Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatments. We hypothesized that the long-term treatments had created distinctly different ecological niches for soil bacteria, suitable for either fast-growing copiotrophic bacteria, or slow-growing oligotrophic bacteria. Based on terminal-restriction fragment length polymorphism of the 16S rRNA genes from the total soil bacterial community and taxa-specific quantitative real-time PCR of seven different groups, all treatments significantly affected the community structure, but nitrogen fertilization was the most important driver for changes in the relative abundances of the studied taxa. According to an indicator species analysis, the changes were largely explained by the decline in the relative abundances of Acidobacteria, Gemmatimonadetes and Verrucomicrobia with nitrogen fertilization. Conditions more favourable for copiotrophic life strategies were indicated in these plots by the decreased metabolic quotient, i.e. the ratio between basal respiration rate and soil biomass. Apart from the Alphaproteobacteria that were significantly associated with peat, no taxa were indicative of organic amendment in general. However, several significant indicators of both peat and straw were identified among the terminal restriction fragments suggesting that changes induced by the organic amendments were mainly manifested at a lower taxonomical level. Our findings strengthen the proposition that certain higher bacterial taxa adapt in an ecologically coherent way in response to changes induced by fertilization.     

Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest

Little is known about the organisms responsible for decomposition in terrestrial ecosystems, or how variations in their relative abundance may influence soil carbon (C) cycling. Here, we altered organic matter in situ by manipulating both litter and throughfall inputs to tropical rain forest soils, and then used qPCR and error-corrected bar-coded pyrosequencing to investigate how the resulting changes in soil chemical properties affected microbial community structure. The plot-scale manipulations drove significant changes in microbial community composition: Acidobacteria were present in greater relative abundance in litter removal plots than in double-litter plots, while Alphaproteobacteria were found in higher relative abundance in double-litter and throughfall reduction plots than in control or litter removal plots. In addition, the bacterial:archaeal ratio was higher in double-litter than no-litter plots. The relative abundances of Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were positively correlated with microbial biomass C and nitrogen (N), and soil N and C pools, while acidobacterial relative abundance was negatively correlated with these same factors. Bacterial:archaeal ratios were positively correlated with soil moisture, total soil C and N, extractable ammonium pools, and soil C:N ratios. Additionally, bacterial:archaeal ratios were positively related to the relative abundance of Actinobacteria, Gammaproteobacteria, and Actinobacteria, and negatively correlated to the relative abundance of Nitrospira and Acidobacteria. Together, our results support the copiotrophic/oligotrophic model of soil heterotrophic microbes suggested by Fierer et al. (2007).     

Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase

The ecological staircase of Mendocino (California, USA) is characterized by a succession of uplifted marine terraces that are derived from the same mineralogical parent material but have different ages, levels of fertility, and types of vegetation, from grassland in the youngest and most fertile terrace to a pygmy forest in the older terraces. Such conditions present a unique opportunity to determine how the structure, abundance, and function of bacterial communities vary with soil fertility along this natural chronosequence. Pyrosequencing analysis of 16S rRNA gene amplicons revealed that Acidobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundantly represented phyla. Bacteroidetes, Firmicutes, Verrucomicrobia were significantly enriched in the grasslands, while the less fertile forested terraces showed higher abundance of Acidobacteria Gp2 and Alphaproteobacteria. The pygmy forest soil harboured significantly more Actinobacteria and OP10 than the non-pygmy forest. Between samples from different terraces, the structure of the bacterial community clearly correlated with soil characteristics. Notably, the number of operational taxonomic units was greater in the fertile terrace, as was the density of culturable bacterial populations. Functional characterization of the soil culturable bacteria from the pygmy and non-pygmy forest terraces revealed that the soil bacteria from the non-pygmy terrace were significantly more effective in solubilizing minerals and more abundant than in the pygmy terrace. Our results provide new information on bacterial community structure as a function of soil age, land cover and fertility, which improve our understanding of soil evolution.     

Long-term effect of plastic film mulching and fertilization on bacterial communities in a brown soil revealed by high through-put sequencing

The objective of this study was to access the effect of long-term fertilization and film mulching application on soil properties and bacterial community structure. We used 16S rRNA gene to investigate soil bacterial community composition by high through-put sequencing. The results demonstrated that predominant groups in the bacterial community were: Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi and Cyanobacteria. Long-term fertilization of combined manure and nitrogen application caused significant decrease in soil bacterial diversity and richness compared to non-fertilization control, though manure fertilization alone played a significant role in restoring bacterial diversity. Film mulching and manure fertilization significantly increased the relative abundances of soil bacterial groups mentioned above. Furthermore, film mulching played significant role in shaping the bacterial community structure regardless of fertilization. Redundancy analysis (RDA) showed that soil moisture content, pH, total N and soil organic C had significant (P < 0.05) influence on dominant bacterial groups. Altogether, plastic film mulching and manure application prevented loss of soil bacterial diversity and abundance during long-term fertilization. These findings showed the detrimental use of combined manure and nitrogen fertilization to soil microbes and the useful application of manure fertilization coupled with film mulching to soil biodiversity in long-term fertilization experiments.     

施肥及秸秆还田对砂姜黑土细菌群落的影响

利用Illumina平台Miseq高通量测序技术对小麦分蘖期砂姜黑土耕层土壤细菌进行高通量测序,结合相关生物信息学分析,探讨了不施化肥秸秆不还田(CK)、施化肥秸秆不还田(F)以及不施化肥秸秆还田(W)3种处理土壤细菌群落组成、多样性和结构的变化。结果显示,测序共获得14 873个OTUs,计173 323条读数,平均读长439 bp。砂姜黑土细菌优势门(相对丰度10%)为变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)和拟杆菌门(Bacteroidetes);优势纲(相对丰度10%)为α-变形菌纲(Alphaproteobacteria)、β-变形菌纲(Betaproteobacteria)、酸杆菌纲(Acidobacteria)、鞘脂杆菌纲(Sphingobacteriia)和γ-变形菌纲(Gammaproteobacteria);优势属(相对丰度1%)共47个,3个处理中均有分布的优势属21个,F处理的细菌优势属的种类最多,为39个。相对丰度最大的门、纲和属分别是变形菌门(38.7%~43.1%)、α-变形菌纲(14.5%~18.1%)和鞘氨醇单胞菌属(Sphingomonas)(4.6%~7.7%)。F处理细菌丰富度指数(Chao1指数和ACE指数)显著低于CK及W处理,W处理和CK处理土壤细菌丰富度指数无显著差异,与CK处理相比,F处理ACE指数降低22.8%。W处理土壤细菌Shannon多样性指数显著大于CK及F处理,W处理Shannon指数较CK处理提高4.1%,而F处理土壤细菌Shannon指数与CK处理无显著差异。F处理Simpson指数显著高于CK及W处理;F处理Simpson指数较CK处理提高38.1%,而W处理细菌Simpson指数最小,显著低于CK处理,较CK降低23.8%。分层聚类图显示在属的水平上,W处理和CK处理土壤细菌群落结构相似性较高,F处理与CK处理及W处理细菌群落结构差异较大。施化肥对土壤细菌优势类群组成、相对丰度及群落结构的影响大于秸秆还田,施化肥显著降低了土壤细菌丰富度,秸秆还田显著提高了土壤细菌的多样性。     

长期施用有机肥潮土细菌的多样性及功能预测

  【目的】  细菌作为土壤中最多的微生物物种,其多样性是土壤质量和土壤健康的标志。施肥不仅为土壤细菌提供了矿质养分,也为细菌提供了不同的碳源。探究长期不同施肥下潮土细菌的多样性及其功能,对于深入理解土壤养分转化的微生物驱动过程及优化施肥管理措施具有重要意义。  【方法】  选取潮土上连续37年不施肥(CK)、单施化学氮肥(N)、单施有机肥(M)、有机肥和化学氮肥配施(MN) 的4个处理,采用高通量测序方法分析土壤细菌丰度(16S rRNA基因拷贝数)、α多样性和β多样性,采用FAPROTAX功能预测的方法分析主要功能种群的丰度在处理间的差异,采用Mantel 检验分析细菌多样性等与产量、土壤养分含量间的相关关系。  【结果】  长期施用有机肥显著提高了土壤细菌丰度,MN和M处理下土壤中的16S rRNA基因拷贝数分别是CK和N处理平均值的11.8和10.7倍(P< 0.05)。土壤细菌多样性指数(Shannon index)和丰富度指数(Chao1 index)均在M处理下最高。潮土中变形菌门、酸杆菌门和放线菌门为优势菌门。与CK相比,施肥处理均提高了潮土拟杆菌门、厚壁菌门和疣微菌门的相对丰度。与N处理相比,MN处理显著提高了潮土变形菌门、厚壁菌门和拟杆菌门的丰度,降低了酸杆菌门的丰度。潮土细菌生态功能以化能异养、有氧化能异养、发酵作用、硝化作用和硝酸盐还原为主,相应种群丰度均在1%以上。MN处理下化能异养功能细菌的丰度较其他处理显著提高2.2%～4.2%。MN和M处理中起发酵作用的种群相对丰度是其他处理的3倍以上。与CK 相比,3个施肥处理均显著增加了光异作用和光异养作用功能种群的相对丰度。土壤细菌β多样性和功能结构均与土壤有机质(SOM)、全氮(TN)、硝态氮(NO₃?-N)含量及作物产量呈显著(P < 0.05)或极显著(P < 0.01)相关。  【结论】  长期施用有机肥提高了潮土中细菌的数量和多样性,提高了土壤中变形菌门、厚壁菌门和拟杆菌门的丰度,降低了酸杆菌门的丰度。有机肥和化肥配施处理中化能异养型细菌丰度较高,可能是施用有机肥后优化土壤养分循环和响应作物产量提高的主要菌群,今后可进一步深入研究其菌群组成和功能调控。     

玉米秸秆分解过程中细菌群落组成演化特征

【目的】土壤中存在着大量的分解秸秆的微生物。研究秸秆分解过程中细菌群落组成的演化规律,对了解和调控农田微生物群体组成以促进秸秆分解具有重要意义。【方法】试验于2014年10月至2015年10月在河南省农业科学院原阳试验基地进行,将成熟期玉米秸秆(茎和叶)烘干,剪成长1~2 cm、宽0.3~1 cm的碎片,称12 g样品(相当于8 t/hm^2)装入15 cm×10 cm的尼龙网包(孔径0.04 mm)内,于10月5日冬小麦出苗后埋置在小麦垄间。分别于埋置后0、1、2、4、7、10和12个月收集秸秆包和土壤样品。测定秸秆样品干物质量和碳氮含量,选择埋置了0、2、4、7和12个月的秸秆及其土壤样品分析细菌丰度及群落组成。【结果】秸秆埋入土壤后的前2个月内分解最快,然后逐步减慢,在1、2、4、7、10和12个月后分别降解了总生物量的19.2%、32.9%、44.2%、52.2%、66.8%和73.8%。秸秆埋入土壤后,秸秆和土壤中细菌丰度均显著增加,分别于第4和7个月达到最高后开始下降。秸秆细菌的丰度指标OTUs、ACE、Chao1和多样性指标Shannon随试验时间的延长逐步增加,而Simpson指数随试验时间延长逐步降低,而土壤中这些指标在试验过程中没有显著变化。与刚埋置秸秆时相比,埋置2个月后的秸秆细菌Bacteroidetes门相对丰度明显增加,主导细菌群为Bacteroidetes和Proteobacteria门。Actinobacteria丰度在埋置2个月后明显降低,然后又随试验时间延长逐步增加。Planctomycetes、Saccharibacteria、Verrucomicrobia、Acidobacteria、Chloroflexi和Gemmatimonadetes丰度在原始秸秆中较低,埋入土壤后随试验时间延长逐步增加。Sphingobacteriia、Gammaproteobacteria、Alphaproteobacteria和Flavobacteriia主导前期细菌纲组成,而Actinobacteria、Anaerolineae和Bacilli纲丰度在后期逐步增加。秸秆分解速率主要受其碳含量影响,秸秆细菌群落组成前期与秸秆碳含量相关,后期与秸秆氮含量相关。随着试验的进展,秸秆细菌群落组成与土壤中的细菌群落组成趋同。【结论】秸秆埋入土壤后前2个月的分解速率最高,随后逐步降低。秸秆分解前期细菌群落由富营养型组分Bacteroidetes和Proteobacteria门和Sphingobacteriia、Gammaproteobacteria、Flavobacteriia和Alphaproteobacteria纲主导,随后被逐步增加的贫营养型组分Actinobacteria、Acidobacteria、Chloroflexi、Saccharibacteria门和Deltaproteobacteria、Actinobacteria纲等代替。秸秆碳氮含量变化是影响秸秆分解及其过程中细菌群落演化的主要原因。     

玉米秸秆分解过程中细菌群落组成演化特征

【目的】土壤中存在着大量的分解秸秆的微生物。研究秸秆分解过程中细菌群落组成的演化规律,对了解和调控农田微生物群体组成以促进秸秆分解具有重要意义。【方法】试验于2014年10月至2015年10月在河南省农业科学院原阳试验基地进行,将成熟期玉米秸秆(茎和叶)烘干,剪成长1~2 cm、宽0.3~1 cm的碎片,称12 g样品(相当于8 t/hm^2)装入15 cm×10 cm的尼龙网包(孔径0.04 mm)内,于10月5日冬小麦出苗后埋置在小麦垄间。分别于埋置后0、1、2、4、7、10和12个月收集秸秆包和土壤样品。测定秸秆样品干物质量和碳氮含量,选择埋置了0、2、4、7和12个月的秸秆及其土壤样品分析细菌丰度及群落组成。【结果】秸秆埋入土壤后的前2个月内分解最快,然后逐步减慢,在1、2、4、7、10和12个月后分别降解了总生物量的19.2%、32.9%、44.2%、52.2%、66.8%和73.8%。秸秆埋入土壤后,秸秆和土壤中细菌丰度均显著增加,分别于第4和7个月达到最高后开始下降。秸秆细菌的丰度指标OTUs、ACE、Chao1和多样性指标Shannon随试验时间的延长逐步增加,而Simpson指数随试验时间延长逐步降低,而土壤中这些指标在试验过程中没有显著变化。与刚埋置秸秆时相比,埋置2个月后的秸秆细菌Bacteroidetes门相对丰度明显增加,主导细菌群为Bacteroidetes和Proteobacteria门。Actinobacteria丰度在埋置2个月后明显降低,然后又随试验时间延长逐步增加。Planctomycetes、Saccharibacteria、Verrucomicrobia、Acidobacteria、Chloroflexi和Gemmatimonadetes丰度在原始秸秆中较低,埋入土壤后随试验时间延长逐步增加。Sphingobacteriia、Gammaproteobacteria、Alphaproteobacteria和Flavobacteriia主导前期细菌纲组成,而Actinobacteria、Anaerolineae和Bacilli纲丰度在后期逐步增加。秸秆分解速率主要受其碳含量影响,秸秆细菌群落组成前期与秸秆碳含量相关,后期与秸秆氮含量相关。随着试验的进展,秸秆细菌群落组成与土壤中的细菌群落组成趋同。【结论】秸秆埋入土壤后前2个月的分解速率最高,随后逐步降低。秸秆分解前期细菌群落由富营养型组分Bacteroidetes和Proteobacteria门和Sphingobacteriia、Gammaproteobacteria、Flavobacteriia和Alphaproteobacteria纲主导,随后被逐步增加的贫营养型组分Actinobacteria、Acidobacteria、Chloroflexi、Saccharibacteria门和Deltaproteobacteria、Actinobacteria纲等代替。秸秆碳氮含量变化是影响秸秆分解及其过程中细菌群落演化的主要原因。     

3种西兰花种植方式对根际土壤细菌群落结构和多样性的影响研究

为明确不同种植方式减缓西兰花的连作障碍,本研究采用Illumina Miseq高通量测序技术,分析和比较了浙江省台州湾滨海滩涂地西兰花种植区单季稻-西兰花水旱轮作、南瓜-西兰花旱旱轮作和西兰花连作3种种植方式对西兰花根际土壤细菌群落结构和多样性的影响。结果表明,3种种植方式西兰花根际土壤共获得28门、92纲、167目、301科、691属土壤细菌。变形菌门、酸杆菌门、放线菌门、芽单胞菌门、拟杆菌门、绿湾菌门、蓝细菌门、厚壁菌门、硝化螺旋菌门、疣微菌门是台州湾滩涂围垦地西兰花根际土壤细菌相对丰度较高的优势菌群。水旱轮作能提高西兰花根际土壤细菌变形菌门、酸杆菌门和绿湾菌门的相对丰度,但降低了西兰花根际土壤细菌放线菌门、芽单胞菌门、拟杆菌门和蓝细菌门的相对丰度。多样性指数和丰富度指数均以水旱轮作为最高,其次是旱旱轮作,以西兰花连作的土壤多样性指数和丰富度指数最低。因此,与西兰花长期连作相比,水旱轮作和旱旱轮作均能改善台州湾滨海滩涂地区西兰花根际土壤细菌群落结构。水稻-西兰花水旱轮作更能增加西兰花根际土壤细菌有益菌丰度,提高其根际土壤细菌多样性指数,以改良西兰花根际生态环境。本研究结果为实现该区域西兰花优质高产栽培提供了理论和实践依据。     

Bacterial and archaeal communities in saline soils from a Los Negritos geothermal area in Mexico

In recent years, there has been a growing need to understand how salinity affects microbial communities in agricultural soils. Archaeal and bacterial community diversities and structures were investigated by high-throughput sequencing analysis of their 16S rRNA in two arable soils with low electrical conductivity(EC)(2.3 and 2.6 dS m^-1) and a saline soil(EC = 17.6 dS m^-1). The dominant bacterial phyla in the soils were Proteobacteria(relative abundance(RA) = 46.2%), followe...     

长期不同施肥黑土细菌和古菌群落结构及主效影响因子分析

【目的】依据黑龙江省农科院34年的长期定位试验,探讨影响东北黑土细菌和古菌区系的主效环境因子。【方法】试验采集不施肥(CK)、施氮磷肥(NP)、施氮钾肥(NK)、施磷钾肥(PK)、施氮磷钾肥(NPK)5个施肥处理的耕层土样借助传统化学分析方法和Illumina Miseq高通量测序技术解析土壤化学性状和细菌与古菌的群落结构特征,并对细菌和古菌群落结构与环境因子进行相关性分析。【结果】1)不同施肥处理土壤细菌和古菌群落结构存在显著差异与CK相比,4种施肥处理均降低了古菌丰富度,NPK处理增加了土壤细菌的丰富度、多样性以及古菌的多样性;变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)是所有土样中的优势菌群,占细菌与古菌总量的38.2%~42.9%。施肥条件下,放线菌门(Actinobacteria)、浮霉菌门(Planctomycetes)、绿弯菌门(Chloroflexi)、蓝藻门(Cyanobacteria)的相对丰度降低芽单胞菌门(Gemmatimonadetes)、厚壁菌门(Firmicutes)的相对丰度升高而其他菌门的相对丰度对不同施肥处理的响应不同。2)施用氮肥显著改变了土壤化学性状,长期施氮(尿素)处理的土壤全氮、速效氮和有机质含量显著高于不施氮处理而pH则显著降低。3)RDA分析结果显示,pH对土壤细菌和古菌群落结构的影响最大解释了66.5%的变化;其他环境因子则共解释了细菌与古菌群落33.5%的变化各因子的贡献率依次为pH速效钾有效磷有机质。Pearson相关性分析结果也表明,细菌和古菌群落与土壤化学指标间存在密切的相关关系。【结论】解析了长期不同施肥条件下土壤细菌和古菌的群落结构特征,确定了pH是影响土壤细菌和古菌区系的主效环境因子,氮磷钾均衡施肥不仅显著提高了作物产量和丰富了土壤养分含量,同时也增加了土壤细菌的丰富度、多样性以及古菌的多样性,有利于维持良好的土壤生态环境。研究结果对揭示东北黑土肥力演变机制、建立合理的施肥制度具有重要的理论价值。     

黄河三角洲刺槐根际与非根际细菌结构及多样性

为精确分析黄河三角洲刺槐根际与非根际土壤细菌群落定殖情况,本研究采用高通量测序方法对刺槐根际与非根际土壤细菌结构及多样性进行了研究。研究表明,根际土壤细菌共有36门214属,非根际土壤细菌共有33门153属。变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)细菌丰度超过15%,是根际与非根际土壤中的优势菌落。根际与非根际土壤中酸杆菌门、硝化螺旋菌门(Nitrospirae)丰度差异显著。根际土壤中红游动菌属(Rhodoplanes)、溶杆菌属(Lysobacter)、热单胞菌属(Thermomonas)、链霉菌属(Streptomyces)及非根际土壤中红游动菌属、溶杆菌属、链霉菌属、Kaistobacter细菌丰度超过4%。根际土壤中固氮菌丰度显著高于非根际土壤,解磷、解钾细菌丰度差异不显著。根际与非根际土壤细菌Chao丰富度分别为2 054、2 376,差异显著。根际与非根际土壤细菌之间的权重(Weighted Unifrac)距离在0.12~0.25之间。综上所述,黄河三角洲刺槐根际与非根际土壤细菌结构具有一定差异,多样性差异显著。     

Effect of long-term fertilization on bacterial composition in rice paddy soil

We investigated the effect of long-term fertilization on bacterial abundance, composition, and diversity in paddy soil. The experiment started in 1990 in Taoyuan Agro-ecosystem Research Station in China (111°33′ E, 28°55′ N). The molecular approaches including real-time quantitative PCR, terminal restriction fragment length polymorphism, and clone library construction were employed using 16S rRNA gene as genetic marker. Application of inorganic fertilizers did not affect bacterial abundance, and rice straw incorporation combined with inorganic fertilizers significantly (P < 0.05) increased bacterial abundance with shifts in bacterial community composition. Among phylogenetic groups, γ-Proteobacteria was responsive to all fertilization regimes while Acidobacteria was relatively stable to fertilization practices. Inorganic fertilizer mainly affected γ-Proteobacteria and δ-Proteobacteria, while rice straw incorporation influenced β-Proteobacteria and Verrucomicrobia. Therefore, long-term fertilization can affect abundance and composition of bacterial communities in paddy soil.     

Distributions and environmental drivers of archaea and bacteria in paddy soils

Purpose

The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.

Materials and methods

Quantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.

Results and discussion

Archaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.

Conclusions

In paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils.

     

Members of soil bacterial communities sensitive to tillage and crop rotation

Pyrosequencing was used to study the effect of rotation and tillage on total bacterial communities. We designed primers to the bacterial 16s rDNA and amplified DNA from soil samples from a long-term tillage/rotation trial in Kansas for two seasons. The 2 × 2 factorial trial had two rotation treatments (wheat-wheat and wheat-soybean) and two tillage treatments (conventional and no-till). A total of 20,180 16s rDNA sequences were generated and 2337 operational taxonomic units (OTUs) were assembled using a 97% similarity cut-off. The phylum Proteobacteria represented 38% of 299 identified taxa. The second most abundant phylum was Acidobacteria, making up 20% of the sequences, the majority of which were Acidobacteria Group 1. The phyla Actinobacteria and Gemmatimonadetes comprised 12% and 3.5% of the sequences. Other groups detected included TM7, Nitrospira, Verrucomicrobia, and Bacteroidetes. Some clusters of Acidobacteria Group 1 were more frequent in continuous wheat versus wheat-soybean rotation, some Acidobacteria Group 2 were more frequent in no-till, and some Acidobacteria Group 4 were more frequent in wheat-soybean rotation. These results were validated by quantitative real-time PCR. Pyrosequencing provided taxonomic information about the overall bacterial community, and detected community shifts resulting from different cropping practices.     

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application

The influence of different systems of fertilization and liming on the changes in the taxonomic structure of prokaryotic community in arable soddy-podzolic soil (Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric)) was studied in a stationary field experiment of Vologda State Dairy Farming Academy with the use of high-performance sequencing method of gene 16S rRNA. The 25-year-old fallow plot, in which the intensity of microbiological processes was close to that in the virgin soddy-podzolic soils, was used as a control. At the first stage, dominant phyla were identified: Proteobacteria (45.3–56.2%), Actinobacteria (13.6–20.4%), Bacteroidetes (7.2–19.3%), Acidobacteria (7.1–11.5%), and Verrucomicrobia (4.3–10.3%). Several groups of microorganisms-indicators, whose portion changes in the arable soil under the influence of liming, fertilizer application, and soil treatment in comparison with the control, were determined. The applied approach made it possible to relate the taxonomic structure of the soil microbial cenosis with external factors for assessing changes in the structure of soil microbial complex under the impact of different uses of the arable soil.     

Taxa-specific changes in soil microbial community composition induced by pyrogenic carbon amendments

The effects of pyrogenic carbon on the microbial diversity of forest soils were examined by comparing two soil types, fire-impacted and non-impacted, that were incubated with laboratory-generated biochars. Molecular and culture-dependent analyses of the biochar-treated forest soils revealed shifts in the relative abundance and diversity of key taxa upon the addition of biochars, which were dependent on biochar and soil type. Specifically, there was an overall loss of microbial diversity in all soils treated with oak and grass-derived biochar as detected by automated ribosomal intergenic spacer analysis. Although the overall diversity decreased upon biochar amendments, there were increases in specific taxa during biochar-amended incubation. DNA sequencing of these taxa revealed an increase in the relative abundance of bacteria within the phyla Actinobacteria and Gemmatimonadetes in biochar-treated soils. Together, these results reveal a pronounced impact of pyrogenic carbon on soil microbial community composition and an enrichment of key taxa within the parent soil microbial community.     

不同茬口和施氮水平对南瓜根际细菌碳分解潜力的影响

为探明根际细菌群落多样性及有机碳分解功能基因对耕作措施的响应特征,以收获小麦和西瓜后种植的南瓜根际土壤为研究对象,以两种施氮水平(纯氮施入量分别为1.0、2.0 g/kg)为处理,结合高通量测序和PICRUSt功能预测解析不同茬口和施氮水平下南瓜根际细菌群落结构和参与有机碳分解代谢细菌的关键功能基因丰度的差异。结果表明:各处理南瓜根际土壤细菌Shannon多样性指数和细菌群落结构无差异;所有处理中变形菌门、拟杆菌门、放线菌门、蓝藻细菌门相对丰度之和达到90%。冗余分析发现,小麦茬土壤中硝态氮的含量、西瓜茬土壤中铵态氮和硝态氮的含量对南瓜根际细菌群落结构的作用高于其他理化指标。高氮水平下,与西瓜茬相比,小麦茬南瓜根际土壤变形菌门的相对丰度降低,但拟杆菌门和放线菌门的相对丰度升高(P<0.05)。无论施氮水平高低,与西瓜茬相比,小麦茬南瓜根际土壤分解半纤维素和淀粉类物质诸如α-淀粉酶和β-半乳糖苷酶等产酶基因丰度提高。因此,施氮水平并未影响不同茬口土壤南瓜根际土壤微环境和细菌种群结构和多样性的稳定性;但高氮处理下,茬口类型影响参与有机碳分解的关键细菌门类相对丰度。与西瓜茬土壤相比,小麦茬土壤可能更能促进南瓜根际土壤有机碳的分解。     

Comparison of bacterial community structures at main habitats in paddy field ecosystem based on DGGE analysis

Bacterial communities at different habitats in a Japanese paddy field ecosystem were compared to understand the bacterial world in the ecosystem as a whole by analyzing data of the denaturing gradient gel electrophoresis (DGGE) band patterns and the sequenced DGGE bands. The habitats were floodwater, percolating water, microcrustacean inhabiting in floodwater, plow layer soil, rice roots, rice straw and rice straw compost incorporated in soil, rice straw placed on the soil surface, plant residues in paddy fields, and rice straw under composting process. Phylotype (band) richness, diversity, evenness, and stability of the bacterial communities at the respective habitats were evaluated based on the DGGE profile data. Phylotype richness was greater near plant residues, rice straw buried in soil and rice straw placed on soil surface, while it was smaller at microcrustacean and rice straw compost buried in soil. The samples from plow layer soil and rice straw compost buried in soil showed considerably higher index values for diversity, evenness, and stability, while those from rice straw placed on soil surface and microcrustacean had lower values of the indices than other habitats. Sequences of totally 250 DGGE bands were assigned to phyla or classes. Distribution of bacterial members to phylogenetic taxa was different among the respective habitats. Inhabitants in plow layer soil were most widely distributed among the groups (nine phyla: Proteobacteria, Chloroflexi, Chlorobi, Verrucomicrobia, Acidobacteria, Nitrospira, candidate division OP10, Cyanobacteria, and Actinobacteria), while those in floodwater and microcrustacean were restricted to only three phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). Proteobacteria and Bacteroidetes were found at all the habitats and the habitats except for plow layer soil, respectively, whereas abundant members belonged to Chloroflexi and Actinobacteria in plow layer soil. “Comprehensive mapping” of DGGE fragments was conducted by principal component analysis based on evolutionary distances of the fragments to 202 reference bacterial strains to overview phylogenetic relationships of bacterial members among the respective habitats. The score plots with the first and second principal components distinctly characterized bacterial members at the respective habitats, and the similarity between the respective communities was clearly demonstrated. Overall, bacterial communities at the respective habitats were distinct and different in the diversity and stability to each other, which may have contributed to the diversity of overall bacterial communities in the paddy field ecosystem.