长期施肥对茶园土壤微生物群落功能多样性的影响

利用BIOLOG研究长期施肥后茶园土壤微生物群落功能多样性变化,结果表明:与清耕(CK)相比,各长期施肥处理AWCD值的变化速度(斜率)和最终能达到的AWCD值均有不同程度提高,其大小顺序为:DWY>DY>W>CK,可见施肥能不同程度提高微生物整体活性和丰富度,以有机无机肥配施效果最好。分析多样性指数表明:各处理对土壤常见微生物种类影响并不大,施有机肥使微生物群落均匀度有所降低。对碳源利用主成分起分异作用的主要是糖类和羧酸类物质。对AWCD值、多样性指数与土壤养分因子的相关性分析表明,在红壤茶园中土壤肥力提高有利于土壤微生物活性的提高。     

紫茎泽兰入侵对土壤细菌的群落组成和多样性的影响

外来生物入侵可能对生物群落结构和生态系统功能产生多种影响, 但入侵植物与土壤微生物群落组成和多样性的关系尚不清楚。为了揭示外来植物紫茎泽兰(Eupatorium adenophorum)入侵对土壤化学性质和细菌群落组成及多样性的影响, 本研究利用第二代高通量测序技术, 比较了紫茎泽兰不同入侵程度的生境(本地植物群落、紫茎泽兰与本地植物混生群落、紫茎泽兰单优群落)土壤中细菌群落的差异。土壤化学性质分析表明, 土壤pH值、有机质、全N和全K随着紫茎泽兰的入侵而逐渐降低, 而土壤全P则在入侵程度最高的生境土壤中最高。通过测序共获得7,755个细菌OUT (operational taxonomic unit)。结果表明, 紫茎泽兰入侵对土壤的细菌多样性影响较小, ACE和Chao指数在3种不同生境间的差异不显著。细菌在紫茎泽兰与本地植物混生群落中的Shannon指数最低, 即细菌的多样性在中等入侵程度的生境最低。此外, 紫茎泽兰入侵改变了土壤细菌组成和结构, 酸杆菌门(Acidobacteria)和疣微菌门(Verrucomicrobia)的相对丰度, 从本地植物群落、混合群落到紫茎泽兰单优群落, 呈现出先增加后减少的趋势。可见, 紫茎泽兰入侵一定程度上改变了土壤微生物的多样性和群落结构, 并改变了土壤的化学性质。     

用PCR-DGGE研究长期施用无机肥对种稻红壤微生物群落多样性的影响

以中国科学院红壤生态试验站的发育于第四纪红粘土的种稻红壤为研究对象,采用PCR-DGGE方法研究了长期施用无机肥对土壤微生物群落多样性的影响。在种植双季稻、连续13a施用不同无机肥后,土壤中细菌、古菌、放线菌和真菌的群落结构发生了较大的变化。未种植水稻的土壤与种稻土壤间四类微生物SSUrDNADGGE带谱相似性只有33%~66%。施磷肥的处理NP、PK、NPK之间微生物群落结构相似性较高,4类微生物的SSUrDNADGGE带谱相似性高达75%~81%。施氮钾肥(NK)、不施肥(CK)处理与施磷肥处理间土壤微生物群落结构的差异较大,其四类微生物的SSUrDNADGGE带谱相似性分别为69%~77%、55%~77%。研究的目的是深入地了解土壤中微生物群落的多样性,为科学施肥、合理利用土壤、保护微生物多样性和实现农业生态系统的可持续发展提供科学依据。     

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils.     

施肥和土壤管理对土壤微生物生物量碳、氮和群落结构的影响

以中国科学院沈阳生态试验站的长期定位试验为平台,研究了不同施肥和土壤管理对潮棕壤微生物生物量碳、氮和群落结构的影响。结果表明,裸地和农田处理的微生物生物量碳、氮较低,但是农田处理下施肥增加了微生物生物量,其中NPK+M效果最明显。DGGE图谱显示,处理间细菌条带分布较相似,其中裸地的细菌多样性最高;长期施肥和土壤管理改变了土壤真菌群落结构,施肥增加了真菌多样性,且有机肥的影响大于化肥;不同处理间氨氧化细菌群落结构差异显著,NPK+M显著增加了氨氧化细菌多样性,且无机肥和有机肥对氨氧化细菌群落影响不同。施肥和土壤管理对细菌影响较小,但显著改变了真菌和氨氧化细菌的群落结构。聚类分析结果显示,土壤管理措施较施肥对细菌、真菌和氨氧化细菌群落的影响更为显著。     

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity.     

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.     

小麦-甘薯轮作长期增施有机肥对碱性土壤固氮菌群落结构及多样性的影响

生物固氮为农业生态系统提供天然的氮素来源,探究长期增施有机肥对土壤固氮菌群落的影响,为合理增施有机肥和维持土壤固氮微生物群落多样性提供科学依据。选取小麦-甘薯轮作中连续37a不施肥对照(CK)、单施化肥(NPK)、化肥+有机肥(NPKM)处理的甘薯季碱性土壤样品为研究对象。采用Illumina MiSeq高通量测序技术,研究土壤固氮菌群落的组成、多样性及其与土壤特性的关系。结果表明:与对照和单施化肥相比,长期增施有机肥降低土壤固氮菌群落丰富度和多样性,且丰富度与土壤pH显著正相关,与有机碳、全氮和有效养分(硝态氮、有效磷和速效钾)显著负相关。主坐标分析表明长期施肥显著改变土壤固氮菌群落结构,与对照相比,增施有机肥比单施化肥对固氮菌群落结构的影响更大。冗余分析表明土壤有机碳和速效钾是影响固氮菌群落结构改变最主要的因素。长期增施有机肥显著降低变形菌门、蓝藻菌门、Beta-变形菌和固氮弧菌属的相对丰度,显著增加硝化螺旋菌门、酸杆菌门和硝化螺菌属的相对丰度,这与土壤pH、有机碳和有效养分显著相关。因此,在碱性土壤上长期增施有机肥对固氮菌群落结构的改变更大,对群落多样性的抑制作用更强。     

长期施用化肥及秸秆还田对砂姜黑土细菌群落的影响

【目的】在施用化肥的基础上进行秸秆还田是提高砂姜黑土肥力的有效措施,以往的研究只注重秸秆还田对土壤结构、肥力等物理化学性状方面的研究,缺少施肥对砂姜黑土微生物群落影响的研究。本研究以安徽蒙城典型的砂姜黑土为研究对象,以期揭示长期施用化肥和秸秆还田对砂姜黑土细菌群落的影响。【方法】采用454高通量测序对砂姜黑土不同农业施肥措施下的细菌群落进行分析研究,并通过生物信息学的分析方法揭示影响砂姜黑土细菌群落的主要因素。【结果】通过对454高通量测序数据的分析,发现砂姜黑土主要的细菌门类为放线菌、变形菌、酸杆菌、绿弯菌和拟杆菌。长期施用化肥显著提高了砂姜黑土肥力和作物产量,但导致了细菌群落结构的显著变化和多样性的显著降低。秸秆还田有利于土壤肥力的进一步提高,但是并没有缓解长期施用化肥对土壤细菌群落产生的不利影响。分析发现土壤pH的变化是导致土壤细菌群落变异的主要因素。【结论】在施用化肥的基础上进行秸秆还田有利于砂姜黑土肥力的提升,然而并没有缓解由施肥导致的土壤酸化对土壤细菌群落组成和多样性产生的不利影响。这暗示秸秆还田可能并未对砂姜黑土微生物生态产生根本性的有益影响,对于秸秆农田的利用方式还需要进一步研究,以达到农业生产效益和生态效益的并重。     

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. This revised version was published online in August 2006 with corrections to the Cover Date.     

不同树盘覆盖对矮砧苹果园土壤微生物群落结构和多样性的影响

以7年生矮化中间砧苹果为试材,研究了不同材质树盘覆盖对土壤微生物丰度、群落结构和多样性的影响。高通量测序结果表明,防水园艺地布和塑膜覆盖处理提高了0-20 cm土层变形菌门的相对丰度和20-40 cm土层变形菌门的相对丰度,防水园艺地布处理还显著提高了土壤细菌Ace和Simpson指数。相较于防水、塑膜覆盖处理,透水园艺地布不仅提高了0-20 cm土层变形菌门、接合菌门的相对丰度,而且提高了土壤细菌Ace、Chao1和Simpson指数,降低了土壤真菌Ace、Chao1和Simpson指数。树状聚类图结果显示,树盘覆盖显著改变了土壤细菌和真菌群落结构,以透水园艺地布覆盖处理的改变最为显著。综合分析认为,不同覆盖措施均有利于提高土壤细菌群落的丰富度和多样性,降低土壤真菌群落的丰富度和多样性,优化土壤微生物群落结构,其中以透水园艺地布覆盖的效果最好。     

盐城滨海滩涂湿地典型植物群落土壤微生物组成与结构特征

土壤微生物是生态系统维持正常结构与功能的重要组成部分,为探究盐城滩涂典型湿地土壤微生物群落结构特征,以江苏盐城滩涂互花米草、藨草、盐地碱蓬、芦苇及淤泥质光滩5种典型群落为对象,采用16S rRNA高通量测序技术分析0—10 cm(表层)、10—30 cm(中层)、30—60 cm(深层)土壤微生物多样性及群落结构。结果表明：(1)几种植物群落间,土壤微生物群落结构差异较大,主要体现在细菌群落结构的差异性,古菌群落结构差异相对较小。光滩与植物群落间,在土壤细菌种类及相对丰度上差异相对较大,互花米草群落与本土植物群落间,在微生物群落的细菌种类组成上存在较大差异;藨草群落土壤表层微生物群落结构与互花米草群落相似,深层与盐地碱蓬、芦苇群落相似。(2)同一群落不同层次土壤微生物群落结构相似,差异小于不同群落间土壤微生物群落的结构差异性;不同群落对应层次间,表深层土壤中五种群落土壤微生物多样性存在显著差异,中层土壤中五种群落微生物多样性差异不显著。总体上,植物群落类型对土壤微生物群落结构的影响大于土壤深度;与本土植物群落相比,互花米草群落土壤主要优势门微生物种类差异较小,但部分优势门微生物相对丰度...     

Influence of Long Term Irrigation with Pulp and Paper Mill Effluent on the Bacterial Community Structure and Catabolic Function in Soil

Microbial communities play a vital role in maintaining soil health. A multiphasic approach to assess the effect of pulp and paper mill effluent on both the structure and function of microbial soil communities is taken. Bacterial communities from agricultural soils irrigated with pulp and paper mill effluent were compared to communities form soils irrigated with well water. Samples were taken from fields in the state of Uttarakhand, India, where pulp and paper mill effluent has been used for irrigation for over 25 years. Comparisons of bacterial community structure were conducted using sequencing of the 16S rRNA gene from both isolates and clone libraries attained from the soil. Community-level physiological profiling was used to characterize the functional diversity and catabolic profile of the bacterial communities. The multiphasic approach using both physiological and molecular techniques proved to be a powerful tool in evaluating the soil bacterial community population and population differences therein. A significant and consistent difference in the population structure and function was found for the bacterial communities from soil irrigated with effluent in comparison to fields irrigated with well water. The diversity index parameters indicated that the microbial community in pulp and paper mill effluent irrigated fields were more diverse in both structure and function. This suggests that the pulp and paper mill effluent is not having a negative effect on the soil microbial community, but in fact may have a positive influence. In terms of soil health, this finding supports the continued use of pulp and paper mill effluent for irrigation. This is however only one aspect of soil health which was evaluated. Further studies on soil resistance and robustness could be undertaken to holistically evaluate soil health in this situation.     

微生物菌剂施用对设施茄子根际土壤养分和细菌群落多样性的影响

[背景]设施茄子连作种植和化学肥料过量施用造成土壤养分失衡、微生物多样性降低、土传病害严重等土壤质量问题,微生物制剂是改善土壤环境质量的一项重要措施。[目的]确定微生物菌剂施用对设施茄子根际土壤养分及细菌群落多样性的影响。[方法]在河北省农林科学院鹿泉大河实验园区,以含有哈茨木霉和巨大芽孢杆菌的微生物菌剂为供试菌剂,采用传统的化学分析方法测定微生物菌剂处理和对照茄子开花期、拉秧期土壤的养分含量;采用稀释涂平板方法测定土壤可培养微生物的数量;采用高通量测序技术测定土壤细菌16S rRNA基因V3-V4区,分析处理和对照土壤的微生物多样性和群落分布规律。[结果]与对照相比,微生物菌剂处理提高了茄子开花期和拉秧期的根际土壤养分含量,拉秧期微生物菌剂处理根际土壤中全氮、碱解氮、有效磷、速效钾含量分别较对照增加13.85%、21.07%、31.51%和55.94%;施用微生物菌剂能够改变土壤可培养微生物的数量和构成,微生物菌剂处理土壤中细菌、真菌、放线菌的数量均显著增加,其中细菌、放线菌在微生物总量中所占比例增加,而真菌的占比则有所降低。微生物菌剂处理能够提高土壤微生物的Shannon指数、降低Simpson指数,ACE指数和Chao1指数差异不显著,表明微生物菌剂能够增加土壤的微生物群落多样性,对微生物群落丰富度影响不明显。从目水平上分析菌剂处理和对照的微生物组成,发现微生物菌剂处理增加了土壤中黄单胞菌目(Xanthomonadales)、红螺菌目(Rhodospirillales)、鞘脂杆菌目(Sphingobacteriales)、芽孢杆菌目(Bacillales)、纤维黏网菌目(Cytophagales)、假单胞菌目(Pseudomonadales)等优势菌目的占比,降低了伯克氏菌目(Burholderiales)、黄杆菌目(Flavobacteriales)等病原菌的占比。微生物菌剂的施入能够促进茄子营养生长,增加茄子的产量,增幅为18.52%。[结论]微生物菌剂作为一种新型环保肥料,具有改善土壤营养状况、增加土壤可培养微生物数量、提高土壤微生物多样性的作用,该结果为微生物菌剂的合理施用提供了科学依据。     

Long-Term Nitrogen Amendment Alters the Diversity and Assemblage of Soil Bacterial Communities in Tallgrass Prairie

Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important implications for both managed and natural grassland ecosystems.     

Impact of chromium-contaminated wastewaters on the microbial community of a river

The influence of chromium on the microbial community structure was analyzed in a river system subjected to long-term chromium contamination, by plating and by sequencing 16S rRNA genes cloned from DNA extracted from the river sediments. We also analyzed the influence of chromium on the ability of the microbial community to resist and reduce Cr(VI) and on its resistance to antibiotics. Shifts in the microbial community structure were analyzed by amplified ribosomal DNA restriction analysis fingerprinting. The isolates obtained were phylogenetically related to Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria, whereas Acidobacteria and Deltaproteobacteria were only revealed by clone analyses. Cr(VI)-resistant and Cr(VI)-reducing strains were isolated in all sites examined. However, each sample site had a microbial community with a different antibiotic resistance pattern. Our study seems to indicate that in this river ecosystem chromium influenced the microbial communities, altering some of their functional characteristics, such as the percentage of the microbial community able to resist or to reduce Cr(VI) and the phylogenetic groups isolated, but it did not affect the structural diversity. Furthermore, the concentration of Cr(VI) in the sediments could not be correlated with a lower number of bacteria or lower index of generic diversity, neither with the ability of the microbial community to resist or to reduce higher Cr(VI) concentrations.     

长期不同施肥制度对潮棕壤微生物生物量碳、氮及细菌群落结构的影响

以沈阳生态站长期定位试验为研究平台,采用传统氯仿熏蒸方法和现代PCR-DGGE技术探讨了长期不同施肥制度对土壤微生物生物量碳和氮及细菌群落结构的影响.结果表明:在整个试验期,土壤微生物生物量碳和氮的动态变化趋势基本相同;长期施用有机肥可显著提高土壤有机碳和土壤微生物生物量碳和氮含量,而长期施用化肥明显降低土壤pH,土壤微生物生物量碳和氮含量也显著降低.DGGE图谱表明:不同施肥处理的细菌16S rDNA多数条带分布相同,28条带中有18条为共有条带,说明潮棕壤中细菌类群较稳定,但其数量受到施肥的影响;长期施用有机肥促进潮棕壤细菌群落结构的多样性,而施用化肥处理则降低了其多样性.     

Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops

Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.     

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities.     

Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences

Microbes are key components of the soil environment and are important contributors to the sustainability of agricultural systems, which is especially significant for biofuel crops growing on marginal lands. We studied bacterial communities in the rhizosphere of five biofuel crops cultivated in four locations in Michigan to determine which factors were correlated to changes in the structure of those communities. Three of these sites were marginal lands in that two were not suitable for conventional agriculture and one was regulated as a brownfield due to prior industrial pollution. Bacterial community composition and structure were assessed by 454 sequencing of the 16S rRNA gene. A total of 387,111 sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as plant species, soil attributes, and location. The most abundant bacterial phyla found in the rhizosphere of all crops were Acidobacteria, Proteobacteria, Actinobacteria, and Verrucomicrobia. Bacterial communities grouped by location rather than by crop and their structures were correlated to soil attributes, principally pH, organic matter, and nutrients. The effect of plant species was low but significant, and interactions between locations, plant species, and soil attributes account for most of the explained variation in the structure of bacterial communities, showing a complex relationship between bacterial populations and their environment. Bacterial diversity was higher in the agricultural sites compared to adjacent forest sites, indicating that the cultivation of those biofuel crops increased the rRNA diversity.