Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.     

Phosphate Addition and Plant Species Alters Microbial Community Structure in Acidic Upland Grassland Soil

Agricultural improvement (addition of fertilizers, liming) of seminatural acidic grasslands across Ireland and the UK has resulted in significant shifts in floristic composition, soil chemistry, and microbial community structure. Although several factors have been proposed as responsible for driving shifts in microbial communities, the exact causes of such changes are not well defined. Phosphate was added to grassland microcosms to investigate the effect on fungal and bacterial communities. Plant species typical of unimproved grasslands (Agrostis capillaris, Festuca ovina) and agriculturally improved grasslands (Lolium perenne) were grown, and phosphate was added 25 days after seed germination, with harvesting after a further 50 days. Phosphate addition significantly increased root biomass (p < 0.001) and shoot biomass (p < 0.05), soil pH (by 0.1 U), and microbial activity (by 5.33 mg triphenylformazan [TPF] g⁻¹ soil; p < 0.001). A slight decrease (by 0.257 mg biomass-C g⁻¹ soil; p < 0.05) in microbial biomass after phosphate addition was found. The presence of plant species significantly decreased soil pH (p < 0.05; by up to 0.2 U) and increased microbial activity (by up to 6.02 mg TPF g⁻¹ soil) but had no significant effect on microbial biomass. Microbial communities were profiled using automated ribosomal intergenic spacer analysis. Multidimensional scaling plots and canonical correspondence analysis revealed that phosphate addition and its interactions with upland grassland plant species resulted in considerable changes in the fungal and bacterial communities of upland soil. The fungal community structure was significantly affected by both phosphate (R = 0.948) and plant species (R = 0.857), and the bacterial community structure was also significantly affected by phosphate (R = 0.758) and plant species (R = 0.753). Differences in microbial community structure following P addition were also revealed by similarity percentage analysis. These data suggest that phosphate application may be an important contributor to microbial community structural change during agricultural management of upland grasslands.     

Effect of Temperature on Structure and Function of the Methanogenic Archaeal Community in an Anoxic Rice Field Soil

Soil temperatures in Italian rice fields typically range between about 15 and 30°C. A change in the incubation temperature of anoxic methanogenic soil slurry from 30°C to 15°C typically resulted in a decrease in the CH₄ production rate, a decrease in the steady-state H₂ partial pressure, and a transient accumulation of acetate. Previous experiments have shown that these changes were due to an alteration of the carbon and electron flow in the methanogenic degradation pathway of organic matter caused by the temperature shift (K. J. Chin and R. Conrad, FEMS Microbiol. Ecol. 18:85–102, 1995). To investigate how temperature affects the structure of the methanogenic archaeal community, total DNA was extracted from soil slurries incubated at 30 and 15°C. The archaeal small-subunit (SSU) rRNA-encoding genes (rDNA) of these environmental DNA samples were amplified by PCR with an archaeal-specific primer system and used for the generation of clone libraries. Representative rDNA clones (n = 90) were characterized by terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis. T-RFLP analysis produced for the clones terminally labeled fragments with a characteristic length of mostly 185, 284, or 392 bp. Sequence analysis allowed determination of the phylogenetic affiliation of the individual clones with their characteristic T-RFLP fragment lengths and showed that the archaeal community of the anoxic rice soil slurry was dominated by members of the families Methanosarcinaceae (185 bp) and Methanosaetaceae (284 bp), the kingdom Crenarchaeota (185 or 284 bp), and a novel, deeply branching lineage of the (probably methanogenic) kingdom Euryarchaeota (392 bp) that has recently been detected on rice roots (R. Großkopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983–4989, 1998). The structure of the archaeal community changed when the temperature was shifted from 30°C to 15°C. Before the temperature shift, the clones (n = 30) retrieved from the community were dominated by Crenarchaeota (70%), “novel Euryarchaeota” (23%), and Methanosarcinacaeae (7%). Further incubation at 30°C (n = 30 clones) resulted in a relative increase in members of the Methanosarcinaceae (77%), whereas further incubation at 15°C (n = 30 clones) resulted in a much more diverse community consisting of 33% Methanosarcinaceae, 23% Crenarchaeota, 20% Methanosaetaceae, and 17% novel Euryarchaeota. The appearance of Methanosaetaceae at 15°C was conspicuous. These results demonstrate that the structure of the archaeal community in anoxic rice field soil changed with time and incubation temperature.     

Effect of Sheep Urine Deposition on the Bacterial Community Structure in an Acidic Upland Grassland Soil

The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (Agrostis capillaris) and agriculturally improved (Lolium perenne) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne-planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.     

Bacterial Activity, Community Structure, and Centimeter-Scale Spatial Heterogeneity in Contaminated Soil

In an anthropogenically disturbed soil (88% sand, 8% silt, 4% clay), 150-mg samples were studied to examine the fine-scale relationship of bacterial activity and community structure to heavy metal contaminants. The soils had been contaminated for over 40 years with aromatic solvents, Pb, and Cr. Samples from distances of <1, 5, 15, and 50 cm over a depth range of 40–90 cm underwent a sequential analysis to determine metabolic potential (from ¹⁴C glucose mineralization), bacterial community structure [using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)], and total extractable Pb and Cr levels. Metabolic potential varied by as much as 10,000-fold in samples <1 cm apart; log–log plots of metal concentration and microbial metabolic potential showed no correlation with each other. Overall, metal concentrations ranged from 9 to 29,000 mg kg⁻¹ for Pb and from 3 to 8500 mg kg⁻¹ for Cr with small zones of high contamination present. All regions exhibited variable metal concentrations, with some soil samples having 30-fold differences in metal concentration in sites <1 cm apart. Geostatistical analysis revealed a strong spatial dependence for all three parameters tested (metabolic activity, Pb, and Cr levels) with a range up to 30 cm. Kriging maps showed that in zones of high metal, the corresponding metabolic activity was low suggesting that metals negatively impacted the microbial community. PCR-DGGE analysis revealed that diverse communities were present in the soils with a random distribution of phylotypes throughout the sampling zones. These results suggest the presence of spatially isolated microbial communities within the soil profile.     

Archaeal Community Structure and Pathway of Methane Formation on Rice Roots

The community structure of methanogenic Archaea on anoxically incubated rice roots was investigated by amplification, sequencing, and phylogenetic analysis of 16S rRNA and methyl-coenzyme M reductase (mcrA) genes. Both genes demonstrated the presence of Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Rice cluster I, an uncultured methanogenic lineage. The pathway of CH₄ formation was determined from the ¹³C-isotopic signatures of the produced CH₄, CO₂ and acetate. Conditions and duration of incubation clearly affected the methanogenic community structure and the pathway of CH₄ formation. Methane was initially produced from reduction of CO₂ exclusively, resulting in accumulation of millimolar concentrations of acetate. Simultaneously, the relative abundance of the acetoclastic methanogens (Methanosarcinaceae, Methanosaetaceae), as determined by T-RFLP analysis of 16S rRNA genes, was low during the initial phase of CH₄ production. Later on, however, acetate was converted to CH₄ so that about 40% of the produced CH₄ originated from acetate. Most striking was the observed relative increase of a population of Methanosarcina spp. (but not of Methanosaeta spp.) briefly before acetate concentrations started to decrease. Both acetoclastic methanogenesis and Methanosarcina populations were suppressed by high phosphate concentrations, as observed under application of different buffer systems. Our results demonstrate the parallel change of microbial community structure and function in a complex environment, i.e., the increase of acetoclastic Methanosarcina spp. when high acetate concentrations become available.     

广东鹤山草坡的群落结构

分析了广东鹤册草坡群落结构。结果表明,该群落有高等植物１８种,分为灌木层和草本层２个层次,以矮高位芽、小型叶植物为主,种类以热带－亚热带分布种为主,Ｓｈａｎｏｎ－Ｗｅｉｎｅｒ多样性指数为１．２５,群落的叶面积指数为２．２８,生物量为１５．２２ｔ／ｈｍ＾２。比较了大陆退化草坡、海鸟退化草坡和当地的人工林的群落结构,提出了退化草坡的改造利用方式。     

松嫩盐碱草地西部的植物群落特征与土壤因子动态关系分析

应用逐步回归法,分析了5~9月松嫩盐碱草地植物群落的生物量、丰富度、多样性和均匀度与同月土壤因子间的关系。松嫩盐碱草地植物群落特征受若干土壤因子的共同影响,不同月份影响因子的变化较复杂。5~7月土壤盐分和养分共同影响着松嫩盐碱草地植物群落生物量,但是土壤盐分因子与群落生物量的相关性更明显（5月的Ca²⁺质量分数,6月和7月的Mg²⁺质量分数）。土壤盐分因子在整个生长季内对松嫩盐碱草地植物群落生物量的直接作用都大于土壤养分因子的。6月时影响松嫩盐碱草地植物群落丰富度、Simpson指数和Shannon指数的土壤养分因子增加,其中土壤全氮质量分数的直接作用是所有土壤因子中最大的。8月植物群落生物量、Simpson指数和Shannon指数仅受土壤盐分因子影响,其中生物量与土壤pH值以及Simpson指数与土壤碱化度都是极显著负相关,Shannon指数与土壤含盐量显著负相关。6~9月的松嫩盐碱草地植物群落均匀度也同时受土壤养分和盐分因子的作用,其中6月和9月时土壤盐分因子对群落均匀度的直接作用更突出。生长末期（9月）松嫩盐碱草地植物群落生物量与土壤因子间的关系以及生长初期（5月）植物群落均匀度与土壤因子间的关系都不明显。     

Linking Microbial Community Structure and Function to Seasonal Differences in Soil Moisture and Temperature in a Chihuahuan Desert Grassland

Global and regional climate models predict higher air temperature and less frequent, but larger precipitation events in arid regions within the next century. While many studies have addressed the impact of variable climate in arid ecosystems on plant growth and physiological responses, fewer studies have addressed soil microbial community responses to seasonal shifts in precipitation and temperature in arid ecosystems. This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency of precipitation within any given year. Carbon utilization by fungi in the cooler winter exceeded use in the warmer summer each year suggesting that soil temperature, rather than soil moisture, strongly influenced fungal carbon use and structure and function dynamics. The structure/function relationship for AM fungi and soil bacteria notably changed across season. Moreover, the abundance of Gram-positive bacteria was lower in the winter compared to Gram-negative bacteria. Bacterial carbon use, however, was highest in the summer and lower during the winter. Enzyme activities did not respond to either annual or seasonal differences in the magnitude or timing of precipitation. Specific structural components of the soil microbiota community became uncoupled from total microbial function during different seasons. This change in the microbial structure/function relationship suggests that different components of the soil microbial community may provide similar ecosystem function, but differ in response to seasonal temperature and precipitation. As soil microbes encounter increased soil temperatures and altered precipitation amounts and timing that are predicted for this region, the ability of the soil microbial community to maintain functional resilience across the year may be reduced in this Chihuahuan Desert ecosystem.     

Nematode Community Structure in a Vineyard Soil

Distribution of the nematode community in a California vineyard was studied over a 13-month period. Omnivorous and microbivorous nematodes were similarly distributed in the root zone, with greatest densities occurring between vine rows and near the soil surface. Greatest densities of plant-parasitic nematodes were found in the vine row, with the individual species differing in their vertical distribution. Total nematode biomass was greatest between rows near the surface. Biomass of plant parasites was greatest in the upper 30 cm of soil in the row, whereas biomass of microbivores was greatest in this region between rows. Of the plant-parasitic nematodes, the variability in distribution among vines was greatest for Paratylenchus hamatus and least for Meloidogyne spp.     

Inoculation with a Native Soil Community Advances Succession in a Grassland Restoration

Restoration on post‐agricultural land may be hindered by the degradation of the soil community, which has been shown to contribute to structuring plant communities and driving succession. Our experiment tested the effect of inoculation with remnant grassland whole soil with or without nurse plants on the survival and growth of uninoculated early and late successional plant species. In 2007 and 2008, we planted uninoculated early, mid, and late successional plant species 0.25–2 m away from a central point of inoculated nurse plants. We found a negative response to inoculation on early successional plants and a positive response to inoculation on mid to late successional plants. This work suggests that the restoration of the soil community is critical to establishing a late successional plant community and that the benefit of inoculated plants can spread to neighbors.     

放牧对草地群落与土壤特征的影响

针对放牧干扰对草地生态系统的影响,采用回归分析和典型对应分析(CCA)方法,研究放牧对草地植物群落物种多样性与生产力、土壤碳氮含量与生物量关系的影响。结果表明:(1)与休牧草地相比,放牧草地的地上生物量降低31.63%,凋落物生物量降低134.29%;放牧草地的禾草类生物量提高19.77%,而杂草类生物量和豆科类生物量分别降低31.09%和23.42%。(2)当物种多样性指数小于1.3时,休牧草地的生产力明显高于放牧草地;当物种多样性指数大于1.3时,放牧草地的生产力高于休牧草地。(3)CCA分析显示,家畜主要通过影响群落地上生物量、凋落物质量和土壤容重进而影响土壤的碳氮含量。(4)当群落地上生物量小于100g·m-2时,休牧草地的土壤有机碳和全氮含量高于放牧草地,当群落地上生物量大于100g·m-2时,放牧草地则略高于休牧草地。(5)当群落地下生物量小于1 200g·m-2时,放牧草地土壤有机碳、全氮含量高于休牧草地;当地下生物量大于1 200g·m-2时,放牧草地则略低于休牧草地。     

垃圾填埋场渗滤液中古细菌群落16S rRNA基因的ARDRA分析

利用特异性的引物对,选择性扩增垃圾填埋场渗滤液中古细菌群落的18S rRNA基因片断,在此基础上建立16S rDNA克隆文库,经古细菌通用寡核苷酸探针的原位杂交筛选后,克隆文库内古细菌16S rDNA扩增片断的多样性通过ARDRA分析（amplified rDNA restriction analysis)而获得,利用PCR将各组重克隆子内的16S rDNA外源片断再扩增出来后,两种限制性内切酶－Hha I和HaeⅢ－被分别用于16S rDNA克隆片断的限制酶切分析,结果表明,随机选出的70个古细菌16S rDNA克隆片断被妥为21个不同的ARDRA型（组）,其中的两个优势型总共占了所有被分析克隆子的60％,而其余19个型的相对丰度均处于较低的水平,当中的14个型更仅含有1个克隆子,通过对16S rRNA基因的PCR扩增,克隆及其ARDRA分析,能快速地获得有关填埋场渗滤液中古细菌群落的结构及其多样性的初步信息。     

荒漠土壤藻群落结构的原生演替

微生物结皮是荒漠化治理中新的热点之一,但其关键形成生物--微型藻类如何通过群落结构的变化向地衣结皮、藓类结皮转变的机理仍是未知的.本文以时空替代法,将沙坡头流沙,4、8、17、34及42龄结皮当作同一群落演替进程中的6个阶段,通过系统聚类、丰分量分析的方法首次对这一问题进行了研究,结果显示该地荒漠藻群落的原生演替朝着蓝藻总丰度和爪哇伪枝藻(Scytonema javanicum)丰度逐渐下降,纤细席藻(Phormidiumtenue)、绿藻、硅藻丰度逐渐增加的方向进行;多样性随群落演替的发展而增高;生物量在初期呈正向演替,后期随地衣、藓类的入侵逐渐下降;演替速度非常缓慢,高龄结皮中的优势种仍是建群种,只是优势度略有下降;水分、植被覆盖、地形、时间,土壤理化性质都影响演替途径和速度,特别是Mn含量对演替有重要的阈值作用.     

荒漠土壤藻群落结构的原生演替

微生物结皮是荒漠化治理中新的热点之一,但其关键形成生物——微型藻类如何通过群落结构的变化向地衣结皮、藓类结皮转变的机理仍是未知的。本文以时空替代法,将沙坡头流沙,4、8、17、34及42龄结皮当作同一群落演替进程中的6个阶段,通过系统聚类、主分量分析的方法首次对这一问题进行了研究,结果显示该地荒漠藻群落的原牛演替朝着蓝藻总丰度和爪畦伪枝藻(Scytonema javanicum)丰度逐渐下降,纤细席藻(Phormidium tenue)、绿藻、硅藻丰度逐渐增加的方向进行;多样性随群落演替的发展而增高;生物量在初期呈正向演替,后期随地衣、藓类的入侵逐渐下降;演替速度非常缓慢,高龄结皮中的优势种仍是建群种,只是优势度略有下降;水分、植被覆盖、地形、时间,土壤理化性质都影响演替徐径和速度．特别是Mn含量对演替有重要的阈值作用。     

Methanogenic Pathway and Archaeal Community Structure in the Sediment of Eutrophic Lake Dagow: Effect of Temperature

Methanogenic degradation of organic matter is an important microbial process in lake sediments. Temperature may affect not only the rate but also the pathway of CH₄ production by changing the activity and the abundance of individual microorganisms. Therefore, we studied the function and structure of a methanogenic community in anoxic sediment of Lake Dagow, a eutrophic lake in north-eastern Germany. Incubation of sediment samples (in situ 7.5°C) at increasing temperatures (4, 10, 15, 25, 30°C) resulted in increasing production rates of CH₄ and CO₂ and in increasing steady-state concentrations of H₂. Thermodynamic conditions for H₂/CO₂ -dependent methanogenesis were only exergonic at 25 and 30°C. Inhibition of methanogenesis with chloroform resulted in the accumulation of methanogenic precursors, i.e., acetate, propionate, and isobutyrate. Mass balance calculations indicated that less CH₄ was formed via H₂ at 4°C than at 30°C. Conversion of ¹⁴CO₂ to ¹⁴CH₄ also showed that H₂/CO₂ -dependent methanogenesis contributed less to total CH₄ production at 4°C than at 30°C. [2–¹⁴ C]Acetate turnover rates at 4°C accounted for a higher percentage of total CH₄ production than at 30°C. Collectively, these results showed a higher contribution of H₂-dependent methanogenesis and a lower contribution of acetate-dependent methanogenesis at high versus low temperature. The archaeal community was characterized by cloning, sequencing, and phylogenetic analysis of the 16S rRNA genes retrieved from the sediment. Sequences were affiliated with Methanosaetaceae, Methanomicrobiaceae, and three deeply branching euryarchaeotal clusters, i.e., group III, Rice cluster V, and a novel euryarchaeotal cluster, the LDS cluster. Terminal restriction fragment length polymorphism (T-RFLP) analysis showed that 16S rRNA genes affiliated to Methanosaetaceae (20–30%), Methanomicrobiaceae (35–55%), and group III (10–25%) contributed most to the archaeal community. Incubation of the sediment at different temperatures (4–30°C) did not result in a systematic change of the archaeal community composition, indicating that change of temperature primarily affected the activity rather than the structure of the methanogenic community.