Soil microbial diversity and community structure across a climatic gradient in western Canada

Soil microbial functional diversity was assessed along a climatic gradient in Western Canada. Mineral soil samples were collected from jack pine (Pinus banksiana Lamb.) stands along an 800km transect between Prince Albert, Saskatchewan and Gillam, Manitoba. Microbial communities were isolated from the soil samples, washed and inoculated into wells of Gram-negative Biolog microplates. Optical density values were used to calculate Shannon diversity indices and to perform principal component analysis. Colour development rank plots (CDR) were created by expressing optical density values as a percentage of total colour development and plotting the wells in descending order. Soil microbial functional diversity decreased with increasing latitude and correlated positively with measures of atmospheric temperature and pH. Soil microbial diversity may be lower in northern sites due to decreased productivity, nutrient limitation and higher acidity. CDR plots are consistent with a trend of increasing environmental harshness moving north along the transect.     

Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to alpha-, beta-, and gamma-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.     

Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient

Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed (R(2) = 0.02, P = 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and the difference in the heavy metal content of hyporheic sediments throughout the year (R(2) = 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the alpha, beta, and gamma-proteobacteria and cyanobacteria) were apparent only during the fall and early winter, when the majority of organic matter is deposited into regional streams. These seasonal data suggest that the abundance of susceptible populations responds to heavy metals primarily during seasons when the potential for growth is highest.     

Soil and plant effects on microbial community structure

We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.     

Carbon sequestration and community composition of ectomycorrhizal fungi across a geothermal warming gradient in an Icelandic spruce forest

Soil warming (0–5.5 °C above controls) effects on ectomycorrhizal growth, carbon sequestration and community composition were examined in a Picea sitchensis forest spanning a geothermal gradient in Iceland. Fungal communities were assayed with sand-filled ingrowth meshbags incubated in the soil for 5 months. Meshbags amended with compost made from maize leaves (a C4 plant enriched in ¹³C) were incubated for 5 or 12 months and used to estimate C sequestration by the fungal community. Despite increases in tree growth, moderate warming only slightly reduced or had no effect on mycelial growth and had no effect on fungal carbon sequestration or overall ectomycorrhizal community composition. Warming was associated with increased abundance of ascomycetes, particularly pyronemataceous ectomycorrhizal fungi, and altered saprotrophic community composition. Increased nitrate availability and root turnover may explain the lack of a positive ectomycorrhizal growth response to increased tree growth and observed shifts in community composition with warming.     

Macroinvertebrate community structure across a wetland hydroperiod gradient in southern New Hampshire,USA

We conducted a field study to examine the influence of hydroperiod and concomitant changes in abiotic (wetland size, pH, conductivity, dissolved oxygen and water temperature) and biotic (predatory fish presence) characteristics on macroinvertebrate communities in isolated wetlands in southern New Hampshire. Invertebrates were sampled using dipnet sweeps in 42 wetlands with short (<4 months), intermediate (4–11 months) or long (permanent) hydroperiods in 1998 and 1999. We found that invertebrate genera richness, and to a lesser degree abundance, increased linearly along the hydrological gradient, and in response to temperature and dissolved oxygen. Relative abundance of genera also differed markedly with respect to hydroperiod. Most notably, invertebrate communities changed from Acilius-dominated communities to Notonecta-dominated communities. Invertebrate relative abundances in permanent wetlands also differed with respect to the occurrence of predatory fish. Some genera (e.g., Libellula, and Dytiscus) were more likely to occur in permanent wetlands without fish, whereas other genera (e.g., Buena, and Basiaeshna) were more likely to occur in wetlands with predatory fish. Because aquatic invertebrate communities differed markedly with respect to wetland hydroperiod, and in relation to the occurrence of predatory fish, it is essential to retain a diversity of wetlands in the landscape to ensure the long-term persistence of aquatic invertebrate biodiversity.     

Modeling microbial community structure and functional diversity across time and space

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways.     

Soil amino-acid availability across a temperate-forest fertility gradient

Despite increasing recognition that free amino acids can be an important source of N for plant uptake, we have a poor understanding of environmental variation in the availability of amino-acid N in soils outside of arctic, alpine and boreal regions. I investigated patterns of amino-acid availability along a temperate forest fertility gradient ranging from low mineral N availability, oak-dominated forests to high mineral N availability, maple-basswood forests (5 sites). I measured standing pools of free amino acids, soluble peptides, ammonium and nitrate, rates of amino acid production (native proteolysis activity) and rates of consumption of a ¹⁵N-labeled leucine tracer. Standing pools of amino acid N decreased consistently along the fertility gradient from the low fertility black oak/white oak system to the high fertility sugar maple/basswood system, with a 25-fold difference in pool sizes between the poorest and richest sites. Standing pools of soluble peptides varied little among sites, instead, the relationship between free amino acids and peptides changed markedly across the gradient. At low fertility sites free amino acids were positively correlated with soluble peptides, whereas free amino acid pools were universally low at high fertility sites, regardless of peptide pools. Assays for native proteolysis activity indicated that amino acid production did not vary significantly among sites. Recovery of leucine tracer in inorganic (NH₄ ⁺ and NO₃ ⁻) pools and in residual soil organic matter both increased with increasing soil fertility; however, total consumption of the added amino-acid tracer did not vary among sites. Results from this study demonstrate that free amino acids can make an important contribution to potentially plant-available N pools in temperate forest soils, particularly at low fertility sites.     

Soil microbial diversity, community structure and denitrification in a temperate riparian zone

Nitrate (NO ₃ ^– ) removal in riparian zones bordering agricultural areas occurs via plant uptake, microbial immobilisation and bacterial denitrification. Denitrification is a desirable mechanism for removal because the bacterial conversion of NO ₃ ^– to N gases permanently removes NO ₃ ^– from the watershed. A field and laboratory study was conducted in riparian soils adjacent to Carroll Creek, Ontario, Canada, to assess the spatial distribution of denitrification relative to microbial community structure and microbial functional diversity. Soil samples were collected in March, June, and August 1997 at varying soil depths and distances from the stream. Denitrification measurements made using the acetylene block technique on intact soil cores were highly variable and did not show any trends with riparian zone location. Microbial community composition and functional diversity were determined using sole carbon source utilization (SCSU) on Biolog® GN microplates. Substrate richness, evenness and diversity (Shannon index) were greatest within the riparian zone and may also have been influenced by a rhizosphere effect. A threshold relationship between denitrification and measures of microbial community structure implied minimum levels of richness, evenness and diversity were required for denitrification.     

Soil microbial biomass and community composition along an anthropogenic disturbance gradient within a long-leaf pine habitat

Some of the finest surviving natural habitat in the United States is on military reservations where land has been protected from development. However, responsibilities of military training often require disturbance of that habitat. Herein, we show how the soil microbial community of a long-leaf pine ecosystem at Fort Benning, Georgia responds to military traffic disturbances. Using the soil microbial biomass and community composition as ecological indicators, reproducible changes showed increasing traffic disturbance decreases soil viable biomass, biomarkers for microeukaryotes and Gram-negative bacteria, while increasing the proportions of aerobic Gram-positive bacterial and Actinomycete biomarkers. Soil samples were obtained from four levels of military traffic (reference, light, moderate, and heavy) with an additional set of samples taken from previously damaged areas that were remediated via planting of trees and ground cover. Utilizing 17 phospholipid fatty acid (PLFA) variables that differed significantly with land usage, a linear discriminant analysis with cross-validation classified the four groups. Wilks’ lambda for the model was 0.032 (P<0.001). Overall, the correct classifications of profiles was 66% (compared to the chance that 25% would be correctly classified). Using this model, 10 observations taken from the remediated transects were classified. One observation was classified as a reference, three as light trafficked, and six as moderately trafficked. Non-linear artificial neural network (ANN) discriminant analysis was performed using the biomass estimates and all of the 61 PLFA variables. The resulting optimal ANN included five hidden nodes and resulted in an r² of 0.97. The prediction rate of profiles for this model was again 66%, and the 10 observations taken from the remediated transects were classified with four as reference (not impacted), two as moderate, and four as heavily trafficked. Although the ANN included more comprehensive data, it classified eight of the 10 remediated transects at the usage extremes (reference or heavy traffic). Inspection of the novelty indexes from the prediction outputs showed that the input vectors from the remediated transects were very different from the data used to train the ANN. This difference suggests as a soil is remediated it does not escalate through states of succession in the same way as it descends following disturbance. We propose to explore this hysteresis between disturbance and recovery process as a predictor of the resilience of the microbial community to repeated disturbance/recovery cycles.     

Changes in community and population responses across a forest-field gradient

The ground-layer vegetation of a forest-old field edge gradient was sampled to determine the effects of the edge on spatial patterns of plant species and community attributes. Species showed individualistic responses to the forest edge, with peak abundance at different spatial positions relative to the edge. Principal components analysis resulted in three axes which explained a total of 63.2% of the variation within the data set. The first two PCA axes were related to distance to the forest edge. The third separated plots into those that were dominated by Solidago canadensis. and those that were dominated by Solidago juncea. All population and community-level attributes varied along the edge gradient. Species richness, Shannon-Wiener diversity, and total percent cover increased from the forest to the edge, with slight declines 60 m from the edge in the field. Among-plot heterogeneity was higher at the edge than in either the forest or the field. Exotic species had peak abundance within 20 m of the edge inside the forest and are restricted to the edge. Most population and community-level attributes showed edge responses on both sides of the edge. This emphasizes the need to study edges as gradients that include both disturbed and undisturbed habitats.     

Changes in soil microbial community structure and function following degradation in a temperate grassland

温带草原退化后土壤微生物群落结构和功能的变化 草原退化是草原生产力维持面临的一个重大挑战,这一过程显著影响着草原生态系统的能量流动和土壤养分变化过程,进而直接或间接地影响着土壤微生物。我们的研究目的首先是调查不同草原退化程度(即未退化、中度退化和严重退化)如何影响着内蒙古温带草原的土壤微生物组成、多样性和功能,其次是阐明哪些生物和非生物因素导致了这些变化。我们的研究主要通过高通量测序技术分析土壤微生物的群落组成,并且采用FAPROTAX工具和FUNGuild工具分别预测细菌群落和真菌群落的功能。研究发现：草原退化显著降低了土壤细菌的多样性,但对真菌多样性影响不大。地下生物量、土壤有机碳和总氮与细菌的多样性变化呈显著正相关关系。草原退化显著增加了绿弯菌门的相对丰度(由2.48%提高到8.40%),降低了厚壁菌门的相对丰度(由3.62%降低到1.08%)。其次,草原退化也显著增加了球囊菌门的相对丰度(从0.17%提高到1.53%),降低了担子菌门的相对丰度(从19.30%降低到4.83%)。致病菌的相对丰度在草原退化过程中显著下降。此外,草原退化对土壤细菌群落的功能有显著的影响,尤其是与土壤碳氮循环相关的土壤细菌群落。我们的结果表明,土壤细菌群落对草原退化的响应比真菌群落更敏感。     

Lipid biomarkers recording marine microbial community structure changes through the Frasnian-Famennian mass extinction event

Studying the response and recovery of marine microbial communities during mass extinction events provides an evolutionary window through which to understand the adaptation and resilience of the marine ecosystem in the face of significant environmental disturbances. The goal of this study is to reconstruct changes in the marine microbial community structure through the Late Devonian Frasnian-Famennian (F-F) transition. We performed a multiproxy investigation on a drill core of the Upper Devonian New Albany Shale from the Illinois Basin (western Kentucky, USA). Aryl isoprenoids show green sulfur bacteria expansion and associated photic zone euxinia (PZE) enhancement during the F-F interval. These changes can be attributed to augmented terrigenous influxes, as recorded collectively by the long-chain/short-chain normal alkane ratio, carbon preference index, C₃₀ moretane/C₃₀ hopane, and diahopane index. Hopane/sterane ratios reveal a more pronounced dominance of eukaryotic over prokaryotic production during the mass extinction interval. Sterane distributions indicate that the microalgal community was primarily composed of green algae clades, and their dominance became more pronounced during the F-F interval and continued to rise in the subsequent periods. The 2α-methylhopane index values do not show an evident shift during the mass extinction interval, whereas the 3β-methylhopane index values record a greater abundance of methanotrophic bacteria during the extinction interval, suggesting enhanced methane cycling due to intensified oxygen depletion. Overall, the Illinois Basin during the F-F extinction experienced heightened algal productivity due to intensified terrigenous influxes, exhibiting similarities to contemporary coastal oceans that are currently undergoing globalized cultural eutrophication. The observed microbial community shifts associated with the F-F environmental disturbances were largely restricted to the extinction interval, which suggests a relatively stable, resilient marine microbial ecosystem during the Late Devonian.     

Temperature effects on fish production across a natural thermal gradient

Global warming is widely predicted to reduce the biomass production of top predators, or even result in species loss. Several exceptions to this expectation have been identified, however, and it is vital that we understand the underlying mechanisms if we are to improve our ability to predict future trends. Here, we used a natural warming experiment in Iceland and quantitative theoretical predictions to investigate the success of brown trout as top predators across a stream temperature gradient (4–25 °C). Brown trout are at the northern limit of their geographic distribution in this system, with ambient stream temperatures below their optimum for maximal growth, and above it in the warmest streams. A five‐month mark‐recapture study revealed that population abundance, biomass, growth rate, and production of trout all increased with stream temperature. We identified two mechanisms that contributed to these responses: (1) trout became more selective in their diet as stream temperature increased, feeding higher in the food web and increasing in trophic position; and (2) trophic transfer through the food web was more efficient in the warmer streams. We found little evidence to support a third potential mechanism: that external subsidies would play a more important role in the diet of trout with increasing stream temperature. Resource availability was also amplified through the trophic levels with warming, as predicted by metabolic theory in nutrient‐replete systems. These results highlight circumstances in which top predators can thrive in warmer environments and contribute to our knowledge of warming impacts on natural communities and ecosystem functioning.     

Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring

Electron microscopy (EM), denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequencing were used to examine the structure and diversity of microbial mats present in an acid-sulphate–chloride (pH 3.1) thermal (58–62°C) spring in Norris Basin, Yellowstone National Park, WY, USA, exhibiting rapid rates of arsenite oxidation. Initial visual assessments, scanning EM and geochemical measurements revealed the presence of three distinct mat types. Analysis of 16S rDNA fragments with DGGE confirmed the presence of different bacterial and archaeal communities within these zones. Changes in the microbial community appeared to coincide with arsenite oxidation activity. Phylogenetic analysis of 1400 bp 16S rDNA sequences revealed that clone libraries prepared from both arsenic redox active and inactive bacterial communities were dominated by sequences phylogenetically related to Hydrogenobacter acidophilus and Desulphurella sp. The appearance of archaeal 16S rDNA sequences coincided with the start of arsenite oxidation, and sequences were obtained showing affiliation with both Crenarchaeota and Euryarchaeota . The majority of archaeal sequences were most similar to sequences obtained from marine hydrothermal vents and other acidic hot springs, although the level of similarity was typically just 90%. Arsenite oxidation in this system may result from the activities of these unknown archaeal taxa and/or the previously unreported arsenic redox activity of H. acidophilus - or Desulphurella -like organisms. If the latter, arsenite oxidation must be inhibited in the initial high-sulphide zone of the spring, where no change in the distribution of arsenite versus arsenate was observed.     

Changes in grassland canopy structure across a precipitation gradient

Abstract. In temperate grasslands, the relative importance of above‐ground competition for light compared to below‐ground competition for water and nutrients is hypothesized to increase with increasing precipitation. Thus, competition for light is likely to exert an increasing influence on canopy structure and species composition as precipitation increases. We quantified canopy structure, light availability and changes in species composition at seven sites across the central grassland region of the United States to determine how these properties change across a precipitation gradient. Across the region, there was a disproportionate increase in leaf area and canopy height with increasing precipitation, indicating that plants become taller and leafier across the gradient. Leaf area index increased by a factor of 12 across the gradient while above‐ground net primary productivity increased by a factor of only 5.5. As precipitation increased, there was decreased light availability at the soil surface, increased seasonal variability in light transmission, increased biomass and leaf area at higher canopy layers and an increased proportion of tallstatured species. These observed changes in canopy structure support the prediction that competition for light increases in importance with increasing precipitation.     

应用PCR与温度梯度凝胶电泳分析龈上菌斑微生物群落

目的应用PCR与温度梯度凝胶电泳(PCR—TGGE)分子技术对成年健康口腔的龈上菌斑中微生物群落组成进行分析。方法8例成年个体包括4男4女,年龄19～29岁,分别采取每例个体上下颌牙周龈上菌斑样品,共18份(个体Subl间隔10天采集2次样品)。提取菌斑DNA,PCR扩增16SrDNAV3可变区,产物经TGGE后进行相似系数分析。结果同一个体的上下颌微生物群落组成相似性系数为81％～95％,而不同个体的龈上菌斑微生物群落组成相似性系数,均在60％以下。结论不同个体具有其独特的牙周微生物群落,而且在一定时期内组成稳定。     

Population structure and physiological changes within a hot spring microbial mat community following disturbance.

The influence of disturbance on a hot spring cyanobacterial mat community was investigated by physically removing the top 3.0 mm, which included the entire cyanobacterial layer. Changes in 16S rRNA-defined populations were monitored by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments. Some previously absent cyanobacterial populations colonized the disturbed areas, while some populations which were present before the disturbance remained absent for up to 40 days. Changes in physiological activity were measured by oxygen microelectrode analyses and by 14CO2 incorporation into cyanobacterial molecular components. These investigations indicated substantial differences between the disturbed and undisturbed mats, including an unexplained light-induced oxygen consumption in the freshly exposed mat, increased carbon partitioning by phototrophs into growth-related macromolecules, bimodal vertical photosynthesis profiles, and delayed recovery of respiration relative to photosynthesis.