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.     

Structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment

Microbial community composition and structure were characterized in marine sediments contaminated for >80 years with cadmium, copper, lead, and zinc. Four sampling sites that encompass a wide range of sediment metal loads were compared in a Norwegian fjord (Sorfjord). HCl-extractable metals and organic matter constantly decreased from the most contaminated site (S1) to the control site (S4). All sampling sites presented low polychlorinated biphenyl (PCB) concentrations (Sigma(7)PCB < 7.0 ng g [dry weight](-1)). The biomass ranged from 4.3 x 10(8) to 13.4 x 10(8) cells g (dry weight) of sediments(-1) and was not correlated to metal levels. Denaturing gradient gel electrophoresis indicated that diversity was not affected by the contamination. The majority of the partial 16S rRNA sequences obtained were classified in the gamma- and delta-Proteobacteria and in the Cytophaga-Flexibacter-Bacteroides (CFB) bacteria. Some sequences were closely related to other sequences from polluted marine sediments. The abundances of seven phylogenetic groups were determined by using fluorescent in situ hybridization (FISH). FISH was impaired in S1 by high levels of autofluorescing particles. For S2 to S4, the results indicated that the HCl-extractable Cu, Pb, and Zn were negatively correlated with the abundance of gamma-Proteobacteria and CFB bacteria. delta-Proteobacteria were not correlated with HCl-extractable metals. Bacteria of the Desulfosarcina-Desulfococcus group were detected in every site and represented 6 to 14% of the DAPI (4',6'-diamidino-2-phenylindole) counts. Although factors other than metals may explain the distribution observed, the information presented here may be useful in predicting long-term effects of heavy-metal contamination in the marine environment.     

Virioplankton community structure along a salinity gradient in a solar saltern

The virioplankton community structure along a salinity gradient from near seawater (40 per thousand ) to saturated sodium chloride brine (370 per thousand ) in a solar saltern was investigated by pulsed-field gel electrophoresis. Viral populations with genome sizes varying from 10 kb to 533 kb were detected. The viral community structure changed along the salinity gradient. Cluster analysis of the viral genome-banding pattern resulted in two main clusters. The virioplankton diversity within the samples with salinity from 40 per thousand to 150 per thousand was on the same cluster of a cladogram. The other group consisted of virioplankton from samples with salinity above 220 per thousand. The virioplankton diversity in the different samples was calculated using the Shannon index. The diversity index demonstrated an increase in diversity in the samples along the gradient from 40 per thousand to 150 per thousand salinity, followed by a decrease in the diversity index along the rest of the salinity gradient. These results demonstrate how viral diversity changes from habitats that are considered one of the most common (seawater) to habitats that are extreme in salt concentrations (saturated sodium brine). The diversity index was highest in the environments that lie in between the most extreme and the most common.     

Microbial community structures in anoxic freshwater lake sediment along a metal contamination gradient

Contamination, such as by heavy metals, has frequently been implicated in altering microbial community structure. However, this association has not been extensively studied for anaerobic communities, or in freshwater lake sediments. We investigated microbial community structure in the metal-contaminated anoxic sediments of a eutrophic lake that were impacted over the course of 80 years by nearby zinc-smelting activities. Microbial community structure was inferred for bacterial, archaeal and eukaryotic populations by evaluating terminal restriction fragment length polymorphism (TRFLP) patterns in near-surface sediments collected in triplicate from five areas of the lake that had differing levels of metal contamination. The majority of the fragments in the bacterial and eukaryotic profiles showed no evidence of variation in association with metal contamination levels, and diversity revealed by these profiles remained consistent even as metal concentrations varied from 3000 to 27 000 mg kg⁻¹ total Zn, 0.125 to 11.2 μ pore water Zn and 0.023 to 5.40 μ pore water As. Although most archaeal fragments also showed no evidence of variation, the prevalence of a fragment associated with mesophilic Crenarchaeota showed significant positive correlation with total Zn concentrations. This Crenarchaeota fragment dominated the archaeal TRFLP profiles, representing between 35% and 79% of the total measured peak areas. Lake DePue 16S rRNA gene sequences corresponding to this TRFLP fragment clustered with anaerobic and soil mesophilic Crenarchaeota sequences. Although Crenarchaeota have been associated with metal-contaminated groundwater and soils, this is a first report (to our knowledge) documenting potential increased prevalence of Crenarchaeota associated with elevated levels of metal contamination.     

Changes in riverine benthic diatom community structure along a chloride gradient

The application of salt is the primary means of deicing roads and highways in colder regions of north-eastern North America. This has increased the chloride concentrations of many lake and stream ecosystems. While this salinization has been documented, less is known about how increased salinity alters benthic communities in downstream ecosystems. Natural thresholds, at which there are large scale changes in community composition, have not yet been established for many types of contaminants, including chloride. The diatom community, which is sensitive to small changes in the ambient environment, has the potential to be a strong indicator of salinization effects on stream ecosystems. In this study, we sampled diatom communities in 41 streams across a salinity gradient throughout south central Ontario, Canada. We sampled benthic diatom assemblages in early May following complete snowmelt, when stream water chloride concentrations ranged from 5 to 502 mg/L. Based on redundancy analysis, we confirmed a strong association between the species composition of the diatom community and water conductivity, a commonly used index of stream salinity. Taxa indicator threshold analyses (TITAN) indicated the community changed substantially at chloride concentrations greater than 35 mg/L. We also found that, an indicator taxa, Meridion circulare, was extremely sensitive to high concentrations of salt and negatively correlated with chloride. In a wide synoptic survey of streams of our region, we found that streams in most developed watersheds exceed tolerance thresholds for benthic diatom communities. This work suggests that current chloride concentrations in urban watersheds are greatly exceeding the benthic community thresholds, for which improved management and regulatory practices are needed. Salinization thus appears to be an important feature of urban streams and needs to be considered as an important ecological driver in future studies.     

Zooplankton community structure along a trophic gradient in a canyon-shaped dam reservoir

The zooplankton community was surveyed along the longitudinalaxis of Rimov Reservoir (Czech Republic) on seven occasionsduring the vegetative season of 1996. The dimictic Rimov Reservoirhas a pronounced trophic gradient along its axis. In nearlyall samples, rotifers were dominant by numbers and formed onaverage 60–95% of the total zooplankton (including copepodnauplii). There was a consistent pattern of increasing relativeabundance of rotifers in the upper regions of the reservoircompared with the downstream parts. Very large rotifer populationscould develop in the upper regions, often associated with floodevents, but also coinciding with reduced abundance of crustaceansassociated with stronger wash-out effects and the advent ofturbid conditions. There was a greater similarity between twoadjacent sites in the proportions of crustacean species thanof rotifer species. This is partially due to the greater speciesdiversity of rotifers than of crustaceans. The timing of theseasonal succession of zooplankton species showed a coherentpattern along the whole longitudinal profile. The site-specificzooplankton patchiness seems to be reduced as there was no sitedependence if average data on zooplankton composition from downstreamlacustrine sites were compared.     

不同海拔缓步动物群落结构的比较

为研究海拔对缓步动物群落结构的影响,对地处秦岭北坡的南五台山缓步动物群落进行了初步调查研究.调查设置3个样区、45个样方,共采集缓步动物919个,个体密度平均816.89个·m-2,隶属缓步动物门2纲2目3科7属11种.其中Macrobiotus hufelandi和M.harmsworthi共占总采量的92.93%,为优势类群.采用Simpson指数、Shannon-Wiener信息指数、Pielou均匀度指数和修正的Hill指数来计算各生境缓步动物群落结构特点.研究表明,海拔对缓步动物群落结构有一定的影响.随着海拔的下降其物种的个体数量、群落优势类群的数量和优势物种数都呈下降趋势;物种多样性的变化趋势为中海拔地区＞低海拔地区＞高海拔地区,而群落优势度的变化趋势完全相反;不同海拔样区的群落相似性较低.     

Temperature and trophic structure are driving microbial productivity along a biogeographical gradient

Temperature is known to influence ecosystem processes through its direct effect on biological rates such as respiration and nutrient cycling. These changes can then indirectly affect ecologically processes by altering trophic dynamics, the persistence of a species in a given environment, and, consequently, its distribution. However, it is not known if this direct effect of temperature on biological rates is singularly the most important factor for the functioning of ecosystems, or if trophic structure and the adaptation of a species to the local environment also play an essential role. Understanding the relative importance of these factors is crucial for predicting the impact that climate change will have on species and ecosystems. To achieve a more complete understanding of the impact of changing temperatures, it is necessary to integrate perspectives from biogeography, such as the influences of species distribution and local adaptation, with ecosystem and community ecology. By using the microbial community inhabiting the water‐filled leaves of Sarracenia purpurea, we tested the importance of temperature, trophic structure, and local adaptation on ecosystem functioning. We accomplished this by collecting communities along a natural temperature gradient and maintaining these communities in a common garden, factorial experiment. To test for the importance of local adaptation and temperature, the origin of each community was crossed with the temperature from each site. Additionally, to test the importance of top‐down trophic regulation for ecosystem functioning, the presence of the mosquito larvae top predator was manipulated. We found that temperature has a greater effect on ecosystem functioning than origin, and that top‐down trophic regulation increased with temperature. Our results emphasize the synergistic effects of temperature and biotic interactions when predicting the consequences of global warming on ecosystem functioning.     

Predictable changes in trophic community structure along a spatial disturbance gradient in streams

1. We assessed insect and resource standing stocks along a spatial gradient of flood disturbance in 19 sub-alpine Swedish streams to test the prediction that change in trophic structure arises from the joint action of disturbance, which affect basal resources, and resource-control, which ties the response of the consumers to the response of the resources.
2. Trophic structure, quantified as scores of non-metric multidimensional scaling based on the biomass of insect trophic groups, changed predictably along the disturbance gradient. In early summer, predators and algae feeders decreased relative to suspension feeders with increasing disturbance; in autumn, algae feeders decreased relative to leaf feeders with increasing disturbance.
3. Across the disturbance gradient, the biomass of algae-, deposit- and leaf-feeders was principally controlled by the availability of the respective resource (algae, fine detritus and coarse detritus), while disturbance only had subsidiary effects on algae feeders in early summer.
4. Overall, patterns in trophic-group biomass along the disturbance gradient were more likely to reflect indirect effects of disturbance via impact on the resources, which reverberated to the consumers because of resource-control, rather than direct effects. In contrast with the view that stream communities are the result of stochastic colonization following disturbance events, in the study streams the trophic structure of insect assemblages is predictable and partly organized by resource-control across a broad range of disturbance conditions.     

Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field

To understand better the in situ microbial functional diversity under oil contamination stress, soils were sampled along a contamination gradient at an oil field in north-east China. Microbial community functional structure was examined with a functional gene array, termed GeoChip. Multivariate statistical analysis and meta-analysis were conducted to study the functional gene responses to oil concentrations. The total functional gene abundance and diversity decreased along the gradient of increasing contamination. The overall abundance of soil bacteria, archaea and fungi decreased to 10%, 40% and 80% of those in the pristine soil. Several functional genes in the families pgl, rbcL, nifH and nor and those encoding cellulase, laccase, chitinase, urease and key enzymes in metabolizing organic compounds were significantly decreased with oil contamination, especially under high contamination stress. However, a few genes encoding key enzymes for catechol, protocatechuate, and biphenyl degradation and in the gene families of nir, rbcL and pgl showed a significant increase at a medium level of oil contamination. Oil content and soil available nitrogen were found to be important factors influencing the microbial community structure. The results provide an insight into microbial functional diversity in oil-contaminated soils, providing potential information for on-site management and remediation measures.     

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.     

Soil microbial community structure across a thermal gradient following a geothermal heating event

In this study microbial species diversity was assessed across a landscape in Yellowstone National Park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. Soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees C at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. Changes in soil microbial diversity across the temperature gradient were qualitatively assessed based on 16S rRNA sequence variation as detected by denaturing gradient gel electrophoresis (DGGE) using both ribosomal DNA (rDNA) and rRNA as PCR templates and primers specific for the Bacteria or Archaea domain. The impact of the major heating disturbance was apparent in that DGGE profiles from heated soils appeared less complex than those from the unaffected soils. Phylogenetic analysis of a bacterial 16S rDNA PCR clone library from a recently heated soil showed that a majority of the clones belonged to the Acidobacterium (51%) and Planctomyces (18%) divisions. Agar plate counts of soil suspensions cultured on dilute yeast extract and R2A agar media incubated at 25 or 50 degrees C revealed that thermophile populations were two to three orders of magnitude greater in the recently heated soil. A soil microcosm laboratory experiment simulated the geothermal heating event. As determined by both RNA- and DNA-based PCR coupled with DGGE, changes in community structure (marked change in the DGGE profile) of soils incubated at 50 degrees C occurred within 1 week and appeared to stabilize after 3 weeks. The results of our molecular and culture data suggest that thermophiles or thermotolerant species are randomly distributed in this area within Yellowstone National Park and that localized thermal activity selects for them.     

中亚热带森林土壤微生物群落多样性随海拔梯度的变化

运用Biolog EcoPlate技术, 对武夷山不同海拔植被带(常绿阔叶林(EBF)、针叶林(CF)、亚高山矮林(DF)、高山草甸(AM))土壤微生物群落多样性差异进行了研究。结果表明: 不同海拔植被带土壤微生物群落功能多样性差异显著。土壤平均颜色变化率(AWCD)随培养时间延长而逐渐增加, 同一深度土层的AWCD值随海拔升高而逐渐降低, 大小顺序依次为EFB > CF > DF > AM。同一海拔植被带, 不同深度土层的AWCD值总体趋势依次为0-10 cm > 10-25 cm > 25-40 cm。土壤微生物群落Simpson指数、Shannon-Wiener指数、丰富度指数和McIntosh指数的总体趋势为EBF最高, CF和DF次之, AM最低。不同海拔植被带土壤微生物对不同碳源利用强度存在较大差异, 其中EBF利用率最高, AM利用率最低, 碳水化合物和羧酸类碳源是各海拔植被带土壤微生物的主要碳源。主成分分析结果表明, 从31个因素中提取的与碳源利用相关的主成分1、主成分2分别能解释变量方差的75.27%和16.14%, 在主成分分离中起主要贡献作用的是胺类和氨基酸类碳源。土壤微生物群落多样性随着海拔上升、土层加深而逐渐下降的原因, 可能是生物量、林分凋落物、土壤养分、微小动物、植物根系等多种因素共同作用的结果。     

Microbial community structure along an altitude gradient in three different localities

The microbial community structure along an altitude gradient was investigated in different localities, in Kalasi lake, Urumqi river and Sangong river, Xingjiang (China). The mean numbers of DAPI (4',6-diamidino-2-phenylindole)-stained cells were lower in Kalasi lake than that in Urumqi river and Sangong river; these differences were attributed to increasing environmental harshness including lower soil organic carbon and nitrogen content, more acidic pH and lower annual temperature. In each locality, the numbers of bacteria and archaea measured with two fluorescence-labeled 16S rRNA oligonucleotide probes (EUB338 and ARCH915) were higher in a coniferous forest and lower in desert vegetation. A significant and positive relationship was found between microbial and soil organic carbon and total nitrogen along the altitudinal gradient, indicating that plant communities and soil nutrients influence the soil microbial structure. The results show that the microbial population in higher latitudinal site was fewer than lower latitudinal one, soil microorganisms were positively correlated to soil organic carbon and total nitrogen, and plant communities had an obviously impact on soil microbes.     

Diversity and phylogenetic community structure of ants along a Costa Rican elevational gradient

The diversity and phylogenetic community structure of many organisms is negatively affected by factors that covary with elevation. On the Pacific slope of the Cordillera Guanacaste within Area de Conservación Guanacaste (ACG) in northwestern Costa Rica we found a negative relationship between elevation and ant diversity on each of three volcanos. This pattern was evident when diversity was measured through molecular operational taxonomic units (MOTU) or by phylogenetic diversity (PD) based on DNA barcodes or a multi‐gene phylogeny. We observed an asymmetrical mid‐elevation peak at approximately 600–800 m and we found high species turnover between sites on the same mountain and among the three mountains. At the highest elevation cloud forest sites we found evidence of significant phylogenetic clustering, the expected result of environmental filtering. The narrow elevational range of each species, coupled with the high diversity at each sampling point, emphasizes that climate change will bring strong changes in the location and composition of biodiversity on these mountains. The structure and composition of the hyperdiverse communities present at any one elevation is extremely vulnerable to a changing climate.     

Scale-dependant control of motile epifaunal community structure along a coral reef fishing gradient

Large-scale fishing is mostly conducted using towed gears that reduce the biomass and diversity of benthic invertebrates. However, it is impossible to differentiate between the physical disturbance effect of towed gears from the effect of fish predator removal upon benthic invertebrate communities. Here we explore the impact of fish removal alone on the community structure of small motile coral reef invertebrates (epifauna) along a subsistence fishing intensity gradient in the Lau group, Fiji. We deployed settlement plates at three areas in each of six fishing grounds and examined the density and class richness of the motile epifaunal communities and the associated algal communities in relation to the structure of fish and benthic communities. Motile epifaunal density was unrelated to fishing intensity. However, at smaller inter-area scale (0.5-10 km) motile epifaunal density was negatively related to plate algal biomass, whereas at the larger inter-fishing-ground scale (4-180 km) motile epifaunal density was positively related to the rugosity (substrate complexity) of the surrounding benthos. The class richness and diversity (Margalef's d) of motile epifaunal communities were negatively related to fishing intensity, but unrelated to grazing intensity, rugosity or algal biomass at either scale. Benthic community structure varied significantly with fishing intensity; hard-coral cover was lower and turf-algal cover was higher at high fishing pressure. The variation in benthic community structure was associated with variation in fish community structure, which in turn varied with fishing intensity. Motile epifaunal community structure upon plates was linked to the structure of the surrounding benthic community, but was not directly linked to the plate algal community. We suggest the decline in richness of the motile epifauna community along the fishing gradient is attributable to either to exploiter-mediated coexistence or the reduction in ‘habitat quality’ of the surrounding benthos. At the large spatial scale substrate complexity is the key determinant of motile epifaunal density, suggesting predation by fishes plays an important structuring role at this scale. Assuming that rugosity is inversely related to predation risk then this study represents the first evidence for spatial-dependence on the top-down (predation) vs. bottom-up (algal biomass) control of community structure. We argue fisheries exploitation, in the absence of a physical disturbance can negatively influence motile epifaunal community structure at large spatial scales.     

Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert

The Namib Desert is considered the oldest desert in the world and hyperarid for the last 5 million years. However, the environmental buffering provided by quartz and other translucent rocks supports extensive hypolithic microbial communities. In this study, open soil and hypolithic microbial communities have been investigated along an East–West transect characterized by an inverse fog-rainfall gradient. Multivariate analysis showed that structurally different microbial communities occur in soil and in hypolithic zones. Using variation partitioning, we found that hypolithic communities exhibited a fog-related distribution as indicated by the significant East–West clustering. Sodium content was also an important environmental factor affecting the composition of both soil and hypolithic microbial communities. Finally, although null models for patterns in microbial communities were not supported by experimental data, the amount of unexplained variation (68–97 %) suggests that stochastic processes also play a role in the assembly of such communities in the Namib Desert.     

Phosphorus availability and microbial community in the rhizosphere of intercropped cereal and legume along a P-fertilizer gradient

Background and aims

Positive below-ground interactions (facilitation) should be more pronounced when resources limit crop growth, according to the stress-gradient hypothesis. Our aim was to test this hypothesis for intercropped durum wheat and faba bean along a P-fertilizer gradient.

Methods

A field experiment was conducted in a long-term P-fertilizer trial with three rates of P-fertilization (No, Low and High P). Microbial biomass was assessed by chloroform fumigation-extraction. Quantitative PCR was applied to evaluate the abundance of relevant microbial groups.

Results

Phosphorus availability and microbial biomass systematically increased in the rhizosphere compared to bulk soil. P-fertilization resulted in higher abundance of targeted bacterial phyla, whole bacterial and fungal communities, and depressed mycorrhizal colonization of durum wheat, but not faba bean. Microbial biomass carbon significantly increased in the rhizosphere only in P-fertilized treatments, pointing to P limitation of microbial communities. Intercropping yielded a significant effect on rhizosphere microbial properties only at High P. Microbial biomass P increased in the rhizosphere of intercropped faba bean only at No P level, and was thus the sole finding supporting the stress-gradient hypothesis.

Conclusions

P-fertilization was the main driver of microbial communities in this field trial, and P-fertilizer application modulated the species-specific effect in the intercrop. Plant performance did not validate the stress-gradient hypothesis as positive plant-plant interactions occurred regardless of the level of P-fertilization.

     

Phylogenetic structure of a palm community in the central Amazon: changes along a hydro-edaphic gradient

The concepts of phylogenetic community structure (PCS) and phylogenetic niche conservatism (PNC) allow ecologists to address the role of species’ evolutionary history in community assembly. It is important to test the role of historical legacies relative to environmental constraints at local scales, where communities are assembled. We studied phylogenetic structure and niche conservatism for palms (Arecaceae) in the 64-km² Ducke Reserve in the central Amazon, near Manaus. The 72 study plots, each covering 0.1 ha, were distributed regularly in a terra firme forest along a hydro-edaphic gradient. We compared the observed palm PCS with assemblages generated by null models. We also analyzed whether morphological and ecological traits are labile or conserved along the phylogeny and quantified the spatial structure of morphological traits in each plot. We found an overall neutral PCS in combination with low PNC (labile traits), suggesting that evolutionary history poses little constraint on palm community assembly in this Amazonian landscape. Still, there was a tendency towards phylogenetic overdispersion in bottomlands, suggesting competitive exclusion among close relatives or, more likely, environmental filtering acting on convergent traits that affect co-occurrence in flood-prone areas. We conclude that (1) PCS of local communities is random as a whole and morphological traits are overall labile, but that (2) the hydro-edaphic gradient within terra firme forests leads to differences in species co-occurrence so that closely related species occur less often than expected in bottomlands due to diffuse competition among close relatives or environmental filtering on convergent traits.