, Shi F, Ruan W, Lu Z, Chai M.2011. Seasonal changes in and relationship between soilmicrobial and microfaunal communities in a Tamarix chinensis community in the Yellow RiverDelta. African Journal of Biotechnology,10:18425-18432.
Caron DA.2009. New accomplishments and approaches for assessing protistan diversity andecology in natural ecosystems. Bioscience,59:287-299.
Caron DA, Worden AZ, Countway PD, Demir E, Heidelberg KB.2009. Protists are microbes too: aperspective. ISME Journal,3:4-12.
Carrigg C, Rice O, Kavanagh S, Collins G, O'Flaherty V.2007. DNA extraction method affectsmicrobial community profiles from soils and sediment. Applied Microbiology andBiotechnology,77:955-964.
Casamayor EO, Massana R, Benlloch S, vre s L, Díez B, Goddard VJ, Gasol JM, Joint I,Rodriguez-Valera F, Pedrós-Alió C.2002. Changes in archaeal, bacterial and eukaryalassemblages along a salinity gradient by comparison of genetic fingerprinting methods in amultipond solar saltern. Environmental Microbiology,4:338-348.
Chandler DP.1998. Redefining relativity: quantitative PCR at low template concentrations forindustrial and environmental microbiology. Journal of Industrial Microbiology&Biotechnology,21:128-140.
Chao A, Li PC, Agatha S, Foissner W.2006. A statistical approach to estimate soil ciliate diversityand distribution based on data from five continents. Oikos,114:479-493.
Chen M, Li X, Yang Q, Chi X, Pan L, Chen N, Yang Z, Wang T, Wang M, Yu S.2012. Soileukaryotic microorganism succession as affected by continuous cropping of peanut-pathogenic and beneficial fungi were selected. PLoS One,7.
Chen X, Daniell TJ, Neilson R, O'Flaherty V, Griffiths BS.2010. A comparison of molecularmethods for monitoring soil nematodes and their use as biological indicators. European Journalof Soil Biology,46:319-324.
Choi JW, Stoecker DK.1989. Effects of fixation on cell-volume of marine planktonic protozoa.Applied and Environmental Microbiology,55:1761-1765.
Clarholm M.2005. Soil protozoa: an under-researched microbial group gaining momentum. SoilBiology&Biochemistry,37:811-817.
Clarke KR.1993. Non-parametric multivariate analyses of changes in community structure.Australian Journal of Ecology,18:117-143.
Coats WD, Heinbokel JF.1982. A study of reproduction and other life cycle phenomena inplanktonic protists using an acridine orange fluorescence technique. Marine Biology,67:71-79.
Coesel PFM, Krienitz L.2008. Diversity and geographic distribution of desmids and other coccoidgreen algae. Biodiversity and Conservation,17:381-392.
Condon RH, Decker MB, Purcell JE.2001. Effects of low dissolved oxygen on survival and asexualreproduction of scyphozoan polyps (Chrysaora quinquecirrha). Hydrobiologia,451:89-95.
Courtois S, Frostegard A, Goransson P, Depret G, Jeannin P, Simonet P.2001. Quantification ofbacterial subgroups in soil: comparison of DNA extracted directly from soil or from cellspreviously released by density gradient centrifugation. Environmental Microbiology,3:431-439.
Countway PD, Gast RJ, Savai P, Caron DA.2005. Protistan diversity estimates based on18S rDNAfrom seawater incubations in the western North Atlantic. Journal of Eukaryotic Microbiology,52:95-106.
Co teaux MM, Palka L.1988. A direct counting method for soil ciliates. Soil Biology&Biochemistry,20:7-10.
Co teaux MM, Darbyshire JF.1998a. Functional diversity amongst soil protozoa. Applied SoilEcology,10:229-237.
Co teaux MM, Raubuch M, Berg M.1998b. Response of protozoan and microbial communities invarious coniferous forest soils after transfer to forests with different levels of atmosphericpollution. Biology and Fertility of Soils,27:179-188.
Cytryn E, Minz D, Oremland RS, Cohen Y.2000. Distribution and diversity of archaeacorresponding to the limnological cycle of a hypersaline stratified lake (Solar Lake, Sinai,Egypt). Applied and Environmental Microbiology,66:3269-3276.
Daniel R.2005. The metagenomics of soil. Nature Reviews Microbiology,3:470-478.
Dang H, Zhang X, Sun J, Li T, Zhang Z, Yang G.2008. Diversity and spatial distribution ofsediment ammonia-oxidizing crenarchaeota in response to estuarine and environmentalgradients in the Changjiang Estuary and East China Sea. Microbiology,154:2084-2095.
Darby BJ, Housman DC, Zaki AM, Shamout, Y., Adl, S. M., Belnap, J., Neher, D. A.2006. Effectsof altered temperature and precipitation on desert protozoa associated with biological soil crusts.Journal of Eukaryotic Microbiology,53:507-514.
De Lipthay JR, Enzinger C, Johnsen K, Aamand J, Sorensen SJ.2004. Impact of DNA extractionmethod on bacterial community composition measured by denaturing gradient gelelectrophoresis. Soil Biology&Biochemistry,36:1607-1614.
Díez B, Pedrós-Alió C, Marsh TL, Massana R.2001. Application of denaturing gradient gelelectrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages andcomparison of DGGE with other molecular techniques. Applied and EnvironmentalMicrobiology,67:2942-2951.
Doherty M, Tamura M, Vriezen JAC, McManus GB, Katz LA.2010. Diversity of Oligotrichia andChoreotrichia ciliates in coastal marine sediments and in overlying plankton. Applied andEnvironmental Microbiology,76:3924-3935.
Dong D, Yan A, Liu H, Zhang X, Xu Y.2006. Removal of humic substances from soil DNA usingaluminium sulfate. Journal of Microbiological Methods,66:217-222.
Dopheide A, Lear G, Stott R, Lewis G.2009. Relative diversity and community structure of ciliatesin stream biofilms according to molecular and microscopy methods. Applied andEnvironmental Microbiology,75:5261-5272.
Du Y, Xu K, Lei Y.2009. Simultaneous enumeration of diatom, protozoa and meiobenthos frommarine sediments using Ludox-QPS method. Chinese Journal of Oceanology and Limnology,27:775-783.
Du Y, Xu K, Warren A, Lei Y, Dai R.2012. Benthic ciliate and meiofaunal communities in twocontrasting habitats of an intertidal estuarine wetland. Journal of Sea Research,70:50-63.
Edgcomb VP, Kysela DT, Teske A, Gomez AD, Sogin ML.2002. Benthic eukaryotic diversity inthe Guaymas Basin hydrothermal vent environment. Proceedings of the National Academy ofSciences of the United States of America,99:7658-7662.
Edgcomb V, Orsi W, Bunge J, Jeon S, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, VarelaR, Epstein S.2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. I.Pyrosequencing vs Sanger insights into species richness. ISME Journal,5:1344-1356.
Edmonds JW, Weston NB, Joye SB, Mou X, Moran MA.2009. Microbial community response toseawater amendment in low-salinity tidal sediments. Microbial Ecology,58:558-68.
Emmerling C, Schloter M, Hartmann A, Kandeler, E.2002. Functional diversity of soil organisms-a review of recent research activities in Germany. Journal of Plant Nutrition and Soil Science,165:408-420.
Epstein S, López-García P.2008."Missing" protists: a molecular prospective. Biodiversity andConservation,17:261-276.
Fawley MJ, Fawley KP, Buchheim MA.2004. Molecular diversity among communities offreshwater microchlorophytes. Microbial Ecology,48:489-499.
Fenchel T, Finlay BJ.2004. The ubiquity of small species: Patterns of local and global diversity.Bioscience,54:777-784.
Feng BW, Li XR, Wang JH, Hu ZY, Meng H, Xiang LY, Quan ZX.2009. Bacterial diversity ofwater and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMSMicrobiology Ecology,70:236-248.
Fierer N, Jackson RB.2006. The diversity and biogeography of soil bacterial communities.Proceedings of the National Academy of Sciences of the United States of America,103:626-631.
Finlay BJ.2002. Global dispersal of free-living microbial eukaryote species. Science,296:1061-1063.
Finlay BJ, Black HIJ, Brown S, Clarke KJ, Esteban GF, Hindle RM, Olmo JL, Rollett A, VickermanK.2000. Estimating the growth potential of the soil protozoan community. Protist,151:69-80.
Finlay BJ, Clarke KJ.1999. Ubiquitous dispersal of microbial species. Nature,400:828-828.
Finlay BJ, Esteban GF, Fenchel T.1996. Global diversity and body size. Nature,383:132-133.
First MR.2008. Benthic microbial food webs: apatial and temporal variations and the role ofheterotrophic protists in salt marsh sediments. The University of Georgia, USA.
Foissner W.1987. Soil protozoa: fundamental problems, ecological significance, adaptations inciliates and testaceans, bioindicators, and guide to the literature. Progress in Protistology,2:69-212.
Foissner W.1991. Basic light and scanning electron microscopic methods for taxonomic studies ofciliated protozoa. European Journal of Protistology,27:313-330.
Foissner W.1993. Colpodea (Ciliophora), Gustav Fischer Verlag, New York.
Foissner W.1997. Protozoa as bioindicators in agroecosystems, with emphasis on farming practices,biocides, and biodiversity. Agriculture Ecosystems&Environment,62:93-103.
Foissner W.1999a. Soil protozoa as bioindicators: Pros and cons, methods, diversity, representativeexamples. Agriculture Ecosystems&Environment,74:95-112.
Foissner W.1999b. Protist diversity: Estimates of the near-imponderable. Protist,150:363-368.
Foissner W.2008. Protist diversity and distribution: some basic considerations. Biodiversity andConservation,17:235-242.
Foissner W, Agatha S, Berger H.2002. Soil ciliates (Protozoa, Ciliophora) from Namibia(Southwest Africa), with emphasis on two contrasting environments, the Etosha Region and theNamib Desert. Denisia5:1-1459.
Foissner W, Chao A, Katz LA.2008. Diversity and geographic distribution of ciliates (Protista:Ciliophora). Biodiversity and Conservation,17:345-363.
Fontaine M, Guillot E.2002. Development of a TaqMan quantitative PCR assay specific forCryptosporidium parvum. FEMS Microbiology Letters,214:13-17.
Frahm JP.2008. Diversity, dispersal and biogeography of bryophytes (mosses). Biodiversity andConservation,17:277-284.
Freeman KR, Martin AP, Karki D, Lynch RC, Mitter MS, Meyer AF, Longcore JE, Simmons DR,Schmidt SK.2009. Evidence that chytrids dominate fungal communities in high-elevation soils.Proceedings of the National Academy of Sciences of the United States of America,106(43):18315-18320.
Fredslund L, Ekelund F, Jacobsen CS, Johnsen K.2001. Development and application of a most-probable-number-PCR assay to quantify flagellate populations in soil samples. Applied andEnvironmental Microbiology,67:1613-1618.
Fortin N, Beaumier D, Lee K, Greer CW.2004. Soil washing improves the recovery of totalcommunity DNA from polluted and high organic content sediments. Journal of MicrobiologicalMethods,56:181-191.
Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S,Gillet F, Aragno M, Rossi P.2002. Statistical analysis of denaturing gel electrophoresis (DGE)fingerprinting patterns. Environmental Microbiology,4:634-643.
Gabor EM, de Vries EJ, Janssen DB.2003. Efficient recovery of environmental DNA for expressioncloning by indirect extraction methods. FEMS Microbiology Ecology,44:153-163.
Gafan GP, Spratt DA.2005. Denaturing gradient gel electrophoresis gel expansion (DGGEGE)-Anattempt to resolve the limitations of co-migration in the DGGE of complex polymicrobialcommunities. FEMS Microbiology Letters,253:303-307.
Gao XL, Song JM.2005. Phytoplankton distributions and their relationship with the environment inthe Changjiang Estuary, China. Marine Pollution Bulletin,50:327-335.
Garstecki T, Verhoeven R, Wickham SA, Arndt H.2000. Benthic-pelagic coupling: a comparison ofthe community structure of benthic and planktonic heterotrophic protists in shallow inlets of thesouthern Baltic. Freshwater Biology,45:147-167.
Griffiths, B.S., Ritz, K.,1988. A technique to extract, enumerate and measure protozoa from mineralsoils. Soil Biology&Biochemistry,20:163-173.
Gomes NC, Fagbola O, Costa R, Rumjanek NG, Buchner A, Mendona-Hagler L, Smalla K.2003.Dynamics of fungal communities in bulk and maize rhizosphere soil in the tropics. Applied andEnvironmental Microbiology,69:3758-3766.
Guidot A, Debaud JC, Marmeisse R.2002. Spatial distribution of the below-ground mycelia of anectomycorrhizal fungus inferred from specific quantification of its DNA in soil samples. FEMSMicrobiology Ecology,42:477-486.
Hall TA.1999. BioEdit: a user-friendly biological sequence alignment editor and analysis programfor Windows95/98/NT. Nucleic Acids Symposium Series,41:95-98.
Hamels I, Sabbe K, Muylaert K, Vyverman W.2004. Quantitative importance, composition, andseasonal dynamics of protozoan communities in polyhaline versus freshwater intertidalsediments. Microbial Ecology,47:18-29.
Hamilton HC, Strickland MS, Wickings K, Bradford MA, Fierer N.2009. Surveying soil faunalcommunities using a direct molecular approach. Soil Biology&Biochemistry,41:1311-1314.
Hatamoto M, Tanahashi T, Murase J, Hayashi M, Kimura M, Asakawa S.2008. Eukaryoticcommunities associated with the decomposition of rice straw compost in a Japanese rice paddyfield estimated by DGGE analysis. Biology and Fertility of Soils,44:527-532.
Hausmann K, Huelsmann N, Radek R.2003. Protistology. Schweizernart’sche Verlagsbuchhandlung,Stuttgart.
Hausmann K, Hülsmann N, Polianski I, Schade S, Weitere M.2002. Composition of benthicprotozoan communities along a depth transect in the eastern Mediterranean Sea. Deep-SeaResearch Part I-Oceanographic Research Papers,49:1959-1970.
He J, Xu Z, Hughes J.2005a. Pre-lysis washing improves DNA extraction from a forest soil. SoilBiology&Biochemistry,37:2337-2341.
He J, Xu Z, Hughes J.2005b. Analyses of soil fungal communities in adjacent natural forest andhoop pine plantation ecosystems of subtropical Australia using molecular approaches based on18S rRNA genes. FEMS Microbiology Letters,247:91-100.
He J.2008. Molecular biological studies of soil microbial communities under different managementpractices in forest ecosystems of Queensland. Germany: VDM Verlag.
He Y, Xu K.2011. Morphology and small subunit rDNA phylogeny of a new soil ciliate, Bistichellavariabilis n. sp.(Ciliophora, Stichotrichia). Journal of Eukaryotic Microbiology,58:332–338.
Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR., Jurkonie DD, Ficke A, Maldonado-RamirezS, Lynch ST, Nelson EB.2000. Methods for assessing the composition and diversity of soilmicrobial communities. Applied Soil Ecology,15:25-36.
Hirsch PR, Mauchline TH, Clark IM.2010. Culture-independent molecular techniques for soilmicrobial ecology. Soil Biology&Biochemistry,42:878-887.
Hollister EB, Engledow AS, Hammett AJM, Provin TL, Wilkinson HH, Gentry TJ.2010. Shifts inmicrobial community structure along an ecological gradient of hypersaline soils and sediments.ISME Journal,4:829-838.
Hunt HW, Coleman DC, Ingham ER, Ingham RE, Elliott ET, Moore JC, Rose SL, Reid CPP, MorleyCR.1987. The detrital food web in a shortgrass prairie. Biology and Fertility of Soils,3:57-68.
Hurt RA, Qiu X, Wu L, Roh Y, Palumbo AV, Tiedje JM, Zhou JH.2001. Simultaneous recovery ofRNA and DNA from soils and sediments. Applied and Environmental Microbiology,67:4495-4503.
Huws SA, McBain AJ, Gilbert P.2005. Protozoan grazing and its impact upon population dynamicsin biofilm communities. Journal of Applied Microbiology,98:238-244.
Ikenaga M, Guevara R, Dean AL, Pisani C, Boyer JN.2010. Changes in community structure ofsediment bacteria along the Florida coastal everglades marsh-mangrove-seagrass salinitygradient. Microbial Ecology,59:284-295.
Inceoglu O, Salles JF, van Overbeek L, van Elsas JD.2010. Effects of plant genotype and growthstage on the Betaproteobacterial communities associated with different potato cultivars in twofields. Applied and Environmental Microbiology,76:3675-3684.
Ishii H, Katsukoshi K.2010. Seasonal and vertical distribution of Aurelia aurita polyps on a pylon inthe innermost part of Tokyo bay. Journal of Oceanography,66:329-336.
Ishii H, Ohba T, Kobayasi T.2008. Effects of low dissolved oxygen on planula settlement, polypgrowth and asexual reproduction of Aurelia aurita. Plankton&Benthos Research,3:107-113.
Jackson CR, Langner HW, Donahoe-Christiansen J, Inskeep WP, McDermott TR.2001. Molecularanalysis of microbial community structure in an arsenite-oxidizing acidic thermal spring.Environmental Microbiology,3:532-542.
Jerome CA, Montagnes DJS, Taylor FJR.1993. The effect of the quantitative protargol stain andLugol’s and Bouin’s fixatives on cell size: a more accurate estimate of ciliate species biomass.Journal of Eukaryotic Microbiology,40:254-259.
Jiao N, Zhang Y, Zeng Y, Gardner W, Mishonov A, Richardson MJ, Hong N, Pan D, Yan X, Jo Y,Chen C, Wang P, Chen Y, Hong H, Bai Y, Chen X, Huang B, Deng H, Shi Y, Yang D.2007.Ecological anomalies in the East China Sea: Impacts of the three gorges dam? Water Research,41:1287-1293.
Jousset A, Lara E, Nikolausz M, Harms H, Chatzinotas A.2010. Application of the denaturinggradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliatecommunities in soil. Science of the Total Environment,408:1221-1225.
Kamiyama T.2011. Planktonic ciliates as a food source for the scyphozoan Aurelia aurita (s.l.):Feeding activity and assimilation of the polyp stage. Journal of Experimental Marine Biologyand Ecology,407:207-215.
Kang S, Mills AL.2006. The effect of sample size in studies of soil microbial community structure.Journal of Microbiological Methods,66:242-250.
Kellogg CA, Griffin DW.2006. Aerobiology and the global transport of desert dust. Trends inEcology&Evolution,21:638-644.
Klammer S, Mondini C, Insam H.2005. Microbial community fingerprints of composts stored underdifferent conditions. Annals of Microbiology,55:299-305.
Kleinsteuber S, Riis V, Fetzer I, Harms H, Müller S.2006. Population dynamics within a microbialconsortium during growth on diesel fuel in saline environments. Applied and EnvironmentalMicrobiology,72:3531-3542.
Lakay FM, Botha A, Prior BA.2007. Comparative analysis of environmental DNA extraction andpurification methods from different humic acid-rich soils. Journal of Applied Microbiology,102:265-273.
Lakhdar A, Rabhi M, Ghnaya T, Montemurro F, Jedidi N, Abdelly C.2009. Effectiveness ofcompost use in salt-affected soil. Journal of Hazardous Materials,171:29-37.
Lara E, Berney C, Harms H, Chatzinotas A.2007a. Cultivation-independent analysis reveals a shiftin ciliate18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil. FEMSMicrobiology Ecology,62:365-373.
Lara E, Berney C, Ekelund F, Harms H, Chatzinotas A.2007b. Molecular comparison of cultivableprotozoa from a pristine and a polycyclic aromatic hydrocarbon polluted site. Soil Biology&Biochemistry,39:139-148.
Lara E, Mitchell EAD, Moreira D, López-García P.2011. Highly diverse and seasonally dynamicprotist community in a pristine peat bog. Protist,162:14-32.
Lara E, Acosta-Mercado D.2012. A molecular perspective on ciliates as soil bioindicators.European Journal of Soil Biology,49:107-111.
Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N.2010. Effect of storage conditions on theassessment of bacterial community structure in soil and human-associated samples. FEMSMicrobiology Letters,307:80-86.
Lawley B, Ripley S, Bridge P, Convey P.2004. Molecular analysis of geographic patterns ofeukaryotic diversity in Antarctic soils. Applied and Environmental Microbiology,70:5963-5972.
Levin LA, Ekau W, Gooday AJ, Jorissen F, Middelburg JJ, Naqvi SWA, Neira C, Rabalais NN,Zhang J.2009. Effects of natural and human-induced hypoxia on coastal benthos.Biogeosciences,6:2063-2098.
Levin LA, Gutiérrez D, Rathburn AE, Neira C, Sellanes J, Munoz P, Gallardo VA, Salamanca MA.2002. Benthic processes on the Peru margin: A transect across the oxygen minimum zoneduring the1997–98El Nino. Progress in Oceanography,53:1-27.
Lim EL, Caron DA, Delong EF.1996. Development and field application of a quantitative methodfor examining natural assemblages of protists with oligonucleotide probes. Applied andEnvironmental Microbiology,62:1416-1423.
Liu L, Yang J, Zhang Y.2011. Genetic diversity patterns of microbial communities in a subtropicalriverine ecosystem (Jiulong River, southeast China). Hydrobiologia,678:113-125.
Liu L, Zhang D, Lv H, Yu X, Yang J.2012. Plankton communities along a subtropical urban river(Houxi River, southeast China) as revealed by morphological and molecular methods. Journalof Freshwater Ecology,28:99-112.
Long LK, Yao Q, Guo J, Yang RH, Huang YH, Zhu HH.2010. Molecular community analysis ofarbuscular mycorrhizal fungi associated with five selected plant species from heavy metalpolluted soils. European Journal of Soil Biology,46:288-294.
López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D.2001. Unexpected diversity ofsmall eukaryotes in deep-sea Antarctic plankton. Nature,409:603-607.
López-García P, Philippe H, Gail F, Moreira D.2003. Autochthonous eukaryotic diversity inhydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge.Proceedings of the National Academy of Sciences of the United States of America,100:697-702.
Lozupone CA, Knight R.2007. Global patterns in bacterial diversity. Proceedings of the NationalAcademy of Sciences of the United States of America,104:11436-11440.
Lueders T, Wagner B, Claus P, Friedrich MW.2004. Stable isotope probing of rRNA and DNAreveals a dynamic methylotroph community and trophic interactions with fungi and protozoa inoxic rice field soil. Environmental Microbiology,6:60-72.
Lüftenegger G, Petz W, Foissner W, Adam H.1988. The efficiency of a direct counting method inestimating the numbers of microscopic soil organisms. Pedobiologia,31:95-101.
Lynn DH, Small EB.2002. Phylum Ciliophora, in: Lee JJ, Bradbury PC, Leedale GF.(ed.), AnIllustrated Guide to the Protozoa, Society of Protozoologists, Lawrence, Kansas.
Magurran AE.1988. Ecological diversity and its measurement. Princeton University Press,Princeton, New Jersey.
Mardis ER.2008. The impact of next-generation sequencing technology on genetics. Trends inGenetics,24:133-141
Maron PA, Schimann H, Ranjard L, Brothier E, Domenach AM, Lensi R, Nazaret S.2006.Evaluation of quantitative and qualitative recovery of bacterial communities from different soiltypes by density gradient centrifugation. European Journal of Soil Biology,42:65-73.
Mayzlish E, Steinberger Y.2004. Effects of chemical inhibitors on soil protozoan dynamics in adesert ecosystem. Biology and Fertility of Soils,39:415-421.
McGrath CL, Katz LA.2004. Genome diversity in microbial eukaryotes. Trends in Ecology&Evolution,19:32-38.
Medinger R, Nolte V, Pandey RV, Jost S, Ottenwaelder B, Schloetterer C, Boenigk J.2010.Diversity in a hidden world: potential and limitation of next-generation sequencing for surveysof molecular diversity of eukaryotic microorganisms. Molecular Ecology,19:32-40.
Meng Z, Xu K, Lei Y.2011. Community composition, distribution, and contribution ofmicrobenthos in offshore sediments from the Yellow Sea. Continental Shelf Research,31:1437-1446.
Meng Z, Xu K, Dai R, Lei Y.2012. Ciliate community structure, diversity and trophic role inoffshore sediments from the Yellow Sea. European Journal of Protistology,48:73-84.
Miller DN.2001. Evaluation of gel filtration resins for the removal of PCR-inhibitory substancesfrom soils and sediments. Journal of Microbiological Methods,44:49-58.
Mitchell KR, Takacs-Vesbach CD.2008. A comparison of methods for total community DNApreservation and extraction from various thermal environments. Journal of IndustrialMicrobiology&Biotechnology,35:1139-1147.
Monroy F, van der Putten WH, Yergeau E, Mortimer SR, Duyts H, Bezemer TM.2012. Communitypatterns of soil bacteria and nematodes in relation to geographic distance. Soil Biology&Biochemistry,45:1-7.
Montagnes DJS, Lynn DH.1987. A quantitative protargol stain (QPS) for ciliates: Methoddescription and test of its quantitative nature. Marine Microbial Food Webs,2:83-93.
Moon-van der Staay SY, Tzeneva VA, van der Staay GWM, de Vos WM, Smidt H, Hackstein JHP.2006. Eukaryotic diversity in historical soil samples. FEMS Microbiology Ecology,57:420-428.
Moreira D, López-García P.2002. The molecular ecology of microbial eukaryotes unveils a hiddenworld. Trends in Microbiology,10:31-38.
Murray SA, Patterson DJ, Thessen AE.2012. Transcriptomics and microbial eukaryote diversity: away forward. Trends in Ecology&Evolution,27:651-652.
Muyzer G, Dewaal EC, Uitterlinden AG.1993. Profiling of complex microbial-populations bydenaturing gradient gel-electrophoresis analysis of polymerase chain reaction-coding for16Sribosomal-RNA. Applied and Environmental Microbiology,59:695-700.
Mylnikov AP, Karpov SA.2004. Review of the diversity and taxonomy of cercomonads.Protistology,3:201-217.
Neira C, Sellanes J, Levin LA, Arntz WE.2001. Meiofaunal distributions on the Peru margin:relationship to oxygen and organic matter availability. Deep-Sea Research Part I,48:2453-2472.
Nekola JC, White PS.1999. The distance decay of similarity in biogeography and ecology. Journalof Biogeography,26:867-878
Ning J, Liebich J, Kastner M, Zhou J, Schaffer A, Burauel P.2009. Different influences of DNApurity indices and quantity on PCR-based DGGE and functional gene microarray in soilmicrobial community study. Applied Microbiology and Biotechnology,82:983-993.
Oren A.2008. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. SalineSystems,4:2.
O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R.2005. Fungal community analysisby large-scale sequencing of environmental samples. Applied and Environmental Microbiology,71:5544-5550.
Oros-Sichler M, Gomes NCM, Neuber G, Smalla, K.2006. A new semi-nested PCR protocol toamplify large18S rRNA gene fragments for PCR-DGGE analysis of soil fungal communities.Journal of Microbiological Methods,65:63-75.
Orsi W, Song Y, Hallam S, Edgcomb V.2012. Effect of oxygen minimum zone formation oncommunities of marine protists. ISME Journal,6:1586-1601.
Pawlowski J, Holzmann M.2008. Diversity and geographic distribution of benthic foraminifera: amolecular perspective. Biodiversity and Conservation,17;317-328.
Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, Guillou L.2011.Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One,6.
Persoh D, Theuerl S, Buscot F, Rambold, G.2008. Towards a universally adaptable method forquantitative extraction of high-purity nucleic acids from soil. Journal of MicrobiologicalMethods,75:19-24.
Petz W, Foissner W.1989. The effects of mancozeb and lindane on the soil microfauna of a spruceforest: a field study using a completely randomized block design. Biology and Fertility of Soils,7:225-231.
Pfister G, Sonntag B, Posch T.1999. Comparison of a direct live count and an improved quantitativeprotargol stain (QPS) in determining abundance and cell volumes of pelagic freshwaterprotozoa. Aquatic Microbial Ecology,18:95-103.
Pokarzhevskii AD, van Straalen NM, Zaboev DP, Zaitsev AS.2003. Microbial links and elementflows in nested detrital food-webs. Pedobiologia,47:213-224.
Porteous LA, Seidler RJ, Watrud LS.1997. An improved method for purifying DNA from soil forpolymerase chain reaction amplification and molecular ecology applications. MolecularEcology,6:787-791.
Puitika T, Kasahara Y, Miyoshi N, Rambold G.2007. A taxon-specific oligonucleotide primer setfor PCR-based detection of soil ciliate. Microbes and Environments,22:78-81.
Putt M, Stoecker DK.1989. An experimentally determined carbon-volume ratio for marineoligotrichous ciliates from estuarine and coastal waters. Limnology and Oceanography,34:1097-1103
Rajendhran J, Gunasekaran P.2008. Strategies for accessing soil metagenome for desiredapplications. Biotechnology Advances,26:576-590.
Ranjard L, Lejon DPH, Mougel C, Schehrer, L., Merdinoglu, D., Chaussod, R.2003. Samplingstrategy in molecular microbial ecology: Influence of soil sample size on DNA fingerprintinganalysis of fungal and bacterial communities. Environmental Microbiology,5:1111-1120.
Richards TA, Bass D.2005. Molecular screening of free-living microbial eukaryotes: diversity anddistribution using a meta-analysis. Current Opinion in Microbiology,8:240-252.
Roose-Amsaleg CL, Garnier-Sillam E, Harry M.2001. Extraction and purification of microbialDNA from soil and sediment samples. Applied Soil Ecology,18:47-60.
Sardinha M, Muller T, Schmeisky H, Joergensen RG.2003. Microbial performance in soils along asalinity gradient under acidic conditions. Applied Soil Ecology,23:237-244.
Sagova-Mareckova M, Cermak L, Novotna J, Plhackova K, Forstova J, Kopecky J.2008. Innovativemethods for soil DNA purification tested in soils with widely differing characteristics. Appliedand Environmental Microbiology,74:2902-2907.
SAS Institute Inc.1989. SAS/STAT Users Guide. Version6,4th ed, vol.2. SAS Institute Inc, Cary,NC.
Schwarz MVJ, Frenzel P.2003. Population dynamics and ecology of ciliates (Protozoa, Ciliophora)in an anoxic rice field soil. Biology and Fertility of Soils,38:245-252.
Segers H, De Smet WH.2008. Diversity and endemism in Rotifera: a review, and Keratella Bory deSt Vincent. Biodiversity and Conservation,17:303-316.
Sherr EB, Sherr BF.1993. Preservation and storage of samples for enumeration of heterotrophicprotists, in: Kemp PF, Sherr BF, Sherr EB, Cole JJ.(Eds.), Handbook of Methods in AquaticMicrobial Ecology, Lewis Publishers.
Shoji J, Kudoh T, Takatsuji H, Kawaguchi O, Kasai A.2010. Distribution of moon jellyfish Aureliaaurita in relation to summer hypoxia in Hiroshima Bay, Seto Inland Sea. Estuarine Coastal andShelf Science,86:485-490.
Shoji J, Masuda R, Yamashita Y, Tanaka M.2005. Effect of low dissolved oxygen concentrations onbehavior and predation rates on red sea bream Pagrus major larvae by the jellyfish Aureliaaurita and by juvenile Spanish mackerel Scomberomorus niphonius. Marine Biology,147:863-868.
Sime-Ngando T, Hartmann HJ, Grolière CA.1990. Rapid quantification of planktonic ciliates:comparison of improved live counting with other methods. Applied and EnvironmentalMicrobiology,56:2234-2242.
Sime-Ngando TS, Grolière CA.1991. Quantitative effects of fixatives on the storage of freshwaterplanktonic ciliates. Archiv Für Protistenkunde,140:109-120.
Simon N, Lebot N, Marie D, Partensky F, Vaulot D.1995. Fluorescent in-situ hybridization withribosomal-RNA-targeted oligonucleotide probes to identify small phytoplankton by flow-cytometry. Applied and Environmental Microbiology,61:2506-2513.
Skibbe O.1994. An improved quantitative protargol stain for ciliates and other planktonic protists.Archiv Für Hydrobiologie,130:339-347.
Skillman LC, Toovey AF, Williams AJ, Wright, ADG.2006. Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability betweenEntodinium populations in sheep offered a hay-based diet. Applied and EnvironmentalMicrobiology,72:200-206.
Smalla K, Cresswell N, Mendoncahagler LC, Wolters A, Vanelsas JD.1993. Rapid DNA extractionprotocol from soil for polymerase chain reaction-mediated amplification. Journal of AppliedBacteriology,74:78-85.
Smith HG, Bobrov A, Lara E.2008. Diversity and biogeography of testate amoebae. Biodiversityand Conservation,17:329-343.
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ.2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedingsof the National Academy of Sciences of the United States of America,103:12115-12120.
Starink M, B r-Gilissen MJ, Bak RPM, Cappenberg TE.1994. Quantitative centrifugation to extractbenthic protozoa from freshwater sediments. Applied and Environmental Microbiology,60:167–173.
Stephenson SL, Schnittler M, Novozhilov YK.2008. Myxomycete diversity and distribution fromthe fossil record to the present. Biodiversity and Conservation,17:285-301.
Stewart FJ, Ulloa O, Delong EF.2012. Microbial metatranscriptomics in a permanent marineoxygen minimum zone. Environmental Microbiology,14:23-40.
Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Breiner HW, Richards TA.2010. Multiplemarker parallel tag environmental DNA sequencing reveals a highly complex eukaryoticcommunity in marine anoxic water. Molecular Ecology,19:21-31.
Stoeck T, Taylor GT, Epstein SS.2003. Novel eukaryotes from the permanently anoxic CariacoBasin (Caribbean sea). Applied and Environmental Microbiology,69:5656-5663.
Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, Epstein S.2007. Protistan diversity in the Arctic: acase of paleoclimate shaping modern biodiversity? PLoS One,2.
Strüder-Kypke MC, Wright ADG, Fokin SI, Lynn DH.2000. Phylogenetic relationships of thegenus Paramecium inferred from small subunit rRNA gene sequences. Molecular Phylogeneticsand Evolution,14:122-130.
Sugano A, Tsuchimoto H, Tun CC, Asakawa S, Kimura M.2007. Succession and phylogeneticprofile of eukaryotic communities in rice straw incorporated into a rice field: Estimation byPCR-DGGE and sequence analyses. Soil Science and Plant Nutrition,53:585-594.
Swofford DL.2002. Paup*. Phylogenetic analysis using parsimony (*and other methods). Version4.Sinauer Associates, Sunderland, MA.
Takishita K, Miyake H, Kawato M, Maruyama T.2005. Genetic diversity of microbial eukaryotes inanoxic sediment around fumaroles on a submarine caldera floor based on the small-subunitrDNA phylogeny. Extremophiles,9:185-196.
Taylor FJR, Hoppenrath M, Saldarriaga JF.2008. Dinoflagellate diversity and distribution.Biodiversity and Conservation,17:407-418.
ter Braak CJF, milauer P.2002. CANOCO reference manual and CanoDraw for windows user'sguide: software for canonical community ordination (version4.5). Microcomputer Power,Ithaca, New York.
Terrado R, Vincent WF, Lovejoy C.2009. Mesopelagic protists: diversity and succession in acoastal Arctic ecosystem. Aquatic Microbial Ecology,56:25-39.
Torsvik VL, Goksoyr J.1978. Determination of bacterial DNA in soil. Soil Biology&Biochemistry,10:7-12.
Tripathi S, Chakraborty A, Chakrabarti K, Bandyopadhyay BK.2007. Enzyme activities andmicrobial biomass in coastal soils of India. Soil Biology&Biochemistry,39:2840-2848.
Tsai YL, Olson BH.1991. Rapid method for direct extraction of DNA from soil and sediments.Applied and Environmental Microbiology,57:1070-1074.
Usher MB, Sier ARJ, Hornung M, Millard P.2006. Understanding biological diversity in soil: theUK's soil biodiversity research programme. Applied Soil Ecology,33:101-113.
Vaerewijck MJM, Sabbe K, Bare J, Houf K.2008. Microscopic and molecular studies of thediversity of free-living protozoa in meat-cutting plants. Applied and EnvironmentalMicrobiology,74:5741-5749.
Valenzuela-Encinas C, Neria-González I, Alcántara-Hernández RJ, Estrada-Alvarado I, Zavala-Díazde la Serna FJ, Dendooven L, Marsch R.2009. Changes in the bacterial populations of thehighly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.Extremophiles,13:609-621.
Vanormelingen P, Verleyen E, Vyverman W.2008. The diversity and distribution of diatoms: fromcosmopolitanism to narrow endemism. Biodiversity and Conservation,17:393-405.
Verhoeven R.2002. Ciliates in coastal dune soils of different stages of development. EuropeanJournal of Soil Biology,38:187-191.
Vigil P, Countway PD, Rose J, Lonsdale DJ, Gobler CJ, Caron DA.2009. Rapid shifts in dominanttaxa among microbial eukaryotes in estuarine ecosystems. Aquatic Microbial Ecology,54:83-100.
Wang J, Yang D, Zhang Y, Shen J, van der Gast C, Hahn MW, Wu Q.2011. Do patterns of bacterialdiversity along salinity gradients differ from those observed for macroorganisms? PLoS ONE,6.
Wang S, Li Q, Liang W, Jiang Y, Jiang S.2008. PCR-DGGE analysis of nematode diversity in Cu-contaminated soil. Pedosphere,18:621--627.
Weston NB, Porubsky WP, Samarkin VA, Erickson M, Macavoy SE, Joye SB.2006. Porewaterstoichiometry of terminal metabolic products, sulfate, and dissolved organic carbon andnitrogen in estuarine intertidal creek-bank sediments. Biogeochemistry,77:375-408.
Wickham S, Gieseke A, Berninger UG.2000. Benthic ciliate identification and enumeration: animproved methodology and its application. Aquatic Microbial Ecology,22:79-91.
Worden AZ, Allen AE.2010. The voyage of the microbial eukaryote. Current Opinion inMicrobiology,13:652-660.
Wu QL, Zwart G, Schauer M, Kamst-van Agterveld MP, Hahn MW.2006. Bacterioplanktoncommunity composition along a salinity gradient of sixteen high-mountain lakes located on theTibetan Plateau, China. Applied and Environmental Microbiology,72:5478-5485.
Wu Q, Chatzinotas A, Wang J, Boenigk J.2009. Genetic diversity of eukaryotic planktonassemblages in eastern Tibetan lakes differing by their salinity and altitude. Microbial Ecology,58:569-581.
Wu RSS.2002. Hypoxia: from molecular responses to ecosystem responses. Marine PollutionBulletin,45:35-45.
Wu T, Ayres E, Li G, Bardgett RD, Wall DH, Garey JR.2009. Molecular profiling of soil animaldiversity in natural ecosystems: incongruence of molecular and morphological results. SoilBiology&Biochemistry,41:849-857.
Xu K, Du Y, Lei Y, Dai R.2010. A practical method of Ludox density gradient centrifugationcombined with protargol staining for extracting and estimating ciliates in marine sediments.European Journal of Protistology,46:263-270.
Xu X, Lin H, Fu Z.2004. Probe into the method of regional ecological risk assessment-a case studyof wetland in the Yellow River delta in China. Journal of Environmental Management,70:253-262.
Yan Q, Yu Y, Feng W, Deng W, Song X.2007. Genetic diversity of plankton community asdepicted by PCR-DGGE fingerprinting and its relation to morphological composition andenvironmental factors in lake Donghu. Microbial Ecology,54:290-297.
Yu Y, Yan Q, Feng W.2008. Spatiotemporal heterogeneity of plankton communities in LakeDonghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation tobiotic and abiotic factors. FEMS Microbiology Ecology,63:328-337.
Zahran HH.1997. Diversity, adaptation and activity of the bacterial flora in saline environments.Biology and Fertility of Soils,25:211-223.
Zeng Y, Chen X, Jiao N.2007. Contrasting diversity pattern of Cytophaga-Flavobacteria in theestuarine and open ocean regions of the East China Sea. Marine Biology Research,3:428-437.
Zhang J, Zhang Z, Liu S, Wu Y, Xiong H, Chen H.1999. Human impacts on the large world rivers:Would the Changjiang (Yangtze River) be an illustration? Global Biogeochemical Cycles,13(4):1099-1106.
Zhang J, Su J.2006. Nutrient dynamics of the Chinese Seas: The Bohai, Yellow Sea, East China Seaand South China Sea, in:The Sea, Robinson AR, Brink KH (eds). Harvard University Press,Cambridge MA.
Zhang J, Liu SM, Ren JL, Wu Y, Zhang GL.2007. Nutrient gradients from the eutrophic Changjiang(Yangtze River) Estuary to the oligotrophic Kuroshio waters and re-evaluation of budgets forthe East China Sea Shelf. Progress in Oceanography,74:449–478.
Zhang L, Xu Z, Patel BKC.2009. An improved method for purifying genomic DNA from forest leaflitters and soil suitable for PCR. Journal of Soils and Sediments,9:261-266.
Zhao B, Chen M, Sun Y, Yang J, Chen F.2011. Genetic diversity of picoeukaryotes in eight lakesdiffering in trophic status. Canadian Journal of Microbiology,57:115-26.
Zhao F, Xu K.2012. Efficiency of DNA extraction methods on the evaluation of soilmicroeukaryotic diversity. Acta Ecologica Sinica,32:209-214.
Zhao F, Xu K, He Y.2012. Application of the Ludox-QPS method for estimating ciliate diversity insoil and comparison with direct count and DNA fingerprinting, European Journal of SoilBiology,49:112-118.
Zhao F, Xu K.2013. Microbial genetic diversity and ciliate community structure along anenvironmental gradient in coastal soil. European Journal of Protistology,doi:10.1016/j.ejop.2013.01.002.
Zhao F, Xu K, Zhang D.2013. Spatio-temporal variations in the molecular diversity ofmicroeukaryotes in particular ciliates in soil of the Yellow River Delta, China. Journal ofEukaryotic Microbiology, doi:10.1111/jeu.12035.
Zhou J, Bruns MA, Tiedje JM.1996. DNA recovery from soils of diverse composition. Applied andEnvironmental Microbiology,62:316-322.
曹志平,陈国康,张凯等.2005.不同土壤培肥措施对华北高产农田原生动物丰度的影响.生态学报,25(11):2992-2996.
陈春辉,王春生,许学伟等,2009.河口缺氧生物效应研究进展.生态学报,29(5):2595-2602.
陈素芳,徐润林.2003.土壤原生动物的研究进展.中山大学学报(自然科学版),42(增刊):187-194.
代仁海,2012.黄东海底栖纤毛虫多样性及微型底栖生物群落结构特点.中国科学院研究生院博士学位论文.
杜萍,刘晶晶,曾江宁等,2011.长江口低氧区异养细菌及氮磷细菌分布.应用生态学报,22(5):1316-1324.
冯伟松,余育和.2000.南极菲尔德斯半岛地区土壤原生动物生态学研究.水生生物学报,24(6):610-615.
冯旭文,于晓果,陈建芳等,2006.河口季节性缺氧在沉积物中记录的研究进展.海洋学研究,24(1):50-61.
高云超,朱文珊,陈文新.2000.土壤原生动物群落及其生态功能.生态学杂志,19(1):59-65.
顾宏堪,1980.黄海溶解氧垂直分布中的最大值.海洋学报,2:70-79.
郭非凡,史雅娟,孟凡乔等.2006.典型POPs物质对土壤原生动物丰度的影响.生态学报,26(1):70-74.
类彦立,徐奎栋.2007.海洋底栖原生动物生态学研究方法综述.海洋科学,31(5):49-57.
类彦立,徐奎栋.2008.底栖纤毛虫原生动物的生态学研究进展.水生生物学报,32:155-160.
类彦立,徐奎栋.2011.海洋微型底栖生物调查方法与操作规范.海洋与湖沼,42(1):157-164.
李洪波,肖天,丁涛等.2006.浮游细菌在黄海冷水团中的分布.生态学报,26(4):1012-1020.
李琦路,宁应之.2008.土壤生态环境中纤毛虫的研究与应用.西北师范大学学报(自然科学版),44(3):82-87.
李新正.2011.我国海洋大型底栖生物多样性研究及展望:以黄海为例.生物多样性,19(6):676–684.
廖庆玉,章金鸿,李玫等.2008.海南东寨港红树林土壤原生动物的群落结构特征.生态环境,17(3):1077-1081.
刘瑞玉等.2008.中国海洋生物名录.科学出版社,北京.
马正学,康瑞琴,孙宏飞等.2007.焦化废水污染土壤中原生动物的群落特征.西北师范大学学报(自然科学版),43(5):90-93.
孟昭翠,2011.黄海夏季微型底栖生物群落结构与生态特点.中国科学院研究生院博士学位论文.
宁应之,沈韫芬.1996.路咖山森林土壤原生动物生态学研究及土壤原生动物定量方法探讨.动物学研究,17(3):225-232.
屈佩,张学雷,王宗灵等.2010.南黄海夏季微微型浮游植物丰度的分布.海洋学报,32(4):155-167.
单秀娟,庄志猛,金显仕等.2011.长江口及其邻近水域大型水母资源量动态变化对渔业资源结构的影响.应用生态学报,22(12):3321-3328.
沈蕴芬等.2000.原生动物学.科学出版社,北京
宋微波等.1999.原生动物学专论.青岛海洋大学出版社,青岛
宋雪英,宋玉芳,孙铁珩等.2004.土壤原生动物对环境污染的生物指示作用.应用生态学报,15(10):1979-1982.
孙宏飞,马正学,宁应之等.2007.皮革废水污染的土壤原生动物生态效应.甘肃科学学报,19(1):82-84.
孙金凤,刘清志.2010.黄河三角洲风能资源评价及开发利用研究.资源与产业,12(4):107-112.
孙松,王荣,张光涛等.2002.黄海中华哲水蚤度夏机制,海洋与湖沼,浮游动物研究专辑,92-100.
唐启生.2006.中国专属经济区海洋生物资源与栖息环境.科学出版社,北京
王冬,宁应之,马正学等.2007.新疆石河子市蘑菇湖混合污水污染土壤中原生动物的群落特征.西北师范大学学报(自然科学版),43(1):83-86.
王家栋,类彦立,徐奎栋等.2011.黄海冷水团及周边海域夏初小型底栖动物现存量及空间分布研究.海洋与湖沼,42(3):359-366.
王丹,孙军,周锋等.2008.2006年6月长江口低氧区及邻近水域浮游植物.海洋与湖沼,39(6):619-627.
王延明,李道季,方涛等.2008.长江口及邻近海域底栖生物分布及与低氧区的关系研究.海洋环境科学,27(2):139-164.
韦钦胜,战闰,魏修华等.2010.夏季长江口东北部海域DO的分布及低氧特征.海洋科学进展,28(1):32-40.
杨庆霄,董娅婕,蒋岳文等.2001.黄海和东海海域溶解氧的分布特征.海洋环境科学,20(3):9-13.
尹文英等.2000.中国土壤动物.科学出版社,北京
徐奎栋.2011.海洋微型底栖生物的多样性和地理分布.生物多样性,19(6):661-675.
徐润林,孙逸湘.2000.大鹏半岛土壤纤毛虫的群落特点.应用生态学报,11(3):428-430.
赵延茂,宋朝枢.1994.黄河三角洲自然保护区科学考察集.中国林业出版社,北京.
张翠霞.2011.我国海区浮游纤毛虫的生态学研究.中国科学院研究生院博士学位论文.
张芳,孙松,李超伦.2009.海洋水母类生态学研究进展.自然科学进展,19(2):121-130.
张莹莹,张经,吴莹等.2007.长江口溶解氧的分布特征及影响因素研究.环境科学,28(8):1649-1654.
张竹琦. l990.黄海和东海北部夏季底层溶解氧最大值和最小值特征分析.海洋通报,9(4):22-26.
赵峰,徐奎栋,孟昭翠.2012.长江口低氧区沉积物表层纤毛虫多样性及其时空变化研究.应用生态学报,23(12):3441-3448.
郑元甲等.2003.东海大陆架生物资源与环境.上海科学技术出版社,上海.
周锋,黄大吉,倪晓波等.2010.影响长江口毗邻海域低氧区多种时间尺度变化的水文因素.生态学报,30(17):4728-4740.
周可新,许木启,曹宏等.2003.土壤原生动物在环境监测中的应用.动物学杂志,38(1):80-84.