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.     

Vertical migration in streams: seasonal use of the hyporheic zone by the spinous loach <Emphasis Type="Italic">Cobitis shikokuensis</Emphasis>

Vertical hydrological connectivity between the surface stream and benthic and hyporheic zones plays a key ecological role in the biodiversity of lotic ecosystems because it allows surface and benthic organisms to use the hyporheic zone as a seasonal habitat and refuge. Use of the hyporheic zone by surface/benthic organisms has been well studied in invertebrates, but little is known about the importance of this connectivity for fishes. We investigated streambed surface and hyporheic densities (5–10, 15–20 and 20–25 cm below the streambed surface) of a stream fish, Cobitis shikokuensis, over a 20-month period in the Shigenobu River, southwestern Japan, to test the hypothesis that it uses the hyporheic zone for spawning and overwintering. In total, 1,804 individuals (13–58 mm total length) were captured from 33 streambed surface samplings and 102 individuals (10–46 mm total length) were present in 1,147 samples of 57 hyporheic samplings. Population densities in both zones peaked in late summer–early autumn due to the recruitment of age 0+ fish and a female with eggs was found in the hyporheic zone during the reproductive season. Both 0+ and older fish were absent from the streambed surface during winter, and fish densities were also lower in the hyporheic zone at this time. However, the vertical distribution of the fish tended to be skewed towards the deeper hyporheic layers from autumn to spring. These findings indicate that C. shikokuensis vertically migrates between the streambed surface and the hyporheic zone for spawning, rearing and overwintering, suggesting that the integrity of vertical hydrological connectivity in lotic systems is crucial for certain fish species.     

Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the estern United States

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6–96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.     

Bacterial community dynamics in the hyporheic zone of an intermittent stream

The dynamics of in situ bacterial communities in the hyporheic zone of an intermittent stream were described in high spatiotemporal detail. We assessed community dynamics in stream sediments and interstitial pore water over a two-year period using terminal-restriction fragment length polymorphism. Here, we show that sediments remained saturated despite months of drought and limited hydrologic connectivity. The intermittency of stream surface water affected interstitial pore water communities more than hyporheic sediment communities. Seasonal changes in bacterial community composition was significantly associated with water intermittency, phosphate concentrations, temperature, nitrate and dissolved organic carbon (DOC) concentrations. During periods of low- to no-surface water, communities changed from being rich in operational taxonomic units (OTUs) in isolated surface pools, to a few OTUs overall, including an overall decline in both common and rare taxa. Individual OTUs were compared between porewater and sediments. A total of 19% of identified OTUs existed in both porewater and sediment samples, suggesting that bacteria use hyporheic sediments as a type of refuge from dessication, transported through hydrologically connected pore spaces. Stream intermittency impacted bacterial diversity on rapid timescales (that is, within days), below-ground and in the hyporheic zone. Owing to the coupling of intermittent streams to the surrounding watershed, we stress the importance of understanding connectivity at the pore scale, consequences for below-ground and above-ground biodiversity and nutrient processing, and across both short- and long-time periods (that is, days to months to years).     

Relationships between bacterial productivity and organic carbon at a soil—stream interface

Microbial communities at soil-stream interfaces may be particularly important in regulating amounts and forms of nutrients that leave upland soils and enter stream ecosystems. While microbial communities are thought to be responsible for key nutrient transformations within near-stream sediments, there is relatively little mechanistic information on factors that control microbial activities in these areas. In this study, we examine the roles of dissolved organic carbon (DOC) vs. particulate organic carbon (POC) as potential controls on rates of bacterial productivity (measured as incorporation of [3H]thymidine into bacterial DNA) and amounts of bacterial biomass (measured as fatty acid yield) in sediments along a transect perpendicular to a soil–stream interface. We hypothesized that spatial patterns in bacterial productivity would vary in response to strong and persistent patterns in pore-water concentrations of DOC that were observed along a soil-stream transect throughout a 2-year period. Our results did not support the existence of such a link between pore-water DOC and bacterial productivity. In contrast, we found bacterial productivity and biomass were related to small-scale spatial variations in sediment POC on 3 of 4 sample dates. While our results indicate that total bacterial productivity in near-stream sediments is not consistently linked to spatial variations in pore-water DOC, it is likely that DOC and POC are not mutually exclusive and the relative contribution of DOC and POC to sedimentary microbes varies temporally and spatially in different riparian habitats. This revised version was published online in July 2006 with corrections to the Cover Date.     

A mixing model analysis of stream solute dynamics and the contribution of a hyporheic zone to ecosystem function*

1. We monitored streamwater and streambed sediment porewaters from White Clay Creek (WCC), SE Pennsylvania, for dissolved organic carbon (DOC), dissolved oxygen (DO) and conductivity to investigate organic matter processing within the hyporheic zone. Dissolved organic carbon and DO concentrations were higher in the streamwater than in the porewaters and, in many cases, concentrations continued to diminish with increasing depth into the streambed. 2. Hydrological exchange data demonstrated that the permeability of the stream bed declines with depth and constrains downwelling, effectively isolating porewaters >30 cm from streamwater. 3. End‐member mixing analysis (EMMA) based on conductivity documented a DOC source and DO sink in the hyporheic zone. We calculated hyporheic streambed DOC fluxes and respiration from the EMMA results and estimates of water flux. Based upon our calculations of biodegradable DOC entering the hyporheic zone, we estimate that DOC supports 39% of the hyporheic zone respiration, with the remaining 61% presumably being supported by entrained particulate organic carbon. Hyporheic respiration averaged 0.38 g C m^?2 d^?1, accounted for 41% of whole ecosystem respiration, and increased baseflow ecosystem efficiency from 46 to 59%. 4. Advective transport of labile organic molecules into the streambed concentrates microbial activity in near‐surface regions of the hyporheic zone. Steep gradients in biogeochemical activity could explain how a shallow and hydrologically constrained hyporheic zone can dramatically influence organic matter processing at the ecosystem scale.     

Sources and seasonal patterns of dissolved organic matter (DOM) in the hyporheic zone

The hyporheic zone is a region underneath streambeds that integrates surface and groundwater. Although its location is central to biogeochemical linkages between the riparian zone, dissolved nutrients, and benthic biota, the seasonal quality and likely sources of dissolved organic matter (DOM) in the hyporheic zone are not well understood. To investigate DOM characteristics in the hyporheic zone, water from the surface and subsurface (at depths 20, 60, and 100 cm below the streambed) was sampled every 4 weeks from 2007 to 2008 in a third-order stream in southern Ontario. Using UV spectroscopy, measures of spectral slopes, aromaticity, and A ₂₅₄/A ₃₆₅ ratios (molecular weight) were obtained. Temporal changes in these measures were consistent with watershed processes such as shedding of leaf litter in the fall, and photochemical and biofilm influence in the spring and summer. The fluorescence index (a measure of relative DOM source) suggested that at the surface and in the downwelling zone, DOM microbial sources increased with depth in the sediment, regardless of the season. Excitation–emission matrices (EEMs) showed seasonally distinct, protein-like DOM components of bacterial origin that were stronger in the fall. Leachates from specific allochthonous DOM sources—leaf litter from Betula papyrifera (white birch) and Thuja occidentalis (white cedar)—and an autochthonous source, biofilm, were isolated and incubated with unfiltered surface water. EEMs from these leachates indicated that these sources could indeed help explain observed patterns of DOM in surface and subsurface waters. These results suggest that although DOM sources were relatively constant, biogeochemical processing within the hyporheic zone resulted a DOM pool that was temporally dynamic and altered the nature of organic matter transported downstream into lakes and rivers.     

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 (R² = 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 (R² = 0.58, P < 0.001). Correlations between heavy-metal contamination and the abundance of four specific phylogenetic groups (most closely related to the α, β, and γ-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.     

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.     

Influence of hyporheic zone characteristics on the structure and activity of microbial assemblages

相似文献   

Spatial responses of hyporheic invertebrates to seasonal changes in environmental parameters

1. Spatial relationships between hyporheic invertebrates and subsurface water flow patterns, sediment characteristics, water physicochemical parameters and several possible food sources were compared over three seasons at one site beneath a riffle. Measures of food sources included particulate organic matter (POM), bacterial activity (aerobic respiration, nitrate respiration and mineralisation of organic nitrogen) and microbial abundance. 2. Patterns of water flow changed significantly over the 9‐month study period, from predominantly upwelling beneath the entire riffle in spring, to distinct differentiation between downwelling and upwelling zones in summer and autumn. Water physicochemical parameters changed accordingly, showing gradually weaker correlations with depth and stronger correlations with zone between spring and autumn. 3. Despite these changes, depth remained the strongest predictor of invertebrate richness, density and taxon composition throughout the study period. However, invertebrate distributions were secondarily correlated with water physicochemical parameters, and a minor gradient in invertebrate distributions between downwelling and upwelling zones became stronger from spring to summer. 4. The correlations between invertebrates and physicochemical parameters changed in both magnitude and direction with season. In spring, invertebrates showed a negative correlation with surface water infiltration, whereas in summer and autumn, the correlation was positive. Correlations were strongest in summer, when interstitial dissolved oxygen concentrations were lowest. 5. No relationships were found between hyporheic invertebrates and POM, microbial abundance or activity. This suggests that at this site, proximity to the streambed surface and physicochemical variables are more important than the abundance of food in controlling invertebrate distributions.     

Nearly a decade‐long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan,China)

Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long‐term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade‐long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance >1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%–82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche‐based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas.     

Habitat Heterogeneity and Associated Microbial Community Structure in a Small-Scale Floodplain Hyporheic Flow Path

The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial β diversity between three different hyporheic flow path locations. Habitat heterogeneity was assessed by measuring soluble reactive phosphorous, nitrate, dissolved organic carbon, dissolved oxygen, and soluble total nitrogen levels seasonally at surface water infiltration, advection, and exfiltration zones. Significant spatial differences were detected in dissolved oxygen and nitrate levels, and seasonal differences were detected in dissolved oxygen, nitrate, and dissolved organic carbon levels. Denaturing gradient gel electrophoresis (DGGE) and cell counts indicated that bacterial diversity increased with abundance, and DGGE fingerprints covaried with nitrate levels where water infiltrated the hyporheic zone. The ribosomal gene phylogeny revealed that hyporheic habitat heterogeneity was sufficient to drive β diversity between bacterial assemblages. Phylogenetic (P) tests detected sequence disparity between the flow path locations. Small distinct lineages of Firmicutes, Actinomycetes, Planctomycetes, and Acidobacteria defined the infiltration zone and α- and β-proteobacterial lineages delineated the exfiltration and advection zone communities. These data suggest that spatial habitat heterogeneity drives hyporheic microbial community development and that attempts to understand functional differences between bacteria inhabiting nutritionally heterogeneous hyporheic environments might begin by focusing on the biology of these taxa.     

山地河流潜流层大型无脊椎动物群落组成及分布

潜流层大型无脊椎动物是河流生态系统重要的组成部分.2013年8月(夏季)、12月(冬季)和2014年4月(春季),在黑水滩河上游河段,采用人工基质法调查潜流层大型无脊椎动物.结果表明: 3个季节共采集大型无脊椎动物27种,其中夏季22种、冬季和春季各16种,各季节水生昆虫种类所占比例均较高,分别为81.8%、75.0%和62.5%;夏季群落密度显著低于冬季和春季,春季最高;冬季群落生物量显著高于夏季和春季,夏季最低;3个季节群落的物种丰富度指数、Shannon多样性指数和Pielou均匀度指数均没有显著性差异.空间分布上,大型无脊椎动物的密度和丰富度均随潜流层深度增加而呈现降低的趋势,大多数个体均分布在0～20 cm深度.群落以滤食者和收集者组成的集食者为绝对优势功能群.动物的相互作用、生活史策略和潜流层的理化条件影响着潜流层大型无脊椎动物的群落结构和时空分布.     

Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains

The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. However, little specific information exists on the diversity of the alpine bacterial community or how it changes during this ecologically important period. We constructed clone libraries of 16S ribosomal DNA from alpine soil collected in winter, spring, and summer. We also cultivated bacteria from the alpine soil and measured the seasonal abundance of selected cultured isolates in hybridization experiments. The uncultured bacterial communities changed between seasons in diversity and abundance within taxa. The Acidobacterium division was most abundant in the spring. The winter community had the highest proportion of Actinobacteria and members of the Cytophaga/Flexibacter/Bacteroides (CFB) division. The summer community had the highest proportion of the Verrucomicrobium division and of beta-PROTEOBACTERIA: As a whole, alpha-Proteobacteria were equally abundant in all seasons, although seasonal changes may have occurred within this group. A number of sequences from currently uncultivated divisions were found, including two novel candidate divisions. The cultured isolates belonged to the alpha-, beta-, and gamma-Proteobacteria, the Actinobacteria, and the CFB groups. The only uncultured sequences that were closely related to the isolates were from winter and spring libraries. Hybridization experiments showed that actinobacterial and beta-proteobacterial isolates were most abundant during winter, while the alpha- and gamma-proteobacterial isolates tested did not vary significantly. While the cultures and clone libraries produced generally distinct groups of organisms, the two approaches gave consistent accounts of seasonal changes in microbial diversity.     

Dissolved organic carbon in streams and groundwater

Minipiezometers installed at different vertical levels within the streambed (20–140 cm) were used to study temporal and spatial variation in the dissolved organic carbon (DOC) content of streamwater and groundwater in three southern Ontario streams. Groundwater, as represented by our streambed samples, contained considerable quantities of DOC but variation between replicate samples was high. Diel fluctuations in DOC content of streamwater were consistent with daytime autochthonous production and night-time uptake by heterotrophs. Water from the streambed neither consistently diluted nor enhanced streamwater levels of DOC. At some stations, DOC variation with depth, including streamwater, seemed to be largely random. At other stations, DOC concentrations from the deepest piezometers were consistently higher than concentrations at intermediate depths, suggesting a loss of DOC from deeper waters to overlying sediments. However, at these stations DOC concentrations were highest at 20 cm and at the surface. Interflow delivery of DOC to the shallow layers of the streambed may be a significant source of carbon for a stream ecosystem, especially in agricultural areas. Late summer diel fluctuations at one station may be related to changing patterns of intermixing of stream and groundwater in the upper layers of the streambed as governed by velocity heads, convective currents and evapotranspiration.     

Spatial and Temporal Patterns in the Microbial Diversity of a Meromictic Soda Lake in Washington State

The microbial community diversity and composition of meromictic Soap Lake were studied using culture-dependent and culture-independent approaches. The water column and sediments were sampled monthly for a year. Denaturing gradient gel electrophoresis of bacterial and archaeal 16S rRNA genes showed an increase in diversity with depth for both groups. Late-summer samples harbored the highest prokaryotic diversity, and the bacteria exhibited less seasonal variability than the archaea. Most-probable-number assays targeting anaerobic microbial guilds were performed to compare summer and fall samples. In both seasons, the anoxic samples appeared to be dominated by lactate-oxidizing sulfate-reducing prokaryotes. High numbers of lactate- and acetate-oxidizing iron-reducing bacteria, as well as fermentative microorganisms, were also found, whereas the numbers of methanogens were low or methanogens were undetectable. The bacterial community composition of summer and fall samples was also assessed by constructing 16S rRNA gene clone libraries. A total of 508 sequences represented an estimated >1,100 unique operational taxonomic units, most of which were from the monimolimnion, and the summer samples were more diverse than the fall samples (Chao1 = 530 and Chao1 = 295, respectively). For both seasons, the mixolimnion sequences were dominated by Gammaproteobacteria, and the chemocline and monimolimnion libraries were dominated by members of the low-G+C-content group, followed by the Cytophaga-Flexibacter-Bacteroides (CFB) group; the mixolimnion sediments contained sequences related to uncultured members of the Chloroflexi and the CFB group. Community overlap and phylogenetic analyses, however, not only demonstrated that there was a high degree of spatial turnover but also suggested that there was a degree of temporal variability due to differences in the members and structures of the communities.     

Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective

Marine planktonic bacteria and archaea commonly exhibit pronounced seasonal succession in community composition. But the existence of seasonality in their assembly processes and between‐domain differences in underlying mechanism are largely unassessed. Using a high‐coverage sampling strategy (including single sample for each station during four cruises in different seasons), 16S rRNA gene sequencing, and null models, we investigated seasonal patterns in the processes governing spatial turnover of bacteria and archaea in surface coastal waters across a sampling grid over ~300 km in the East China Sea. We found that archaea only bloomed in prokaryotic communities during autumn and winter cruises. Seasonality mostly overwhelmed spatial variability in the compositions of both domains. Bacterial and archaeal communities were dominantly governed by deterministic and stochastic assembly processes, respectively, in autumn cruise, probably due to the differences in niche breadths (bacteria < archaea) and relative abundance (bacteria > archaea). Stochasticity dominated assembly mechanisms of both domains but was driven by distinct processes in winter cruise. Determinism‐dominated assembly mechanisms of bacteria rebounded in spring and summer cruises, reflecting seasonal variability in bacterial community assembly. This could be attributed to seasonal changes in bacterial niche breadths and habitat heterogeneity across the study area. There were seasonal changes in environmental factors mediating the determinism‐stochasticity balance of bacterial community assembly, holding a probability of the existence of unmeasured mediators. Our results suggest contrasting assembly mechanisms of bacteria and archaea in terms of determinism‐vs.‐stochasticity pattern and its seasonality, highlighting the importance of seasonal perspective on microbial community assembly in marine ecosystems.     

Recurring seasonal dynamics of microbial communities in stream habitats

Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations associated with streambed sediments and rocks (epilithon) were identified using terminal restriction length polymorphism (tRFLP) and sequencing of 16S rRNA genes selectively amplified with primers for the bacterial domain. Analyses of the relative magnitudes of tRFLP peak areas by using nonmetric multidimensional scaling resolved clear seasonal trends in epilithic and sediment populations. Oscillations between two dominant groups of epilithic genotypes, explaining 86% of the seasonal variation in the data set, were correlated with temperature and dissolved organic carbon. Sequences affiliated with epilithic phototrophs (cyanobacteria and diatom chloroplasts), a Rhodoferax sp., and a Bacillus species clustered in the summer, whereas sequences most closely related to "Betaproteobacteria" (putative Burkholderia sp.), and a putative cyanobacterium clustered in the fall/spring. The sediment genotypes also clustered into two groups, and these explained 85% of seasonal variation but correlated only with temperature. A summer tRFLP pattern was characterized by prevalence of "Betaproteobacteria," "Gammaproteobacteria," and a Bacillus sp., whereas the winter/spring pattern was characterized by phylotypes most closely related to "Firmicutes," "Gammaproteobacteria," and "Nitrospirae." A close association between these headwater streams and their watersheds was suggested by the recovery of sequences related to microbial populations provisionally attributed to not only freshwaters but also terrestrial habitats.     

Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer

Seasonal patterns of groundwater and sediment microbial communities were explored in a hydrologically dynamic alpine oligotrophic porous aquifer, characterized by pronounced groundwater table fluctuations. Rising of the groundwater level in consequence of snow melting water recharge was accompanied by a dramatic drop of bacterial Shannon diversity in groundwater from H' = 3.22 ± 0.28 in autumn and winter to H' = 1.31 ± 0.35 in spring and summer, evaluated based on T-RFLP community fingerprinting. Elevated numbers of bacteria in groundwater in autumn followed nutrient inputs via recharge from summer rains and correlated well with highest concentrations of assimilable organic carbon. Sterile sediments incubated to groundwater in monitoring wells were readily colonized reaching maximum cell densities within 2 months, followed by a consecutive but delayed increase and leveling-off of bacterial diversity. After 1 year of incubation, the initially sterile sediments exhibited a similar number of bacteria and Shannon diversity when compared to vital sediment from a nearby river incubated in parallel. The river bed sediment microbial communities hardly changed in composition, diversity, and cell numbers during 1 year of exposure to groundwater. Summing up, the seasonal hydrological dynamics were found to induce considerable dynamics of microbial communities suspended in groundwater, while sediment communities seem unaffected and stable in terms of biomass and diversity.