The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi‐arid soils

Biogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi‐arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β‐glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi‐arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high‐DOC sites probably fuelled by metabolism of one‐C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient.     

Do temperate tree species diversity and identity influence soil microbial community function and composition?

Studies of biodiversity–ecosystem function in treed ecosystems have generally focused on aboveground functions. This study investigates intertrophic links between tree diversity and soil microbial community function and composition. We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR ), functional diversity (FD ), community‐weighted mean trait value (CWM ), and tree identity. The site was a 4‐year‐old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community‐level physiological profiles, and respiration were evaluated using phospholipid fatty acid (PLFA ) analysis and the MicroResp^? system, respectively. The relationship between tree species richness and glucose‐induced respiration (GIR ), basal respiration (BR ), metabolic quotient (qCO ₂) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration [BR ]), with higher biomass (glucose‐induced respiration [GIR ]), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA ) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR . In general, the CWM of traits had stronger effects than did FD , suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD . Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR ) and identity (species and functional identity—leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified functional traits related to life‐history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR .     

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long‐term plant diversity experiment

Stable provisioning of ecosystem functions and services is crucial for human well‐being in a changing world. Two essential ecological components driving vital ecosystem functions in terrestrial ecosystems are plant diversity and soil microorganisms. In this study, we tracked soil microbial basal respiration and biomass over a time period of 12 years in a grassland biodiversity experiment (the Jena Experiment) and examined the role of plant diversity and plant functional group composition for the spatial and temporal stability of soil microbial properties (basal respiration and biomass) in bulk‐soil. Spatial and temporal stability were calculated as the inverse coefficient of variation (CV^?1) of soil microbial respiration and biomass measured from soil samples taken over space and time, respectively. We found that 1) plant species richness consistently increased soil microbial properties after a time lag of four years since the establishment of the experimental plots, 2) plant species richness had minor effects on the spatial stability of soil microbial properties, whereas 3) the functional composition of plant communities significantly affected spatial stability of soil microbial properties, with legumes and tall herbs reducing both the spatial stability of microbial respiration and biomass, while grasses increased the latter, and 4) the effect of plant diversity on temporal stability of soil microbial properties turned from being negative to neutral, suggesting that the recovery of soil microbial communities from former arable land‐use takes more than a decade. Our results highlight the importance of plant functional group composition for the spatial and temporal stability of soil microbial properties, and hence for microbially‐driven ecosystem processes, such as decomposition and element cycling, in temperate semi‐natural grassland.     

Above‐ and belowground linkages in Sphagnum peatland: climate warming affects plant‐microbial interactions

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above‐ and belowground linkages that regulate soil organic carbon dynamics and C‐balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top‐predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum‐polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above‐ and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands     

Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO₂ given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short‐term effects of wildfire to the long‐term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both ¹³C lignin decomposition and microbial respiration in incubation studies. Taken together, these results indicate that reductions in fungal biomass in postfire soils and lower soil moisture in nonpermafrost soils reduced the potential of soil heterotrophs to decompose soil carbon. Although in the field increased rates of microbial respiration can be observed in postfire soils due to warmer soil conditions, reductions in fungal biomass and activity may limit rates of decomposition.     

Vegetation feedbacks of nutrient addition lead to a weaker carbon sink in an ombrotrophic bog

To study vegetation feedbacks of nutrient addition on carbon sequestration capacity, we investigated vegetation and ecosystem CO₂ exchange at Mer Bleue Bog, Canada in plots that had been fertilized with nitrogen (N) or with N plus phosphorus (P) and potassium (K) for 7–12 years. Gross photosynthesis, ecosystem respiration, and net CO₂ exchange were measured weekly during May–September 2011 using climate‐controlled chambers. A substrate‐induced respiration technique was used to determine the functional ability of the microbial community. The highest N and NPK additions were associated with 40% less net CO₂ uptake than the control. In the NPK additions, a diminished C sink potential was due to a 20–30% increase in ecosystem respiration, while gross photosynthesis rates did not change as greater vascular plant biomass compensated for the decrease in Sphagnum mosses. In the highest N‐only treatment, small reductions in gross photosynthesis and no change in ecosystem respiration led to the reduced C sink. Substrate‐induced microbial respiration was significantly higher in all levels of NPK additions compared with control. The temperature sensitivity of respiration in the plots was lower with increasing cumulative N load, suggesting more labile sources of respired CO₂. The weaker C sink potential could be explained by changes in nutrient availability, higher woody : foliar ratio, moss loss, and enhanced decomposition. Stronger responses to NPK fertilization than to N‐only fertilization for both shrub biomass production and decomposition suggest that the bog ecosystem is N‐P/K colimited rather than N‐limited. Negative effects of further N‐only deposition were indicated by delayed spring CO₂ uptake. In contrast to forests, increased wood formation and surface litter accumulation in bogs seem to reduce the C sink potential owing to the loss of peat‐forming Sphagnum.     

Influence of corn,switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side‐by‐side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipid analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.     

Ecosystem properties and microbial community changes in primary succession on a glacier forefront

We studied microbial community composition in a primary successional chronosequence on the forefront of Lyman Glacier, Washington, United States. We sampled microbial communities in soil from nonvegetated areas and under the canopies of mycorrhizal and nonmycorrhizal plants from 20- to 80-year-old zones along the successional gradient. Three independent measures of microbial biomass were used: substrate-induced respiration (SIR), phospholipid fatty acid (PLFA) analysis, and direct microscopic counts. All methods indicated that biomass increased over successional time in the nonvegetated soil. PLFA analysis indicated that the microbial biomass was greater under the plant canopies than in the nonvegetated soils; the microbial community composition was clearly different between these two types of soils. Over the successional gradient, the microbial community shifted from bacterial-dominated to fungal-dominated. Microbial respiration increased while specific activity (respiration per unit biomass) decreased in nonvegetated soils over the successional gradient. We proposed and evaluated new parameters for estimating the C use efficiency of the soil microbial community: “Max” indicates the maximal respiration rate and “Acc” the total C released from the sample after a standard amount of substrate is added. These, as well as the corresponding specific activities (calculated as Max and Acc per unit biomass), decreased sharply over the successional gradient. Our study suggests that during the early stages of succession the microbial community cannot incorporate all the added substrate into its biomass, but rapidly increases its respiration. The later-stage microbial community cannot reach as high a rate of respiration per unit biomass but remains in an “energy-saving state,” accumulating C to its biomass. Received: 4 June 1998 / Accepted: 11 January 1999     

模拟酸雨对我国亚热带毛竹林土壤呼吸及微生物多样性的影响

酸沉降造成的土壤持续酸化对毛竹林生态系统碳循环具有重要的影响,为量化酸沉降我国亚热带毛竹林土壤的影响,于2016年在浙江省杭州临安天目山国家级自然保护区毛竹林持续开展了2年野外模拟酸雨淋溶土壤实验,设置pH 4.0(T1)和pH 2.0(T2)两个模拟酸雨处理,以pH 5.8天然湖水为对照(CK),分析酸雨作用下土壤CO_2排放及土壤微生物多样性的变化趋势,并明确毛竹林土壤呼吸、土壤微生物及土壤理化性质三者之间的关系。结果表明:土壤呼吸速率在酸雨作用下经过缓冲期后呈现先促进后抑制的变化,作用强度表现为:T2T1。不同处理的土壤呼吸对温度的敏感性由高到低依次是:T2、CK、T1。PCR-DGGE分析表明,模拟酸雨改变了土壤微生物菌群结构,T2处理抑制了土壤细菌的多样性和丰富度,而T1处理对土壤真菌多样性和丰富度具有促进作用。土壤pH值、有效钾、可溶有机碳、微生物量碳、碱解氮和有效磷对土壤微生物群落结构及土壤呼吸具有显著的影响(P0.05)。综上所述,模拟酸雨能够显著抑制毛竹林的土壤呼吸,并改变土壤微生物群落结构及多样性,这些结果为进一步研究毛竹林土壤生态系统对环境问题响应机制提供理论基础。     

Successional changes in the soil microbial community along a vegetation development sequence in a subalpine volcanic desert on Mount Fuji, Japan

Aims

To study the relationship between vegetation development and changes in the soil microbial community during primary succession in a volcanic desert, we examined successional changes in microbial respiration, biomass, and community structure in a volcanic desert on Mount Fuji, Japan.

Methods

Soil samples were collected from six successional stages, including isolated island-like plant communities. We measured microbial respiration and performed phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE) analysis, and community-level physiological profile (CLPP) analysis using Biolog microplates.

Results

Microbial biomass (total PLFA content) increased during plant succession and was positively correlated with soil properties including soil water and soil organic matter (SOM) contents. The microbial respiration rate per unit biomass decreased during succession. Nonmetric multidimensional scaling based on the PLFA, DGGE, and CLPP analyses showed a substantial shift in microbial community structure as a result of initial colonization by the pioneer herb Polygonum cuspidatum and subsequent colonization by Larix kaempferi into central areas of island-like communities. These shifts in microbial community structure probably reflect differences in SOM quality.

Conclusions

Microbial succession in the volcanic desert of Mt. Fuji was initially strongly affected by colonization of the pioneer herbaceous plant (P. cuspidatum) associated with substantial changes in the soil environment. Subsequent changes in vegetation, including the invasion of shrubs such as L. kaempferi, also affected the microbial community structure.     

Plant functional diversity enhances associations of soil fungal diversity with vegetation and soil in the restoration of semiarid sandy grassland

The trait‐based approach shows that plant functional diversity strongly affects ecosystem properties. However, few empirical studies show the relationship between soil fungal diversity and plant functional diversity in natural ecosystems. We investigated soil fungal diversity along a restoration gradient of sandy grassland (mobile dune, semifixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China, using the denaturing gradient gel electrophoresis of 18S rRNA and gene sequencing. We also examined associations of soil fungal diversity with plant functional diversity reflected by the dominant species' traits in community (community‐weighted mean, CWM) and the dispersion of functional trait values (FD_is). We further used the structure equation model (SEM) to evaluate how plant richness, biomass, functional diversity, and soil properties affect soil fungal diversity in sandy grassland restoration. Soil fungal richness in mobile dune and semifixed dune was markedly lower than those of fixed dune and grassland (P < 0.05). Soil fungal richness was positively associated with plant richness, biomass, CWM plant height, and soil gradient aggregated from the principal component analysis, but SEM results showed that plant richness and CWM plant height determined by soil properties were the main factors exerting direct effects. Soil gradient increased fungal richness through indirect effect on vegetation rather than direct effect. The negative indirect effect of FDis on soil fungal richness was through its effect on plant biomass. Our final SEM model based on plant functional diversity explained nearly 70% variances of soil fungal richness. Strong association of soil fungal richness with the dominant species in the community supported the mass ratio hypothesis. Our results clearly highlight the role of plant functional diversity in enhancing associations of soil fungal diversity with community structure and soil properties in sandy grassland ecosystems.     

喀斯特地区三种人工林土壤微生物群落结构特征

为揭示不同人工植被修复模式对喀斯特土壤微生物群落的影响,采用氯仿熏蒸提取法和磷脂脂肪酸(phospholipid fatty acid, PLFA)法研究人工构建的降香黄檀(Dalbergia odorifera)纯林(PDOP)、顶果木(Acrocarpus fraxinifolius)纯林(PAFP)、顶果木×降香黄檀混交林(MADP)对土壤微生物生物量及土壤微生物群落结构的影响。结果表明:(1)PDOP的土壤微生物生物量碳(MBC)和微生物生物量氮(MBN)含量显著高于PAFP和MADP,PAFP显著高于MADP。(2)三种人工林土壤真菌、丛枝菌根真菌和总PLFA含量无显著差异,但PDOP土壤细菌、放线菌、丛枝菌根真菌和总PLFA含量均高于PAFP和MADP,PAFP高于MADP。PDOP的土壤细菌、革兰氏阳性菌、革兰氏阴性菌、放线菌的PLFA含量显著高于MADP。MADP的真菌细菌比显著高于PDOP,但与PAFP无显著差异。(3)冗余分析表明,土壤阳离子交换量、pH和C:N是影响土壤微生物群落组成的最主要影响因子。从三种人工林的土壤微生物生物量及微生物群落结构来看,在喀斯特地区MADP并未显示出酸性土地区混交林提高土壤微生物生物量、改善土壤微生物群落结构的优势,但混交林的真菌细菌比最高,更有利于提高土壤生态系统的稳定性。     

Differential sensitivity of total and active soil microbial communities to drought and forest management

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning—that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 60 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community‐based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought‐plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.     

Relationship between plant species diversity and soil microbial functional diversity along a longitudinal gradient in temperate grasslands of Hulunbeir,Inner Mongolia,China

Numerous experiments have been established to examine the effect of plant diversity on the soil microbial community. However, the relationship between plant diversity and microbial functional diversity along broad spatial gradients at a large scale is still unexplored. In this paper, we examined the relationship of plant species diversity with soil microbial biomass C, microbial catabolic activity, catabolic diversity and catabolic richness along a longitudinal gradient in temperate grasslands of Hulunbeir, Inner Mongolia, China. Preliminary detrended correspondence analysis (DCA) indicated that plant composition showed a significant separation along the axis 1, and axis 1 explained the main portion of variability in the data set. Moreover, DCA-axis 1 was significantly correlated with soil microbial biomass C (r = 0.735, P = 0.001), microbial catabolic activity (average well color development; r = 0.775, P < 0.001) and microbial functional diversity (catabolic diversity: r = 0.791, P < 0.001 and catabolic richness: r = 0.812, P < 0.001), which suggested thatsome relationship existed between plant composition and the soil microbial community along the spatial gradient at a large scale. Soil microbial biomass C, microbial catabolic activity, catabolic diversity and catabolic richness showed a significant, linear increase with greater plant species richness. However, many responses that we observed could be explained by greater aboveground plant biomass associated with higher levels of plant diversity, which suggested that plant diversity impacted the soil microbial community mainly through increases in plant production.     

Accumulation of organic matter along a pollution gradient: Application of odum's theory of ecosystem energetics

Forest soil biology in Scots pine forests of the Empetrum-Vaccinium type was studied around the industrialized city of Oulu, northern Finland since 1987. The forest sites lie along a sulphur and nitrogen concentration gradient in the mor humus ranging from 1.6 to 3.9 mg S g^–1 organic matter (OM) and from 14 to 23 mg N g^–1 OM. A number of biological parameters have earlier been found to vary along this gradient, thus indicating that the ecosystems are subjected to a pollution stress. Total microbial biomass and various activity parameters were studied in 1991. The different methods are discussed and the results interpreted within the light of Odum's theory of the energetic stabilization of ecosystems. Microbial biomass C determined by the fumigation-extraction (FE) technique varied from 5 to 10 mg g^–OM, N from 0.5 to 1.0 mg g^–1OM, and basal respiration rate from 0.040 to 0.097 mg CO₂ h^–1 g^–1OM. All decreased along the pollution gradient. Substrate induced respiration values (SIR) varied from 0.025 to 0.085 mg CO₂-C h^–1 g^–1dw. SIR correlated well with the biomass values determined by the FE technique. The lag time of the microbial community after glucose addition (varying from 13 to 22 h) was shortened and the specific respiration increment of the microbial community in response to glucose addition increased along the gradient. The metabolic quotient (respiration/biomass) of the microflora strongly depended on the technique and equation used in calculating the microbial biomass. The results show a reduced biomass, but a more intensive regeneration and intensified activity per biomass unit of microorganisms in polluted forest soil. This in turn denotes an alteration in the microbial community in favor of a higher proportion of r-strategists under the disturbed conditions. In contrast, K-strategists may be more dominant under less polluted conditions. This interpretation is presented with some reservations concerning methodology. There is a need for the calibration of each method for determining microbial biomass in different types of soil.     

Elevated atmospheric CO2 increases microbial growth rates in soil: results of three CO2 enrichment experiments

Increasing the belowground translocation of assimilated carbon by plants grown under elevated CO₂ can cause a shift in the structure and activity of the microbial community responsible for the turnover of organic matter in soil. We investigated the long‐term effect of elevated CO₂ in the atmosphere on microbial biomass and specific growth rates in root‐free and rhizosphere soil. The experiments were conducted under two free air carbon dioxide enrichment (FACE) systems: in Hohenheim and Braunschweig, as well as in the intensively managed forest mesocosm of the Biosphere 2 Laboratory (B2L) in Oracle, AZ. Specific microbial growth rates (μ) were determined using the substrate‐induced respiration response after glucose and/or yeast extract addition to the soil. For B2L and both FACE systems, up to 58% higher μ were observed under elevated vs. ambient CO₂, depending on site, plant species and N fertilization. The μ‐values increased linearly with atmospheric CO₂ concentration at all three sites. The effect of elevated CO₂ on rhizosphere microorganisms was plant dependent and increased for: Brassica napus=Triticum aestivum<Beta vulgaris<Populus deltoides. N deficiency affected microbial growth rates directly (N limitation) and indirectly (changing the quantity of fine roots). So, 50% decrease in N fertilization caused the overall increase or decrease of microbial growth rates depending on plant species. The μ‐value increase was lower for microorganisms growing on yeast extract then for those growing on glucose, i.e. the effect of elevated CO₂ was smoothed on rich vs. simple substrate. So, the r/K strategies ratio can be better revealed by studying growth on simple (glucose) than on rich substrate mixtures (yeast extract). Our results clearly showed that the functional characteristics of the soil microbial community (i.e. specific growth rates) rather than total microbial biomass amount are sensitive to increased atmospheric CO₂. We conclude that the more abundant available organics released by roots at elevated CO₂ altered the ecological strategy of the soil microbial community specifically a shift to a higher contribution of fast‐growing r‐selected species was observed. These changes in functional structure of the soil microbial community may counterbalance higher C input into the soil under elevated atmospheric CO₂ concentration.     

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel‐contaminated soil

Ecotoxicology is primarily concerned with predicting the effects of toxic substances on the biological components of the ecosystem. In remote, high latitude environments such as Antarctica, where field work is logistically difficult and expensive, and where access to adequate numbers of soil invertebrates is limited and response times of biota are slow, appropriate modeling tools using microbial community responses can be valuable as an alternative to traditional single‐species toxicity tests. In this study, we apply a Bayesian nonparametric model to a soil microbial data set acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. We model community change in terms of OTUs (operational taxonomic units) in response to a range of total petroleum hydrocarbon (TPH) concentrations. The Shannon diversity of the microbial community, clustering of OTUs into groups with similar behavior with respect to TPH, and effective concentration values at level x, which represent the TPH concentration that causes x% change in the community, are presented. This model is broadly applicable to other complex data sets with similar data structure and inferential requirements on the response of communities to environmental parameters and stressors.     

川西亚高山森林土壤呼吸和微生物生物量碳氮对施氮的响应

随着全球大气氮沉降的明显增加,将有可能显著影响我国西部地区受氮限制的亚高山森林生态系统。土壤微生物是生态系统的重要组成部分,是土壤物质循环和能量流动的重要参与者。由于生态系统类型、土壤养分、氮沉降背景值等的差异,土壤呼吸和土壤生物量碳氮对施氮的响应存在许多不确定性。而施氮会不会促进亚高山森林生态系统中土壤呼吸和微生物对土壤碳氮的固定?基于此假设,选择了川西60年生的四川红杉(Larix mastersiana)亚高山针叶林为研究对象,通过4个水平的土壤施氮控制试验(CK:0 g m~(-2) a~(-1)、N1:2 g m~(-2)a~(-1)、N2:5 g m~(-2) a~(-1)、N3:10 g m~(-2)a~(-1)),监测了土壤呼吸及土壤微生物生物量碳氮在一个生长季的动态情况。结果表明:施氮对土壤呼吸各指标和土壤微生物碳氮都有极显著的影响,施氮能促进土壤全呼吸、自养呼吸、异养呼吸通量和土壤微生物生物量碳氮的增长,施氮使土壤呼吸通量提高了11%—15%,土壤微生物量碳提高了5%—9%,土壤微生物量氮提高了23%—34%。在中氮水平下(5 g m~(-2) a~(-1))对土壤呼吸的促进最显著。相关分析发现,土壤呼吸与微生物生物量碳氮和微生物代谢商极呈显著正相关,微生物量碳氮与土壤温度呈极显著的正相关,与土壤湿度呈极显著负相关。通过一般线性回归拟合土壤呼吸速率与土壤10 cm温湿度的关系,发现土壤呼吸速率与土壤温度呈极显著的正相关,与土壤湿度极显著负相关(P0.001),中氮水平下土壤温度敏感性系数Q_(10)值(7.10)明显高于对照(4.26)。     

The effect of anthropogenic arsenic contamination on the earthworm microbiome

Earthworms are globally distributed and perform essential roles for soil health and microbial structure. We have investigated the effect of an anthropogenic contamination gradient on the bacterial community of the keystone ecological species Lumbricus rubellus through utilizing 16S rRNA pyrosequencing for the first time to establish the microbiome of the host and surrounding soil. The earthworm‐associated microbiome differs from the surrounding environment which appears to be a result of both filtering and stimulation likely linked to the altered environment associated with the gut micro‐habitat (neutral pH, anoxia and increased carbon substrates). We identified a core earthworm community comprising Proteobacteria (～50%) and Actinobacteria (～30%), with lower abundances of Bacteroidetes (～6%) and Acidobacteria (～3%). In addition to the known earthworm symbiont (Verminephrobacter sp.), we identified a potential host‐associated Gammaproteobacteria species (Serratia sp.) that was absent from soil yet observed in most earthworms. Although a distinct bacterial community defines these earthworms, clear family‐ and species‐level modification were observed along an arsenic and iron contamination gradient. Several taxa observed in uncontaminated control microbiomes are suppressed by metal/metalloid field exposure, including eradication of the hereto ubiquitously associated Verminephrobacter symbiont, which raises implications to its functional role in the earthworm microbiome.     

A High Arctic soil ecosystem resists long‐term environmental manipulations

We evaluated above‐ and belowground ecosystem changes in a 16 year, combined fertilization and warming experiment in a High Arctic tundra deciduous shrub heath (Alexandra Fiord, Ellesmere Island, NU, Canada). Soil emissions of the three key greenhouse gases (GHGs) (carbon dioxide, methane, and nitrous oxide) were measured in mid‐July 2009 using soil respiration chambers attached to a FTIR system. Soil chemical and biochemical properties including Q₁₀ values for CO₂, CH₄, and N₂O, Bacteria and Archaea assemblage composition, and the diversity and prevalence of key nitrogen cycling genes including bacterial amoA, crenarchaeal amoA, and nosZ were measured. Warming and fertilization caused strong increases in plant community cover and height but had limited effects on GHG fluxes and no substantial effect on soil chemistry or biochemistry. Similarly, there was a surprising lack of directional shifts in the soil microbial community as a whole or any change at all in microbial functional groups associated with CH₄ consumption or N₂O cycling in any treatment. Thus, it appears that while warming and increased nutrient availability have strongly affected the plant community over the last 16 years, the belowground ecosystem has not yet responded. This resistance of the soil ecosystem has resulted in limited changes in GHG fluxes in response to the experimental treatments.