Microbial characteristics of soils on a latitudinal transect in Siberia

Soil microbial properties were studied from localities on a transect along the Yenisei River, Central Siberia. The 1000 km‐long transect, from 56°N to 68°N, passed through tundra, taiga and pine forest characteristic of Northern Russia. Soil microbial properties were characterized by dehydrogenase activity, microbial biomass, composition of microbial community (PLFAs), respiration rates, denitrification and N mineralization rates. Relationships between vegetation, latitude, soil quality (pH, texture), soil organic carbon (SOC) and the microbial properties were examined using multivariate analysis. In addition, the temperature responses of microbial growth (net growth rate) and activity (soil respiration rate) were tested by laboratory experiments. The major conclusions of the study are as follows: 1. Multivariate analysis of the data revealed significant differences in microbial activity. SOC clay content was positively related to clay content. Soil texture and SOC exhibited the dominant effect on soil microbial parameters, while the vegetation and climatic effects (expressed as a function of latitude) were weaker but still significant. The effect of vegetation cover is linked to SOC quality, which can control soil microbial activity. 2. When compared to fine‐textured soils, coarse‐textured soils have (i) proportionally more SOC bound in microbial biomass, which might result in higher susceptibility of SOC transformation to fluctuation of environmental factors, and (ii) low mineralization potential, but with a substantial part of the consumed C being transformed to microbial products. 3. The soil microbial community from the northernmost study region located within the permafrost zone appears to be adapted to cold conditions. As a result, microbial net growth rate became negative when temperature rose above 5 °C and C mineralization then exceeded C accumulation.     

Carbon Mineralization in Peatlands: Does the Soil Microbial Community Composition Matter?

Peat from four geographically separated peatlands (up to 1,500 km apart) with distinct vegetation across North America was sterilized and inoculated with microbial consortia from either the home site or from the other sites. This reciprocal inoculation microcosm experiment examined how different microbial communities adapted to various peat substrates and how this in turn influenced C-mineralization patterns. The experimental approach allows distinctions to be made as to whether microbial community structure, peat properties, or imposed environmental conditions are primary drivers of peat C mineralization. Two additional inocula collected from other freshwater environments (industrially polluted harbor and lake sediments) were also added to each peat type to investigate the response of clearly disparate microbial communities. We hypothesized that the peat properties, such as substrate quality and physical structure, would dictate microbial community composition and activity, thus inoculations from different sites into the same peat soil would lead to the establishment of very similar microbial communities both phylogenetically and functionally. Post-incubation, the bacterial communities in each site converged towards a similar community regardless of the inoculum source, with the exception of peat inoculated with polluted harbor sediment. Inoculum type had no effect on C mineralization rates compared with controls, except for the two disparate inocula, which had lower rates in all peat types. Variation in microbial community structure measured as nonmetric multidimensional scaling axes scores or richness did not correlate significantly with microbial activity. Overall, these findings suggest that abiotic variables (e.g., pH, aeration, moisture content, and temperature) are the dominant control on peatland microbial activity and community composition, and in natural peatlands the microbial community can quickly adapt to future environmental change.     

黄土丘陵沟壑区地形变化对土壤微生物群落功能多样性的影响

研究黄土高原丘陵沟壑区破碎地形对土壤微生物功能多样性的影响,对于理解复杂地形区生态过程与系统功能的空间变化具有重要意义。选择陕西省安塞县陈家洼为研究区,依据坡面地形变化选择不同坡位土壤,采用Biolog微平板培养法探究地形变化对土壤微生物群落功能多样性的影响。实验发现,土壤微生物群落培养的平均颜色变化率(AWCD)增长曲线总的呈现出坡下部坡中部坡上部的规律,且坡下部AWCD值与坡中部、坡上部间差异显著(P0.05);坡下部土壤微生物群落功能多样性显著高于坡中部和坡上部,但不同土层深度(0—10 cm、10—20 cm)间无显著性差异(P0.05);对土壤微生物群落功能多样性差异贡献较大的碳源是糖类、羧酸类和多酚化合物类碳源;土壤含水率高低是不同坡位土壤微生物群落功能多样性差异显著的主要原因;微生物群落丰富度(H)和均一度(D)与土壤全氮含量正相关,优势度(U)反之,土壤全碳、全磷和p H对土壤微生物群落结构和功能多样性差异作用不显著。     

Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use

Abstract The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone. Received: 1 December 1999; Accepted: 6 June 2000; Online Publication: 28 August 2000     

Spatial Heterogeneity and Soil Nitrogen Dynamics in a Burned Black Spruce Forest Stand: Distinct Controls at Different Scales

We evaluated spatial patterns of soil N and C mineralization, microbial community composition (phospholipid fatty acids), and local site characteristics (plant/forest floor cover, soil pH, soil %C and %N) in a 0.25-ha burned black spruce forest stand in interior Alaska. Results indicated that factors governing soil N and C mineralization varied at two different scales. In situ net N mineralization was autocorrelated with microbial community composition at relatively broad scales (∼ ∼8 m) and with local site characteristics (`site' axis 1 of non-metric scaling ordination) at relatively fine scales (2–4 m). At the scale of the individual core, soil moisture was the best predictor of in situ net N mineralization and laboratory C mineralization, explaining between 47 and 67% of the variation (p < 0.001). Ordination of microbial lipid data showed that bacteria were more common in severely burned microsites, whereas fungi were more common in low fire severity microsites. We conclude that C and N mineralization rates in this burned black spruce stand were related to different variables depending on the scale of analysis, suggesting the importance of considering multiple scales of variability among key drivers of C and N transformations.     

Monitoring of accelerated naphthalene-biodegradation in a bioaugmented soil slurry

The effect of microbial inoculation on the mineralization of naphthalene in a bioslurry treatment was evaluated in soil slurry microcosms. Inoculation by Pseudomonas putida G7 carrying the naphthalene dioxygenase (nahA) gene resulted in rapid mineralization of naphthalene, whereas indigenous microorganisms in the PAH-contaminated soil required a 28 h adaptation period before significant mineralization occurred. The number of nahA-like gene copies increased in both the inoculated and non-inoculated soil as mineralization proceeded, indicating selection towards naphthalene dioxygenase producing bacteria in the microbial community. In addition, 16S rRNA analysis by denaturing gradient gel electrophoresis (DGGE) analysis showed that significant selection occurred in the microbial community as a result of biodegradation. However, the indigenous soil bacteria were not able to compete with the P. putida G7 inoculum adapted to naphthalene biodegradation, even though the soil microbial community slightly suppressed naphthalene mineralization by P. putida G7.     

The Effects of Soil Bacterial Community Structure on Decomposition in a Tropical Rain Forest

Soil microorganisms are key drivers of terrestrial biogeochemical cycles, yet it is still unclear how variations in soil microbial community composition influence many ecosystem processes. We investigated how shifts in bacterial community composition and diversity resulting from differences in carbon (C) availability affect organic matter decomposition by conducting an in situ litter manipulation experiment in a tropical rain forest in Costa Rica. We used bar-coded pyrosequencing to characterize soil bacterial community composition in litter manipulation plots and performed a series of laboratory incubations to test the potential functional significance of community shifts on organic matter decomposition. Despite clear effects of the litter manipulation on soil bacterial community composition, the treatments had mixed effects on microbial community function. Distinct communities varied in their ability to decompose a wide range of C compounds, and functional differences were related to both the relative abundance of the two most abundant bacterial sub-phyla (Acidobacteria and Alphaproteobacteria) and to variations in bacterial alpha-diversity. However, distinct communities did not differ in their ability to decompose native dissolved organic matter (DOM) substrates that varied in quality and quantity. Our results show that although resource-driven shifts in soil bacterial community composition have the potential to influence decomposition of specific C substrates, those differences may not translate to differences in DOM decomposition rates in situ. Taken together, our results suggest that soil bacterial communities may be either functionally dissimilar or equivalent during decomposition depending on the nature of the organic matter being decomposed.     

种植阔叶树种和毛竹对土壤有机碳矿化与微生物群落结构的影响

为探明种植阔叶树种和毛竹对土壤有机碳矿化与微生物群落特征的影响,本研究通过盆栽试验和室内培养法比较分析种植香樟、木荷、青冈等阔叶树种与毛竹的土壤有机碳矿化速率和累计矿化量,并结合末端限制性片段长度多态性(T-RFLP)以及荧光定量PCR技术,分析土壤细菌、真菌群落组分与数量特征.结果表明:与种植阔叶树种的土壤相比,种植...     

蚂蚁筑巢对西双版纳热带森林土壤碳矿化动态的影响

蚂蚁作为生态系统工程师,能够通过筑巢定居活动增加有机物的输入、改变理化环境及刺激微生物活动,进而影响土壤有机碳矿化动态.本研究以西双版纳高檐蒲桃热带森林群落为研究对象,比较了蚁巢地与非巢地土壤有机碳矿化速率的动态特征,分析蚂蚁筑巢引起的土壤理化性质改变对土壤碳矿化速率的影响.结果表明: 蚂蚁筑巢显著影响土壤有机碳的矿化,相较于非巢地,蚁巢地平均土壤有机碳矿化速率提高19.2%;巢地与非巢地土壤有机碳矿化速率均表现为6月>9月>3月>12月;蚁巢地土壤有机碳矿化速率最大值出现在10～15 cm土层,而非巢地土壤有机碳矿化速率0～5 cm土层最高;蚂蚁筑巢对土壤理化性质产生了显著影响,相较于非蚁巢地,蚁巢地土壤温度、水分、有机碳、微生物生物量碳、全氮、水解氮、硝态氮和铵态氮平均增加幅度分别为7.6%、5.4%、9.9%、14.8%、13.4%、9.9%、24.1%、6.6%和19.4%,而土壤容重和pH平均降幅分别为1.4%和2.5%.相关性分析及主成分分析表明,土壤有机碳和土壤微生物量碳是影响土壤有机碳矿化速率的主控因子,土壤全氮、水解氮、铵态氮、硝态氮、温度和土壤含水率对土壤有机碳矿化的贡献次之.蚂蚁筑巢主要显著改变有机碳矿化的底物组分(土壤有机碳和土壤微生物生物量碳),进而调控西双版纳热带森林土壤有机碳矿化速率的时空动态.     

Soil microbial responses to elevated phosphorus and pH in acidic temperate deciduous forests

Although northern temperate forests are generally not considered phosphorus (P) limited, ecosystem P limitation may occur on highly weathered or strongly acidic soils where bioavailable inorganic P is low. In such environments, soil organisms may compensate by increasing the utilization of organic P via the production of extracellular enzymes to prevent limitation. In this study, we experimentally increased available P and/or pH in several acidic eastern deciduous forests underlain by glaciated and unglaciated soils in eastern Ohio, USA. We hypothesized that where inorganic P is low; soil microbes are able to access organic P by increasing production of phosphatase enzymes, thereby overcoming biogeochemical P limitations. We measured surface soil for: available P pools, N mineralization and nitrification rates, total C and N, enzymes responsible for C, N, and P hydrolysis, and microbial community composition (PLFA). Increasing surface soil pH a whole unit had little effect on microbial community composition, but increased N cycling rates in unglaciated soils. Phosphorus additions suppressed phosphatase activities over 60% in the unglaciated soils but were unchanged in the glaciated soils. All treatments had minimal influence on microbial biomass, but available pools of P strongly correlated with microbial composition. Microbes may be dependent on sources of organic P in some forest ecosystems and from a microbial perspective soil pH might be less important overall than P availability. Although our sampling was conducted less than 1 year after treatment initiation, microbial community composition was strongly influenced by available P pools and these effects may be greater than short-term increases in soil pH.     

Microbial communities show parallels at sites with distinct litter and soil characteristics

Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated by erm resistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.     

Biochar amendment to soils with contrasting organic matter level: effects on N mineralization and biological soil properties

Four biochar types, produced by slow pyrolysis of poultry litter (PL) and pine chips (P) at 400 or 500 °C, were added to two adjacent soils with contrasting soil organic matter (SOM) content (8.9 vs. 16.1 g C kg^?1). The N mineralization rate was determined during 14‐week incubations and assessments were made of the microbial biomass C, dehydrogenase activity, and the microbial community structure (PLFA‐extraction). The addition of PL biochars increased the net N mineralization (i.e., compared to the control treatment) in both soils, while for treatments with P biochars net N immobilization was observed in both soils. Increasing the pyrolysis temperature of both feedstock types led to a decrease in net N mineralization. The ratio of Bacterial to Fungal PLFA biomarkers also increased with addition of biochars, and particularly in the case of the 500 °C biochars. Next to feedstock type and pyrolysis temperature, SOM content clearly affected the assessed soil biological parameters, viz. net N mineralization or immobilization, MBC and dehydrogenase activity were all greater in the H soil. This might be explained by an increased chance of physical contact between the microbial community activated by SOM mineralization upon incubation and discrete biochar particles. However, when considering the H soil's double C and N content, these responses were disproportionally small, which may be partly due to the L soil's, somewhat more labile SOM. Nonetheless, increasing SOM content and microbial biomass and activity generally appears to result in greater mineralization of biochar. Additionally, higher N mineralization after PL addition to the H soil with lower pH than the L soil can be due to the liming effect of the PL biochars.     

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose (¹³C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO₃ ^? as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.     

Bacterial communities in Arctic fjelds of Finnish Lapland are stable but highly pH-dependent

The seasonal and spatial variations of microbial communities in Arctic fjelds of Finnish Lapland were studied. Phospholipid fatty acid analysis (PLFA) and terminal restriction fragment analysis (T-RFLP) of amplified 16S rRNA genes were used to assess the effect of soil conditions and vegetation on microbial community structures along different altitudes of two fjelds, Saana and Jehkas. Terminal restriction fragments were additionally analysed from c. 160 cloned sequences and isolated bacterial strains and matched with those of soil DNA samples. T-RFLP and PLFA analyses indicated relatively similar microbial communities at various altitudes and under different vegetation of the two fjelds. However, soil pH had a major influence on microbial community composition. Members of the phylum Acidobacteria dominated especially in the low pH soils (pH 4.6-5.2), but above pH 5.5, the relative amount of terminal restriction fragments corresponding to acidobacterial clones was substantially lower. Both T-RFLP and PLFA analysis indicated stable microbial communities as the DNA and fatty acid profiles were similar in spring and late summer samples sampled over 3 years. These results indicate that differences in microbial community composition could be explained primarily by variation in the bedrock materials that cause variation in the soil pH.     

Effect of soil macroaggregates crushing on C mineralization in a tropical deciduous forest ecosystem

Soil aggregates strongly influence C dynamics by affecting microbial activity. Our study tested the effect of soil crushing on C mineralization by laboratory incubation experiments of soil samples from a tropical deciduous forest ecosystem in Western Mexico. Soil samples were taken in January (dry season) and in October (rainy season). For each sampling date, the incubation experiment had a two factorial design with litter and macroaggregates (>250 μm) crushing as the main factors, both with two levels (with and without). At both sampling dates, the soil samples with intact macroaggregates had significantly higher C mineralization than the soil samples in which macroaggregates were crushed. The pH of leached solution was higher in the crushed soil samples than in uncrushed soil samples. The reduction of C mineralization caused by the disruption of soil aggregates is explained by the disturbance of environmental conditions within macroaggregates. The effect of macroaggregates crushing also reduced the differences of C mineralization between both seasons. We concluded that macroaggregates promote microbial activity by reducing the impact of variations in soil chemical and physical environmental conditions.     

Soil aggregates in a tropical deciduous forest: effects on C and N dynamics, and microbial communities as determined by t-RFLPs

The aim of this study was to analyze C and N dynamics, as well as, soil bacterial community structure within soil micro- and macro-aggregates in a tropical deciduous forest in México. We measured, for three landscape positions and three seasons of the year: total, microbial and available forms of C and N; potential C and N mineralization; and soil bacterial communities by using t-RFLPs. The highest total C concentrations were found in the north-slopes and in the dry season (DS) samples. In general, micro-aggregates had higher concentrations than macro-aggregates of available C and N forms, and microbial C. Similarly, micro-aggregates had the highest potential C mineralization and net N mineralization. We detected 149 different OTUs (operational taxonomic units) from which 50% was shared by the two aggregate size fractions, 25% was exclusive to micro-aggregates and the 25% left was found only in macro-aggregates. Top-hills were richer in OTUs than north and south-slopes. The Unweighted Pair Group Method with Arithmetic mean (UPGMA) analysis indicated clear differences in community composition between the two aggregate size-fractions in relation to the presence of OTUs. These results suggest that the main difference between micro- and macro-aggregates is due to the community structure within each soil fraction and this difference could affect soil nutrients dynamics.     

广西典型喀斯特地区深层土壤有机碳矿化及其影响因素

以广西典型峰丛洼地草地和原生林深层土壤(70～100cm)为对象,利用微生物交叉接种培养试验,研究不同土地利用类型、土壤微生物群落和通气条件对深层土壤有机碳矿化的影响。在124d的培养期内,微生物接种改变了0～28d原生林和0～81d草地深层土壤有机碳矿化速率,而通气条件变化对这一过程没有明显影响。3因素方差分析结果显示,深层土壤有机碳累积矿化率受土地利用类型、微生物群落和通气条件的影响显著(P<0.01),且存在3因素间交互效应。研究结果对于深入认识喀斯特深层土壤有机碳稳定机制和评估碳储量及其周转具有重要意义。     

Microbial activity and soil respiration under nitrogen addition in Alaskan boreal forest

Climate warming could increase rates of soil organic matter turnover and nutrient mineralization, particularly in northern high‐latitude ecosystems. However, the effects of increasing nutrient availability on microbial processes in these ecosystems are poorly understood. To determine how soil microbes respond to nutrient enrichment, we measured microbial biomass, extracellular enzyme activities, soil respiration, and the community composition of active fungi in nitrogen (N) fertilized soils of a boreal forest in central Alaska. We predicted that N addition would suppress fungal activity relative to bacteria, but stimulate carbon (C)‐degrading enzyme activities and soil respiration. Instead, we found no evidence for a suppression of fungal activity, although fungal sporocarp production declined significantly, and the relative abundance of two fungal taxa changed dramatically with N fertilization. Microbial biomass as measured by chloroform fumigation did not respond to fertilization, nor did the ratio of fungi : bacteria as measured by quantitative polymerase chain reaction. However, microbial biomass C : N ratios narrowed significantly from 16.0 ± 1.4 to 5.2 ± 0.3 with fertilization. N fertilization significantly increased the activity of a cellulose‐degrading enzyme and suppressed the activities of protein‐ and chitin‐degrading enzymes but had no effect on soil respiration rates or ¹⁴C signatures. These results indicate that N fertilization alters microbial community composition and allocation to extracellular enzyme production without affecting soil respiration. Thus, our results do not provide evidence for strong microbial feedbacks to the boreal C cycle under climate warming or N addition. However, organic N cycling may decline due to a reduction in the activity of enzymes that target nitrogenous compounds.     

Quantifying the Contribution of Entire Free-Living Nematode Communities to Carbon Mineralization under Contrasting C and N Availability

To understand the roles of nematodes in organic matter (OM) decomposition, experimental setups should include the entire nematode community, the native soil microflora, and their food sources. Yet, published studies are often based on either simplified experimental setups, using only a few selected species of nematode and their respective prey, despite the multitude of species present in natural soil, or on indirect estimation of the mineralization process using O₂ consumption and the fresh weight of nematodes. We set up a six-month incubation experiment to quantify the contribution of the entire free living nematode community to carbon (C) mineralization under realistic conditions. The following treatments were compared with and without grass-clover amendment: defaunated soil reinoculated with the entire free living nematode communities (+Nem) and defaunated soil that was not reinoculated (-Nem). We also included untreated fresh soil as a control (CTR). Nematode abundances and diversity in +Nem was comparable to the CTR showing the success of the reinoculation. No significant differences in C mineralization were found between +Nem and -Nem treatments of the amended and unamended samples at the end of incubation. Other related parameters such as microbial biomass C and enzymatic activities did not show significant differences between +Nem and -Nem treatments in both amended and unamended samples. These findings show that the collective contribution of the entire nematode community to C mineralization is small. Previous reports in literature based on simplified experimental setups and indirect estimations are contrasting with the findings of the current study and further investigations are needed to elucidate the extent and the mechanisms of nematode involvement in C mineralization.