Changes in Sediment Bacterial Community in Response to Long-Term Nutrient Enrichment in a Subtropical Seagrass-Dominated Estuary

Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m² plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community structures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band sequences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial communities with increased capability to degrade polymeric organic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in community composition tended to be proportional to the amount of P limitation obviated by the nutrient additions.     

Nutrient Enrichment and Planktonic Biomass Ratios in Lakes

Phosphorus (P) to chlorophyll ratios and zooplankton–phytoplankton (Z:P) biomass ratios were assessed in 400 temperate lakes over a gradient of phosphorus (P) and with different fish communities. Most of the lakes in this survey were oligotrophic, with a median total P of 7.3 μg P L⁻¹. Thus, the survey provided information on food web effects during the early phase of eutrophication. There was no tendency toward a reduced yield of autotrophs per unit of P over the gradient covered in this survey. The zooplankton yield per unit of P or chlorophyll a decreased slightly with increased nutrient concentrations, and Z:P biomass ratios decreased with fish community classes, reflecting increased fish predation pressure. However, the variability in biomass ratios within a given range of P and fish class was some 100 times higher than the difference over the gradients. This finding suggests that lake-specific properties, community composition, and food quality are by far the most important determinants of biomass ratios and probably also trophic efficiency in lakes; it further suggests that these factors are superimposed on the general effect of eutrophication, at least up to 30 μg P L⁻¹.     

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

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

Carbon Catabolite Control is Important for Listeria monocytogenes Biofilm Formation in Response to Nutrient Availability

The foodborne pathogen Listeria monocytogenes has the ability to develop biofilm in food-processing environment, which becomes a major concern for the food safety. The biofilm formation is strongly influenced by the availability of nutrients and environmental conditions, and particularly enhanced in poor minimal essential medium (MEM) containing glucose rather than in rich brain heart infusion (BHI) broth. To gain better insight into the conserved protein expression profile in these biofilms, the proteomes from biofilm- and planktonic-grown cells from MEM with 50?mM glucose or BHI were compared using two-dimensional polyacrylamide gel electrophoresis followed by MALDI-TOF/TOF analysis. 47 proteins were successfully identified to be either up (19 proteins) or down (28 proteins) regulated in the biofilm states. Most (30 proteins) of them were assigned to the metabolism functional category in cluster of orthologous groups of proteins. Among them, up-regulated proteins were mainly associated with the pentose phosphate pathway and glycolysis, whereas a key enzyme CitC involved in tricarboxylic acid cycle was down-regulated in biofilms compared to the planktonic states. These data implicate the importance of carbon catabolite control for L. monocytogenes biofilm formation in response to nutrient availability.     

Bacteriophage Latent-Period Evolution as a Response to Resource Availability

Bacteriophages (phages) modify microbial communities by lysing hosts, transferring genetic material, and effecting lysogenic conversion. To understand how natural communities are affected it is important to develop predictive models. Here we consider how variation between models—in eclipse period, latent period, adsorption constant, burst size, the handling of differences in host quantity and host quality, and in modeling strategy—can affect predictions. First we compare two published models of phage growth, which differ primarily in terms of how they model the kinetics of phage adsorption; one is a computer simulation and the other is an explicit calculation. At higher host quantities (~10⁸ cells/ml), both models closely predict experimentally determined phage population growth rates. At lower host quantities (10⁷ cells/ml), the computer simulation continues to closely predict phage growth rates, but the explicit model does not. Next we concentrate on predictions of latent-period optima. A latent-period optimum is the latent period that maximizes the population growth of a specific phage growing in the presence of a specific quantity and quality of host cells. Both models predict similar latent-period optima at higher host densities (e.g., 17 min at 10⁸ cells/ml). At lower host densities, however, the computer simulation predicts latent-period optima that are much shorter than those suggested by explicit calculations (e.g., 90 versus 1,250 min at 10⁵ cells/ml). Finally, we consider the impact of host quality on phage latent-period evolution. By taking care to differentiate latent-period phenotypic plasticity from latent-period evolution, we argue that the impact of host quality on phage latent-period evolution may be relatively small.     

The Impact of Resource Availability on Bacterial Resistance to Phages in Soil

Resource availability can affect the coevolutionary dynamics between host and parasites, shaping communities and hence ecosystem function. A key finding from theoretical and in vitro studies is that host resistance evolves to greater levels with increased resources, but the relevance to natural communities is less clear. We took two complementary approaches to investigate the effect of resource availability on the evolution of bacterial resistance to phages in soil. First, we measured the resistance and infectivity of natural communities of soil bacteria and phage in the presence and absence of nutrient-providing plants. Second, we followed the real-time coevolution between defined bacteria and phage populations with resource availability manipulated by the addition or not of an artificial plant root exudate. Increased resource availability resulted in increases in bacterial resistance to phages, but without a concomitant increase in phage infectivity. These results suggest that phages may have a reduced impact on the control of bacterial densities and community composition in stable, high resource environments.     

Bacterial Community Structure in Patagonian Andean Lakes Above and Below Timberline: From Community Composition to Community Function

Lakes located above the timberline are remote systems with a number of extreme environmental conditions, becoming physically harsh ecosystems, and sensors of global change. We analyze bacterial community composition and community-level physiological profiles in mountain lakes located in an altitude gradient in North Patagonian Andes below and above the timberline, together with dissolved organic carbon (DOC) characterization and consumption. Our results indicated a decrease in 71 % of DOC and 65 % in total dissolved phosphorus (TDP) concentration as well as in bacteria abundances along the altitude range (1,380 to 1,950 m a.s.l.). Dissolved organic matter (DOM) fluorescence analysis revealed a low global variability composed by two humic-like components (allochthonous substances) and a single protein-like component (autochthonous substances). Lakes below the timberline showed the presence of all the three components, while lakes above the timberline the protein-like compound constituted the main DOC component. Furthermore, bacterial community composition similarity and ordination analysis showed that altitude and resource concentration (DOC and TDP) were the main variables determining the ordination of groups. Community-level physiological profiles showed a mismatch with bacteria community composition (BCC), indicating the absence of a relationship between genetic and functional diversity in the altitude gradient. However, carbon utilization efficiencies varied according to the presence of different compounds in DOM bulk. The obtained results suggest that the different bacterial communities in these mountain lakes seem to have similar metabolic pathways in order to be able to exploit the available DOC molecules.     

Disturbance Promotes Non-Indigenous Bacterial Invasion in Soil Microcosms: Analysis of the Roles of Resource Availability and Community Structure

Background

Invasion-biology is largely based on non-experimental observation of larger organisms. Here, we apply an experimental approach to the subject. By using microbial-based microcosm-experiments, invasion-biology can be placed on firmer experimental, and hence, less anecdotal ground. A better understanding of the mechanisms that govern invasion-success of bacteria in soil communities will provide knowledge on the factors that hinder successful establishment of bacteria artificially inoculated into soil, e.g. for remediation purposes. Further, it will yield valuable information on general principles of invasion biology in other domains of life.

Methodology/Principal Findings

Here, we studied invasion and establishment success of GFP-tagged Pseudomonas fluorescens DSM 50090 in laboratory microcosms during a 42-day period. We used soil heating to create a disturbance gradient, and hypothesized that increased disturbance would facilitate invasion; our experiments confirmed this hypothesis. We suggest that the key factors associated with the heating disturbance that explain the enhanced invasion success are increased carbon substrate availability and reduced diversity, and thus, competition- and predation-release. In a second experiment we therefore separated the effects of increased carbon availability and decreased diversity. Here, we demonstrated that the effect of the indigenous soil community on bacterial invasion was stronger than that of resource availability. In particular, introduced bacteria established better in a long term perspective at lower diversity and predation pressure.

Conclusion

We propose increased use of microbial systems, for experimental study of invasion scenarios. They offer a simple and cost-efficient way to study and understand biological invasion. Consequently such systems can help us to better predict the mechanisms controlling changes in stability of communities and ecosystems. This is becoming increasingly relevant since anthropogenic disturbance causes increasing global change, which promotes invasion. Moreover, a thorough understanding of factors controlling invasion and establishment of artificially amended micro-organisms will mean a major step forward for soil-remediation microbiology.     

Phosphorus Availability Determines the Response of Tundra Ecosystem Carbon Stocks to Nitrogen Enrichment

Northern permafrost soils contain important carbon stocks. Here we report the long-term response of carbon stocks in high Arctic dwarf shrub tundra to short-term, low-level nutrient enrichment. Twenty years after experimental nitrogen addition, carbon stocks in vegetation and organic soil had almost halved. In contrast, where phosphorus was added with nitrogen, carbon storage increased by more than 50%. These responses were explained by changes in the depths of the moss and organic soil layers. Nitrogen apparently stimulated decomposition, reducing carbon stocks, whilst phosphorus and nitrogen co-stimulated moss productivity, increasing organic matter accumulation. The altered structure of moss and soil layers changed soil thermal regimes, which may further influence decomposition of soil carbon. If climate warming increases phosphorus availability, any increases in nitrogen enrichment from soil warming or expanding human activity in the Arctic may result in increased carbon sequestration. Where phosphorus is limiting in tundra areas, however, nitrogen enrichment may result in carbon loss.     

匍匐茎草本蛇莓对基质养分条件的克隆可塑性

A pot experiment with three levels of nutrient (N, P, K) supply was carried out to investigate clonal plasticity of stoloniferous herb Duchesnea indica Focke in response to nutrient availability. The plants had greater biomass at higher levels of nutrient availability. The root/shoot ratio of the plants changed with the nutrient availability in the following order: low level > high level > medium level. They had the largest biomass allocation to stolon at the medium level of nutrient availability. The biomass allocation to petiole did not respond to the treatments. The plants formed more stolons and ramets at the high and medium levels than the low level of nutrient availability. The petiole length, specific petiole weight（mg/cm）and stolon internode length of the plants did not respond to the treatments, while the specific stolon weight (mg/cm）of the plants was greater at the high and medium levels than the low level of nutrient availability. The results have been discussed in the context of adaptation of clonal plants to environmental heterogeneity.     

Responses to CO2 Enrichment by Two Genotypes of Arabidopsis thaliana Differing in their Sensitivity to Nutrient Availability

The responses of two genotypes of Arabidopsis thaliana, whichdiffer in their sensitivities to nutrients to present and predictedfuture CO₂ concentration were determined under rich vs. poornutrient regimes on the basis of both single traits and thewhole plant. Based on individual traits, the two genotypes respondedsimilarly to CO₂ enrichment for all the traits measured exceptfor rate of increase in crown diameter, for which a decreasewas observed in the less nutrient-sensitive genotype grown atincreased CO₂. Based on the overall response of the whole plant,by analysing groups of plant traits using multivariate analysis,the two genotypes differed substantially from one another andboth responded more strongly to nutrient availability than toCO₂ concentration, especially for traits measured at harvestthat related to reproductive fitness. The less nutrient-sensitivegenotype also showed a weaker overall response to CO₂, and thepattern of the overall response was strikingly similar at differentnutrient supply. In contrast, the more nutrient-sensitive genotyperesponded more strongly to CO₂ than the less nutrient-sensitivegenotype, and responded differently to CO₂ at low vs. high nutrientavailability.Copyright 1995, 1999 Academic Press Plasticity, CO₂ enrichment, nutrient status, nutrient x CO₂ interaction, Arabidopsis thaliana, canonical analysis     

资源异质性环境中三种匍匐茎草本植物克隆内资源共享和分株功能特化

研究了3种来自中国北方林下、草地和碱化草甸匍匐茎型克隆草本植物绢毛匍匐委陵菜 (Potentilla reptans L. var. sericophylla Franch.)、鹅绒委陵菜 (P. anserina L.) 和金戴戴 (Halerpestes ruthenica (Jacq.) Qvcz.) 对由高光照低养分斑块和低光照高养分斑块组成的资源交互斑块性生境的适应性对策.当生长于高光照低养分条件下分株 (HL分株) 与生长于低光照高养分条件下分株 (LH分株) 之间的匍匐茎连接时, 3种克隆植物HL分株、LH分株以及整个分株对系统 (HL分株 + LH分株) 的生物量均得到显著提高.同时, LH分株根冠比显著增加, 而HL分株根冠比显著下降.这表明, 当互连分株置于由低光照高养分斑块和高光照低养分斑块组成的异质性环境中时, 3种植物克隆分株均发生了环境诱导的功能特化.克隆内资源共享以及克隆内不同分株的功能特化有利于整个分株系统对局部丰富资源的获取, 从而能够缓解资源交互斑块性生境对克隆植物的不利影响.     

资源异质性环境中三种匍匐茎草本植物克隆内资源共享和分株功能特化(英文)

研究了 3种来自中国北方林下、草地和碱化草甸匍匐茎型克隆草本植物绢毛匍匐委陵菜 (PotentillareptansL .var.sericophyllaFranch .)、鹅绒委陵菜 (P .anserinaL .)和金戴戴 (Halerpestesruthenica (Jacq .)Qvcz .)对由高光照低养分斑块和低光照高养分斑块组成的资源交互斑块性生境的适应性对策。当生长于高光照低养分条件下分株(HL分株 )与生长于低光照高养分条件下分株 (LH分株 )之间的匍匐茎连接时 ,3种克隆植物HL分株、LH分株以及整个分株对系统 (HL分株 LH分株 )的生物量均得到显著提高。同时 ,LH分株根冠比显著增加 ,而HL分株根冠比显著下降。这表明 ,当互连分株置于由低光照高养分斑块和高光照低养分斑块组成的异质性环境中时 ,3种植物克隆分株均发生了环境诱导的功能特化。克隆内资源共享以及克隆内不同分株的功能特化有利于整个分株系统对局部丰富资源的获取 ,从而能够缓解资源交互斑块性生境对克隆植物的不利影响     

Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity

Vertical and latitudinal differences in bacterial community composition (BCC) in Lake Tanganyika were studied during the dry season of 2002 by means of denaturing gradient gel electrophoresis analysis of PCR-amplified 16S RNA fragments. Dominant bands were sequenced and identified as members of the Cyanobacteria, Actinobacteria, Nitrospirae, green nonsulfur bacteria, and Firmicutes divisions and the Gamma- and Deltaproteobacteria subdivisions. The BCC in the lake displayed both vertical and latitudinal variation. Vertical changes in BCC were related to the thermal water column stratification, which influences oxygen and nutrient concentrations. Latitudinal variation was related to upwelling of deep water and increased primary production in the south of the lake. The number of bands per sample increased with bacterial production in the epilimnion of the lake, suggesting a positive diversity-productivity relationship.     

Experimental Examination of Bacteriophage Latent-Period Evolution as a Response to Bacterial Availability

For obligately lytic bacteriophage (phage) a trade-off exists between fecundity (burst size) and latent period (a component of generation time). This trade-off occurs because release of phage progeny from infected bacteria coincides with destruction of the machinery necessary to produce more phage progeny. Here we employ phage mutants to explore issues of phage latent-period evolution as a function of the density of phage-susceptible bacteria. Theory suggests that higher bacterial densities should select for shorter phage latent periods. Consistently, we have found that higher host densities (≥~10⁷ bacteria/ml) can enrich stocks of phage RB69 for variants that display shorter latent periods than the wild type. One such variant, dubbed sta5, displays a latent period that is ~70 to 80% of that of the wild type—which is nearly as short as the RB69 eclipse period—and which has a corresponding burst size that is ~30% of that of the wild type. We show that at higher host densities (≥~10⁷ bacteria/ml) the sta5 phage can outcompete the RB69 wild type, though only under conditions of direct (same-culture) competition. We interpret this advantage as corresponding to slightly faster sta5 population growth, resulting in multifold increases in mutant frequency during same-culture growth. The sta5 advantage is lost, however, given indirect (different-culture) competition between the wild type and mutant or given same-culture competition but at lower densities of phage-susceptible bacteria (≤~10⁶ bacteria/ml). From these observations we suggest that phage displaying very short latent periods may be viewed as specialists for propagation when bacteria within cultures are highly prevalent and transmission between cultures is easily accomplished.     

Spatial Physiological Heterogeneity in Pseudomonas aeruginosa Biofilm Is Determined by Oxygen Availability

The role of oxygen availability in determining the local physiological activity of Pseudomonas aeruginosa growing in biofilms was investigated. Biofilms grown in an ambient-air environment expressed approximately 1/15th the alkaline phosphatase specific activity of planktonic bacteria subjected to the same phosphate limitation treatment. Biofilms grown in a gaseous environment of pure oxygen exhibited 1.9 times the amount of alkaline phosphatase specific activity of air-grown biofilms, whereas biofilms grown in an environment in which the air was replaced with pure nitrogen prior to the inducing treatment did not develop alkaline phosphatase activity. Frozen cross sections of biofilms stained for alkaline phosphatase activity with a fluorogenic stain demonstrated that alkaline phosphatase activity was concentrated in distinct bands adjacent to the gaseous interfaces. These bands were approximately 30 μm thick with biofilms grown in air, 2 μm thick with biofilms grown in pure nitrogen, and 46 μm thick with biofilms grown in pure oxygen. Overall biofilm thickness ranged from approximately 117 to approximately 151 μm. Measurements with an oxygen microelectrode indicated that oxygen was depleted locally within the biofilm and that the oxygen-replete zone was of a dimension similar to that of the biologically active zone, as indicated by alkaline phosphatase induction. These experiments revealed marked spatial physiological heterogeneity within P. aeruginosa biofilms in which active protein synthesis was restricted by oxygen availability to the upper 30 μm of the biofilm. Such physiological heterogeneity has implications for microbial ecology and for understanding the reduced susceptibilities of biofilms to antimicrobial agents.     

Spatial Heterogeneity and Peptide Availability Determine CTL Killing Efficiency In Vivo

The rate at which a cytotoxic T lymphocyte (CTL) can survey for infected cells is a key ingredient of models of vertebrate immune responses to intracellular pathogens. Estimates have been obtained using in vivo cytotoxicity assays in which peptide-pulsed splenocytes are killed by CTL in the spleens of immunised mice. However the spleen is a heterogeneous environment and splenocytes comprise multiple cell types. Are some cell types intrinsically more susceptible to lysis than others? Quantitatively, what impacts are made by the spatial distribution of targets and effectors, and the level of peptide-MHC on the target cell surface? To address these questions we revisited the splenocyte killing assay, using CTL specific for an epitope of influenza virus. We found that at the cell population level T cell targets were killed more rapidly than B cells. Using modeling, quantitative imaging and in vitro killing assays we conclude that this difference in vivo likely reflects different migratory patterns of targets within the spleen and a heterogeneous distribution of CTL, with no detectable difference in the intrinsic susceptibilities of the two populations to lysis. Modeling of the stages involved in the detection and killing of peptide-pulsed targets in vitro revealed that peptide dose influenced the ability of CTL to form conjugates with targets but had no detectable effect on the probability that conjugation resulted in lysis, and that T cell targets took longer to lyse than B cells. We also infer that incomplete killing in vivo of cells pulsed with low doses of peptide may be due to a combination of heterogeneity in peptide uptake and the dissociation, but not internalisation, of peptide-MHC complexes. Our analyses demonstrate how population-averaged parameters in models of immune responses can be dissected to account for both spatial and cellular heterogeneity.