Functional Gene Composition,Diversity and Redundancy in Microbial Stream Biofilm Communities

We surveyed the functional gene composition and diversity of microbial biofilm communities in 18 New Zealand streams affected by different types of catchment land use, using a comprehensive functional gene array, GeoChip 3.0. A total of 5,371 nutrient cycling and energy metabolism genes within 65 gene families were detected among all samples (342 to 2,666 genes per stream). Carbon cycling genes were most common, followed by nitrogen cycling genes, with smaller proportions of sulphur, phosphorus cycling and energy metabolism genes. Samples from urban and native forest streams had the most similar functional gene composition, while samples from exotic forest and rural streams exhibited the most variation. There were significant differences between nitrogen and sulphur cycling genes detected in native forest and urban samples compared to exotic forest and rural samples, attributed to contrasting proportions of nitrogen fixation, denitrification, and sulphur reduction genes. Most genes were detected only in one or a few samples, with only a small minority occurring in all samples. Nonetheless, 42 of 65 gene families occurred in every sample and overall proportions of gene families were similar among samples from contrasting streams. This suggests the existence of functional gene redundancy among different stream biofilm communities despite contrasting taxonomic composition.     

Sampling and Complementarity Effects of Plant Diversity on Resource Use Increases the Invasion Resistance of Communities

BackgroundAlthough plant diversity is postulated to resist invasion, studies have not provided consistent results, most of which were ascribed to the influences of other covariate environmental factors.Conclusions/SignificanceThe results of this study suggest that plant diversity confers resistance to invasion, which is mainly ascribed to the sampling effect of particular species and the complementarity effect among species on resources use.     

Effects of Warming on Stream Biofilm Organic Matter Use Capabilities

The understanding of ecosystem responses to changing environmental conditions is becoming increasingly relevant in the context of global warming. Microbial biofilm communities in streams play a key role in organic matter cycling which might be modulated by shifts in flowing water temperature. In this study, we performed an experiment at the Candal stream (Portugal) longitudinally divided into two reaches: a control half and an experimental half where water temperature was 3 °C above that of the basal stream water. Biofilm colonization was monitored during 42 days in the two stream halves. Changes in biofilm function (extracellular enzyme activities and carbon substrate utilization profiles) as well as chlorophyll a and prokaryote densities were analyzed. The biofilm in the experimental half showed a higher capacity to decompose cellulose, hemicellulose, lignin, and peptidic compounds. Total leucine-aminopeptidase, cellobiohydrolase and β-xylosidase showed a respective 93, 66, and 61 % increase in activity over the control; much higher than would be predicted by only the direct temperature physical effect. In contrast, phosphatase and lipase activity showed the lowest sensitivity to temperature. The biofilms from the experimental half also showed a distinct functional fingerprint and higher carbon usage diversity and richness, especially due to a wider use of polymers and carbohydrates. The changes in the biofilm functional capabilities might be indirectly affected by the higher prokaryote and chlorophyll density measured in the biofilm of the experimental half. The present study provides evidence that a realistic stream temperature increase by 3 °C changes the biofilm metabolism to a greater decomposition of polymeric complex compounds and peptides but lower decomposition of lipids. This might affect stream organic matter cycling and the transfer of carbon to higher trophic levels.     

Watershed-scale Land Use Change Increases Ecosystem Metabolism in an Agricultural Stream

Ecosystems - Stream metabolism, in the form of gross primary production (GPP) and ecosystem respiration (ER), is an important metric of stream ecosystem function, given GPP and ER are integrative...     

Aggregation of Cricket Activity in Response to Resource Addition Increases Local Diversity

Crickets are often found feeding on fallen fruits among forest litter. Fruits and other sugar-rich resources are not homogeneously distributed, nor are they always available. We therefore expect that crickets dwelling in forest litter have a limited supply of sugar-rich resource, and will perceive this and displace towards resource-supplemented sites. Here we evaluate how sugar availability affects cricket species richness and abundance in old-growth Atlantic forest by spraying sugarcane syrup on leaf litter, simulating increasing availability, and collecting crickets via pitfall trapping. We found an asymptotic positive association between resource addition and species richness, and an interaction between resource addition and species identity on cricket abundance, which indicates differential effects of resource addition among cricket species. Our results indicate that 12 of the 13 cricket species present in forest litter are maintained at low densities by resource scarcity; this highlights sugar-rich resource as a short-term driver of litter cricket community structure in tropical forests. When resource was experimentally increased, species richness increased due to behavioral displacement. We present evidence that the density of many species is limited by resource scarcity and, when resources are added, behavioral displacement promotes increased species packing and alters species composition. Further, our findings have technical applicability for increasing sampling efficiency of local cricket diversity in studies aiming to estimate species richness, but with no regard to local environmental drivers or species-abundance characteristics.     

Species-Specific Traits Rather Than Resource Partitioning Mediate Diversity Effects on Resource Use

Background

The link between biodiversity and ecosystem processes has firmly been established, but the mechanisms underpinning this relationship are poorly documented. Most studies have focused on terrestrial plant systems where resource use can be difficult to quantify as species rely on a limited number of common resources. Investigating resource use at the bulk level may not always be of sufficient resolution to detect subtle differences in resource use, as species-specific nutritional niches at the biochemical level may also moderate diversity effects on resource use.

Methodology/Principal Findings

Here we use three co-occurring marine benthic echinoderms (Brissopsis lyrifera, Mesothuria intestinalis, Parastichopus tremulus) that feed on the same phytodetrital food source, to determine whether resource partitioning is the principal mechanism underpinning diversity effects on resource use. Specifically we investigate the use of phytodetrital pigments (chlorophylls and carotenoids) because many of these are essential for biological functions, including reproduction. Pigments were identified and quantified using reverse-phase high performance liquid Chromatography (HPLC) and data were analysed using a combination of extended linear regression with generalised least squares (GLS) estimation and standard multivariate techniques. Our analyses reveal no species-specific selectivity for particular algal pigments, confirming that these three species do not partition food resources at the biochemical level. Nevertheless, we demonstrate increased total resource use in diverse treatments as a result of selection effects and the dominance of one species (B. lyrifera).

Conclusion

Overall, we found no evidence for resource partitioning at the biochemical level, as pigment composition was similar between individuals, which is likely due to plentiful food availability. Reduced intra-specific competition in the species mixture combined with greater adsorption efficiency and differences in feeding behaviour likely explain the dominant use of resources by B. lyrifera.     

Early Life-History Consequences of Growth-Hormone Transgenesis in Rainbow Trout Reared in Stream Ecosystem Mesocosms

There is persistent commercial interest in the use of growth modified fishes for shortening production cycles and increasing overall food production, but there is concern over the potential impact that transgenic fishes might have if ever released into nature. To explore the ecological consequences of transgenic fish, we performed two experiments in which the early growth and survival of growth-hormone transgenic rainbow trout (Oncorhynchus mykiss) were assessed in naturalized stream mesocosms that either contained predators or were predator-free. We paid special attention to the survival bottleneck that occurs during the early life-history of salmonids, and conducted experiments at two age classes (first-feeding fry and 60 days post-first-feeding) that lie on either side of the bottleneck. In the late summer, the first-feeding transgenic trout could not match the growth potential of their wild-type siblings when reared in a hydrodynamically complex and oligotrophic environment, irrespective of predation pressure. Furthermore, overall survival of transgenic fry was lower than in wild-type (transgenic = 30% without predators, 8% with predators; wild-type = 81% without predators, 31% with predators). In the experiment with 60-day old fry, we explored the effects of the transgene in different genetic backgrounds (wild versus domesticated). We found no difference in overwinter survival but significantly higher growth by transgenic trout, irrespective of genetic background. We conclude that the high mortality of GH-transgenic trout during first-feeding reflects an inability to sustain the basic metabolic requirements necessary for life in complex, stream environments. However, when older, GH-transgenic fish display a competitive advantage over wild-type fry, and show greater growth and equal survival as wild-type. These results demonstrate how developmental age and time of year can influence the response of genotypes to environmental conditions. We therefore urge caution when extrapolating the results of GH-transgenesis risk assessment studies across multiple life-history or developmental stages.     

Relative Diversity and Community Structure of Ciliates in Stream Biofilms According to Molecular and Microscopy Methods

Ciliates are an important component of aquatic ecosystems, acting as predators of bacteria and protozoa and providing nutrition for organisms at higher trophic levels. Understanding of the diversity and ecological role of ciliates in stream biofilms is limited, however. Ciliate diversity in biofilm samples from four streams subject to different impacts by human activity was assessed using microscopy and terminal restriction fragment length polymorphism (T-RFLP) analysis of 18S rRNA sequences. Analysis of 3′ and 5′ terminal fragments yielded very similar estimates of ciliate diversity. The diversity detected using microscopy was consistently lower than that suggested by T-RFLP analysis, indicating the existence of genetic diversity not apparent by morphological examination. Microscopy and T-RFLP analyses revealed similar relative trends in diversity between different streams, with the lowest level of biofilm-associated ciliate diversity found in samples from the least-impacted stream and the highest diversity in samples from moderately to highly impacted streams. Multivariate analysis provided evidence of significantly different ciliate communities in biofilm samples from different streams and seasons, particularly between a highly degraded urban stream and less impacted streams. Microscopy and T-RFLP data both suggested the existence of widely distributed, resilient biofilm-associated ciliates as well as ciliate taxa restricted to sites with particular environmental conditions, with cosmopolitan taxa being more abundant than those with restricted distributions. Differences between ciliate assemblages were associated with water quality characteristics typical of urban stream degradation and may be related to factors such as nutrient availability and macroinvertebrate communities. Microscopic and molecular techniques were considered to be useful complementary approaches for investigation of biofilm ciliate communities.Heterotrophic microeukaryotes such as ciliates are thought to be of considerable importance in aquatic ecosystems, as they are major predators of bacteria and constitute a nutritional resource for other protozoa, invertebrates, and probably fish larvae (9, 22, 36, 52, 62, 63, 71). In addition, protozoan bacterivory contributes to enhanced decomposition of leaf detritus—a vital nutrient resource in streams—by increasing turnover of bacterial populations through predation (57). It is not well understood, however, how ciliate diversity and community structure in streams are affected by changing environmental conditions, or how ciliate communities affect other stream biota and processes. The effects of various physical, chemical, and biological factors on freshwater protozoan communities have been considered by a number of studies, but most of these have focused upon planktonic organisms in lentic habitats (for example, see references 2, 11, and 44). However, the complex microbial communities in biofilms have been recognized as important contributors to critical ecological processes, such as auxotrophic primary production, nitrogen fixation, and nutrient cycling, and may underpin the function of stream food webs (31, 45, 61). The few studies which have investigated benthic habitats in lotic systems have found evidence of the existence of diverse communities of abundant ciliates (3, 20, 56) and shifts in community structure in response to ecophysiological parameters (30, 42, 43). With one exception, however, these investigations were based on aquatic sediments, and the organisms within epilithic biofilms have continued to receive little attention.Most studies of ciliate diversity and ecology have utilized microscopy-based methods of identification (for example, see references 3 and 56), as ciliate cells are relatively large and morphologically diverse. Such methods demand a high level of taxonomic expertise, however, and are difficult and time-consuming—for example, many ciliates are fragile and fast moving, and they often require difficult fixing and staining protocols for reliable identification. Molecular biological tools offer the possibility of more accurate and efficient methods for protozoan study and may provide a useful complement to traditional approaches (12, 18, 28, 65), yet we know of only a few molecular studies of environmental ciliate diversity (18, 20, 37). A series of recent investigations used culture-independent analysis of 18S rRNA gene sequences to reveal the existence of diverse microeukaryote communities in assorted marine, anoxic, and extreme environments (40, 48, 66, 69, 70, 72). Furthermore, a growing body of evidence suggests the existence of significant genetic diversity among various ciliate taxa which has escaped detection by microscopy (14, 18, 23, 34, 60, 64, 78), pointing to the potential for molecular techniques to generate new insights into ciliate diversity and ecology, and suggesting a need for comparison of the effectiveness of these different techniques in environmental samples.Terminal restriction fragment length polymorphism (T-RFLP) analysis provides an efficient, inexpensive, and semiquantitative means for comparing microbial molecular diversity between different samples and has been widely used to investigate bacterial communities, although only a few studies have applied T-RFLP methods to the analysis of microeukaryote diversity (6, 16, 17). In this study, ciliate diversity and community structure were investigated in biofilm samples from streams representing a range of levels of anthropogenic degradation, with the objective of testing the null hypothesis that human impacts have no effect upon this important heterotrophic component of stream ecosystems. To achieve this, ciliate-targeted PCR primers were used in conjunction with T-RFLP and multivariate statistical analyses. Additionally, ciliate diversity measures obtained using molecular techniques were compared with those derived from microscopy-based methods in order to assess the relative effectiveness of these approaches.     

New Insights into the Molecular Mechanisms of Evolution: Stress Increases Genetic Diversity

The mechanisms of stress-induced mutagenesis in prokaryotes and realization of reserved (preaccumulated) genetic variation in eukaryotes are considered. In prokaryotes, replication becomes error-prone in stress because of the induction of the SOS response and the inactivation of the mismatch repair system; stress also increases the transposition rate and the efficiency of interspecific gene transfer. In eukaryotes, chaperone HSP90, which restores the native folding of mutant proteins (e.g., signal transduction and morphogenetic proteins) in normal conditions, fails to do so in stress, which leads to abrupt expression of multiple mutations earlier reserved in the corresponding genes. The role of these mechanisms in the evolution of prokaryotes and eukaryotes is discussed.     

Light Increases Energy Transfer Efficiency in a Boreal Stream

Periphyton communities of a boreal stream were exposed to different light and nutrient levels to estimate energy transfer efficiency from primary to secondary producers using labeling with inorganic ¹³C. In a one-day field experiment, periphyton grown in fast-flow conditions and dominated by opportunistic green algae were exposed to light levels corresponding to sub-saturating (forest shade) and saturating (open stream section) irradiances, and to N and P nutrient additions. In a two-week laboratory experiment, periphyton grown in low-flow conditions and dominated by slowly growing diatoms were incubated under two sub-saturating light and nutrient enrichment levels as well as grazed and non-grazed conditions. Light had significant positive effect on ¹³C uptake by periphyton. In the field experiment, P addition had a positive effect on ¹³C uptake but only at sub-saturating light levels, whereas in the laboratory experiment nutrient additions had no effect on the periphyton biomass, ¹³C uptake, biovolume and community composition. In the laboratory experiment, the grazer (caddisfly) effect on periphyton biomass specific ¹³C uptake and nutrient content was much stronger than the effects of light and nutrients. In particular, grazers significantly reduced periphyton biomass and increased biomass specific ¹³C uptake and C:nutrient ratios. The energy transfer efficiency, estimated as a ratio between ¹³C uptake by caddisfly and periphyton, was positively affected by light conditions, whereas the nutrient effect was not significant. We suggest that the observed effects on energy transfer were related to the increased diet contribution of highly palatable green algae, stimulated by higher light levels. Also, high heterotrophic microbial activity under low light levels would facilitate energy loss through respiration and decrease overall trophic transfer efficiency. These findings suggest that even a small increase in light intensity could result in community-wide effects on periphyton in boreal streams, with a subsequent increase in energy transfer and system productivity.     

Phenotypic Heterogeneity in Biofilm Consortia of E. coli

Microbiology - In this study, a total of seventeen (17) waterborne, biofilm-producing isolates of Escherichia coli were used. The population analysis showed that biofilm consortia harbour three...     

Stability and Change in Estuarine Biofilm Bacterial Community Diversity

Biofouling communities contribute significantly to aquatic ecosystem productivity and biogeochemical cycling. Our knowledge of the distribution, composition, and activities of these microbially dominated communities is limited compared to other components of estuarine ecosystems. This study investigated the temporal stability and change of the dominant phylogenetic groups of the domain Bacteria in estuarine biofilm communities. Glass slides were deployed monthly over 1 year for 7-day incubations during peak tidal periods in East Sabine Bay, Fla. Community profiling was achieved by using 16S rRNA genes and terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes in combination with ribotyping, cloning, and sequencing to evaluate diversity and to identify dominant microorganisms. Bacterial community profiles from biofilms grown near the benthos showed distinct periods of constancy within winter and summer sampling periods. Similar periods of stability were also seen in T-RFLP patterns from floating biofilms. Alternating dominance of phylogenetic groups between seasons appeared to be associated with seasonal changes in temperature, nutrient availability, and light. The community structure appeared to be stable during these periods despite changes in salinity and in dissolved oxygen.     

Microbial Diversity and Heterogeneity in Sandy Subsurface Soils

Microbial community diversity and heterogeneity in saturated and unsaturated subsurface soils from Abbott's Pit in Virginia (1.57, 3.25, and 4.05 m below surface) and Dover Air Force Base in Delaware (6.00 and 7.50 m below surface) were analyzed using a culture-independent small-subunit (SSU) rRNA gene (rDNA)-based cloning approach. Four to six dominant operational taxonomic units (OTUs) were identified in 33 to 100 unique SSU rDNA clones (constituting about 40 to 50% of the total number of SSU rDNA clones in the clone library) from the saturated subsurface samples, whereas no dominant OTUs were observed in the unsaturated subsurface sample. Less than 10% of the clones among samples from different depths at the same location were identical, and the proportion of overlapping OTUs was lower for the samples that were vertically far apart than for adjacent samples. In addition, no OTUs were shared between the Abbott's Pit and Dover samples. The majority of the clones (80%) had sequences that were less than 5% different from those in the current databases. Phylogenetic analysis indicated that most of the bacterial clones were affiliated with members of the Proteobacteria family (90%), gram-positive bacteria (3%), and members of the Acidobacteria family (3%). Principal component analysis revealed that samples from different geographic locations were well separated and that samples from the same location were closely grouped together. In addition, the nonsaturated subsurface samples from Abbott's Pit clustered together and were well separated from the saturated subsurface soil sample. Finally, the overall diversity of the subsurface samples was much lower than that of the corresponding surface soil samples.     

Microbial Diversity in the Early In Vivo-Formed Dental Biofilm

Although the mature dental biofilm composition is well studied, there is very little information on the earliest phase of in vivo tooth colonization. Progress in dental biofilm collection methodologies and techniques of large-scale microbial identification have made new studies in this field of oral biology feasible. The aim of this study was to characterize the temporal changes and diversity of the cultivable and noncultivable microbes in the early dental biofilm. Samples of early dental biofilm were collected from 11 healthy subjects at 0, 2, 4, and 6 h after removal of plaque and pellicle from tooth surfaces. With the semiquantitative Human Oral Microbiome Identification Microarray (HOMIM) technique, which is based on 16S rRNA sequence hybridizations, plaque samples were analyzed with the currently available 407 HOMIM microbial probes. This led to the identification of at least 92 species, with streptococci being the most abundant bacteria across all time points in all subjects. High-frequency detection was also made with Haemophilus parainfluenzae, Gemella haemolysans, Slackia exigua, and Rothia species. Abundance changes over time were noted for Streptococcus anginosus and Streptococcus intermedius (P = 0.02), Streptococcus mitis bv. 2 (P = 0.0002), Streptococcus oralis (P = 0.0002), Streptococcus cluster I (P = 0.003), G. haemolysans (P = 0.0005), and Stenotrophomonas maltophilia (P = 0.02). Among the currently uncultivable microbiota, eight phylotypes were detected in the early stages of biofilm formation, one belonging to the candidate bacterial division TM7, which has attracted attention due to its potential association with periodontal disease.     

西双版纳乡村河溪利用方式及变化研究

西双版纳地处中国西南横断山脉向南延伸的帚状山地,没有气势宏大的高山峡谷,却有由坝子(或沟谷)与低山山地相间排列构成的地貌格局[1].     

Relationship of Farm Level Pesticide Use and Physical Habitat on Benthic Community Status in a California Agricultural Stream

The objectives of this study were to: (1) evaluate temporal and spatial trends in water quality parameters, physical habitat metrics, and benthic community metrics in the Orestimba Creek from years 2000 to 2005, and (2) assess the relationship of benthic community condition from ten Orestimba Creek stations and both pesticide use at the farm level and physical habitat conditions. Significant year effects were reported for temperature, pH, dissolved oxygen, and turbidity. In general, most of the 17 physical habitat metrics did not show statistical variability over the 6-year period. Most of the benthic metrics were variable over the 6-year period. A total of 41 herbicides, 14 organophosphorus (OP) insecticides, and 5 pyrethroids were applied to 23 sections of land bordering the Orestimba Creek from 2000 to 2004. The OP insecticides showed the strongest relationship to benthic metrics using univariate regression models when all three classes of pesticides were compared; however, these statistical relationships had low R² values. Stepwise regression analysis showed statistically significant relationships between most benthic metrics and habitat metrics. In general, both pesticide applications and physical habitat have a similar but modest statistical association with benthic communities. However, the relationship of both pesticide applications and physical habitat on benthic communities in the Orestimba Creek appear to be insignificant compared to the magnitude of spatiotemporal patterns reported.     

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.