Temporal variability in the diversity and composition of stream bacterioplankton communities

Bacterioplankton in freshwater streams play a critical role in stream nutrient cycling. Despite their ecological importance, the temporal variability in the structure of stream bacterioplankton communities remains understudied. We investigated the composition and temporal variability of stream bacterial communities and the influence of physicochemical parameters on these communities. We used barcoded pyrosequencing to survey bacterial communities in 107 streamwater samples collected from four locations in the Colorado Rocky Mountains from September 2008 to November 2009. The four sampled locations harboured distinct communities yet, at each sampling location, there was pronounced temporal variability in both community composition and alpha diversity levels. These temporal shifts in bacterioplankton community structure were not seasonal; rather, their diversity and composition appeared to be driven by intermittent changes in various streamwater biogeochemical conditions. Bacterial communities varied independently of time, as indicated by the observation that communities in samples collected close together in time were no more similar than those collected months apart. The temporal turnover in community composition was higher than observed in most previously studied microbial, plant or animal communities, highlighting the importance of stochastic processes and disturbance events in structuring these communities over time. Detailed temporal sampling is important if the objective is to monitor microbial community dynamics in pulsed ecosystems like streams.     

Temporal Patterns and Environmental Correlates of Macroinvertebrate Communities in Temporary Streams

Temporary streams are characterised by short periods of seasonal or annual stream flow after which streams contract into waterholes or pools of varying hydrological connectivity and permanence. Although these streams are widespread globally, temporal variability of their ecology is understudied, and understanding the processes that structure community composition in these systems is vital for predicting and managing the consequences of anthropogenic impacts. We used multivariate and univariate approaches to investigate temporal variability in macroinvertebrate compositional data from 13 years of sampling across multiple sites from autumn and spring, in South Australia, the driest state in the driest inhabited continent in the world. We examined the potential of land-use, geographic and environmental variables to predict the temporal variability in macroinvertebrate assemblages, and also identified indicator taxa, that is, those highly correlated with the most significantly associated physical variables. Temporal trajectories of macroinvertebrate communities varied within site in both seasons and across years. A combination of land-use, geographic and environmental variables accounted for 24% of the variation in community structure in autumn and 27% in spring. In autumn, community composition among sites were more closely clustered together relative to spring suggesting that communities were more similar in autumn than in spring. In both seasons, community structure was most strongly correlated with conductivity and latitude, and community structure was more associated with cover by agriculture than urban land-use. Maintaining temporary streams will require improved catchment management aimed at sustaining seasonal flows and critical refuge habitats, while also limiting the damaging effects from increased agriculture and urban developments.     

Long-term changes in macroinvertebrate communities across high-latitude streams

Long-term records of benthic macroinvertebrates in high-latitude streams are essential for understanding climatic changes, including extreme events (e.g. floods). Data extending over multiple decades are typically scarce. Here, we investigated macroinvertebrate community structural change (including alpha and beta diversity and gain and loss of species) over 22 years (1994–2016) in 10 stream systems across Denali National Park (Alaska, USA) in relation to climatological and meteorological drivers (e.g. air temperature, snowpack depth, precipitation). We hypothesised that increases in air temperature and reduced snowpack depth, due to climatic change, would reduce beta and gamma diversity but increase alpha diversity. Findings showed temporal trends in alpha diversity were variable across streams, with oscillating patterns in many snowmelt- and rainfall runoff-fed streams linked to climatic variation (temperature and precipitation), but increased over time in several streams supported by a mixture of water sources, including more stable groundwater-fed streams. Beta-diversity over the time series was highly variable, yet marked transitions were observed in response to extreme snowpack accumulation (1999–2000), where species loss drove turnover. Gamma diversity did not significantly increase or decrease over time. Investigating trends in individual taxa, several taxa were lost and gained during a relative constrained time period (2000–2006), likely in response to climatic variability and significant shifts in instream environmental conditions. Findings demonstrate the importance of long-term biological studies in stream ecosystems and highlight the vulnerability of high-latitude streams to climate change.     

Variation in parasite communities and health indices of juvenile Lepomis gibbosus across a gradient of watershed land-use and habitat quality

Parasites of fishes vary in community structure and species abundance in response to environmental conditions and pollutants. As a result, the use of parasites as bioindicators of habitat degradation has been proposed and successfully applied in recent years. Here, helminth parasites of juvenile pumpkinseed Lepomis gibbosus from three streams representing a gradient of watershed development and habitat quality were examined to assess variation in parasite communities. Health assessment indices were also generated for each host to quantify the influence of habitat on the observed health of individuals. A total of 22 parasite taxa were recovered from examined fish, comprising 11 digeneans, 3 cestodes, 2 acanthocephalans, 5 monogeneans and 1 crustacean. In the most disturbed stream, parasite species richness was lowest and total abundance was highest, while parasite abundance was lowest and diversity highest in the least disturbed stream. There was no significant difference in health indices among streams. Analysis of similarities (ANOSIM) and Bray–Curtis dissimilarity in species composition (SIMPER) identified Posthodiplostomum spp. and Actinocleidus sp. as the species driving parasite community dissimilarity. These taxa are relatively easy to identify to genus level and thus could be appropriate for use as indicators of environmental health, where increased abundance would suggest negative changes in habitat quality. However, larger scale study including more streams would be necessary to establish baseline community data before such implementation would be feasible.     

Inter-annual patterns in macroinvertebrate communities of wilderness streams in Idaho, U.S.A.

This study examined the inter-annual variation in macroinvertebrate assemblages in six wilderness streams in central Idaho over a 6-year period (1990–1995). Benthic macroinvertebrates and associated environmental correlates were sampled during baseflow each summer. Little environmental change, as assessed using coefficients of variation (CVs) for substrate size and embeddedness, width, depth and periphyton standing crops, occurred in the streams over the period of study. There was also little temporal change in macroinvertebrate assemblages based on the relative abundance of the 10 most abundant taxa, all shredder taxa and all plecopteran taxa. CVs for individual taxa were substantially greater than those of most community measures, with rare taxa contributing 30–50% of the variation for any one stream. Frequency distributions for taxa CVs excluding rare taxa were more normally distributed. Differences in assemblage structure among streams were attributed to stream size (shift in shredder assemblages) and temperature (shift in plecopteran taxa). These data indicate a long-term (multi-year) persistence in the macroinvertebrate composition of these pristine streams, thus supporting the premise that such streams are excellent references for use in long-term biomonitoring programs.     

Stability and Persistence of Alpine Stream Macroinvertebrate Communities and the Role of Physicochemical Habitat Variables

Macroinvertebrate communities in alpine streams have rarely been examined over more than two consecutive years or at sub-monthly temporal resolution during the summer melt season, in relation to a range of stream physicochemical habitat measurements. This paper addresses these research gaps by investigating the inter- (late melt season, 1996–2003) and intra-annual (bi-weekly; June–September, 2002–2003) community compositional stability and persistence of three alpine streams fed from different water sources (snow, glaciers and groundwater) in the Taillon–Gabiétous catchment, French Pyrénées. Inter-annual community stability and persistence decreased from 1996 to 2003; however, groundwater stream communities changed less than those in the main glacial stream. Intra-annual community stability varied spatially and temporally, particularly in relation to water quality variables (water temperature and suspended sediment concentration); water quantity (stream discharge) was less important perhaps due to taxa possessing adaptations to flow variability. The 15 most abundant taxa were consistently more stable and persistent than the entire stream community suggesting a common pool of taxa in these streams. Overall, the results support the view that streams originating from different alpine water sources are characterised by distinct benthic macroinvertebrate assemblages, and demonstrate the value of sampling at nested temporal scales (inter-annual to bi-weekly) for understanding how these stream ecosystems function.     

Physical and biological changes to a lengthening stream gradient following a decade of rapid glacial recession

In mountains, environmental gradients are steep in both terrestrial and aquatic systems, and climate change is causing upward shifts of physical and biological features of these gradients. Glacial streams are an interesting system to evaluate such shifts both because streams have a linear nature (for simplicity of analysis), and because the stream habitat will at least temporarily lengthen as it follows receding glaciers upward. The Tschierva Glacier, Swiss Alps, receded 482 m upstream from 1997 to 2008. We tested the null hypothesis that the physical and biological stream gradient below this glacier maintained the same structure between these time periods, but simply shifted upward following the glacial source. We compared longitudinal patterns of water temperature and zoobenthic community structure in 1997 and 2007–2008 during three seasons (spring, summer, fall) along the uppermost ca. 5 stream km. Upward shifts were evident, including colonization of the newly exposed stream reaches by cold‐adapted taxa, and the appearance in 2007/2008 of four lower‐altitude species that were previously absent. Overall, however, results rejected the null hypothesis, instead revealing significant changes in gradient structures. These included a more steeply increasing temperature profile downstream of the glacier and increased amplitude of seasonal community turnover in 2007/2008 vs. 1997. Long‐term (1955–2007) flow records revealed increasing short‐term and seasonal hydrologic variability, which might have influenced the increased intra‐annual community variability. The steepening of the temperature gradient was likely caused by a warming lake‐outlet tributary upon which glacial influence was diminished between 1997 and 2007/2008. These results suggest that upward‐shifting gradients in glacial streams can involve complex interactions with other landscape elements and that local‐scale climate response can progress even more rapidly than the rate of glacial recession.     

Seasonal response of stream biofilm communities to dissolved organic matter and nutrient enrichments

Dissolved organic matter (DOM) and inorganic nutrients may affect microbial communities in streams, but little is known about the impact of these factors on specific taxa within bacterial assemblages in biofilms. In this study, nutrient diffusing artificial substrates were used to examine bacterial responses to DOM (i.e., glucose, leaf leachate, and algal exudates) and inorganic nutrients (nitrate and phosphate singly and in combination). Artificial substrates were deployed for five seasons, from summer 2002 to summer 2003, in a northeastern Ohio stream. Differences were observed in the responses of bacterial taxa examined to various DOM and inorganic nutrient treatments, and the response patterns varied seasonally, indicating that resources that limit the bacterial communities change over time. Overall, the greatest responses were to labile, low-molecular-weight DOM (i.e., glucose) at times when chlorophyll a concentrations were low due to scouring during significant storm events. Different types of DOM and inorganic nutrients induced various responses among bacterial taxa in the biofilms examined, and these responses would not have been apparent if they were examined at the community level or if seasonal changes were not taken into account.     

Characterizing seasonal changes in physicochemistry and bacterial community composition in hyporheic sediments

The hyporheic zone of stream ecosystems is a critical habitat for microbial communities. However, the factors influencing hyporheic bacterial communities along spatial and seasonal gradients remain poorly understood. We sought to characterize patterns in bacterial community composition among the sediments of a small stream in southern Ontario, Canada. We used sampling cores to collect monthly hyporheic water and sediment microbial communities in 2006 and 2007. We described bacterial communities terminal-restriction fragment length polymorphism (TRFLP) and tested for spatial and seasonal relationships with physicochemical parameters using multivariate statistics. Overall, the hyporheic zone appears to be a DOC, oxygen, and nitrogen sink. Microbial communities were distinct from those at the streambed surface and from soil collected in the adjacent watershed. In the sediments, microbial communities were distinct between the fall, spring, and summer seasons, and bacterial communities were more diverse at streambed surface and near-surface sites compared with deeper sites. Moreover, bacterial communities were similar between consecutive fall seasons despite shifting throughout the year, suggesting recurring community assemblages associated with season and location in the hyporheic zone. Using canonical correspondence analysis, seasonal patterns in microbial community composition and environmental parameters were correlated in the following way: temperature was related to summer communities; DOC (likely from biofilm and allochthonous inputs) influenced most fall communities; and nitrogen associated strongly with winter and spring communities. Our results also suggest that labile DOC entering the hyporheic zone occurred in concert with shifts in the bacterial community. Generally, seasonal patterns in hyporheic physicochemistry and microbial biodiversity remain largely unexplored. Therefore, we highlight the importance of seasonal and spatial resolution when assessing surface- and groundwater interactions in stream ecosystems.     

Environmental effects on biofilm bacterial communities: a comparison of natural and anthropogenic factors in New Zealand streams

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The effects of catchment liming on the chemistry and biology of upland Welsh streams: testing model predictions

1. The catchments of three acidified streams in mid Wales were limed in 1987/88. Here we assess their chemical and biological response in comparison with unmanipulated reference streams over a period of 5 years post-liming. 2. Stream chemistry was measured weekly/fortnightly between 1985 and 1992, while macroinvertebrates were sampled annually. Colonization by acid-sensitive taxa was assessed and trends in community structure were monitored by TWINSPAN. Real biological responses were compared with those predicted by an empirical model constructed using chemical data. 3. There were marked changes in stream chemistry following liming: calcium concentrations and pH values increased, while aluminium concentrations decreased to levels similar to those in naturally circumneutral streams. These conditions have persisted since liming. 4. Empirical models predicted that stream invertebrates would respond to the altered stream chemistry, with the establishment of communities typical of circumneutral conditions. 5. Following liming, the taxon richness and abundance of acid-sensitive taxa was significantly higher in limed compared with reference streams. Colonization by, and persistence of acid-sensitive taxa was patchy, however, and richness was still substantially lower than in naturally circumneutral streams. Moreover, contrary to the model predictions, there were no wholesale changes in the structure of macroinvertebrate communities. 6. We conclude that liming has created and maintained chemical conditions suitable for macroinvertebrate communities typical of circumneutral streams, but these chemical changes have not been matched by sustained responses among the biota. The views expressed in this article are those of the authors and do not necessarily reflect those of the NRA.     

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient

A majority of environmental studies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), ignoring key ecological knowledge gained from finer-scales and microbial indicator taxa. Here, we characterized the distribution of 940 bacterial taxa from 41 streams along an urbanization gradient (0%–83% developed watershed area) in the Raleigh-Durham area of North Carolina (USA). Using statistical approaches derived from macro-organismal ecology, we found that more bacterial taxa were classified as intolerant than as tolerant to increasing watershed urbanization (143 vs 48 OTUs), and we identified a threshold of 12.1% developed watershed area beyond which the majority of intolerant taxa were lost from streams. Two bacterial families strongly decreased with urbanization: Acidobacteriaceae (Acidobacteria) and Xanthobacteraceae (Alphaproteobacteria). Tolerant taxa were broadly distributed throughout the bacterial phylogeny, with members of the Comamonadaceae family (Betaproteobacteria) presenting the highest number of tolerant taxa. Shifts in microbial community structure were strongly correlated with a stream biotic index, based on macroinvertebrate composition, suggesting that microbial assemblages could be used to establish biotic criteria for monitoring aquatic ecosystems. In addition, our study shows that classic methods in community ecology can be applied to microbiome datasets to identify reliable microbial indicator taxa and determine the environmental constraints on individual taxa distributions along environmental gradients.     

Seasonal Response of Stream Biofilm Communities to Dissolved Organic Matter and Nutrient Enrichments

Dissolved organic matter (DOM) and inorganic nutrients may affect microbial communities in streams, but little is known about the impact of these factors on specific taxa within bacterial assemblages in biofilms. In this study, nutrient diffusing artificial substrates were used to examine bacterial responses to DOM (i.e., glucose, leaf leachate, and algal exudates) and inorganic nutrients (nitrate and phosphate singly and in combination). Artificial substrates were deployed for five seasons, from summer 2002 to summer 2003, in a northeastern Ohio stream. Differences were observed in the responses of bacterial taxa examined to various DOM and inorganic nutrient treatments, and the response patterns varied seasonally, indicating that resources that limit the bacterial communities change over time. Overall, the greatest responses were to labile, low-molecular-weight DOM (i.e., glucose) at times when chlorophyll a concentrations were low due to scouring during significant storm events. Different types of DOM and inorganic nutrients induced various responses among bacterial taxa in the biofilms examined, and these responses would not have been apparent if they were examined at the community level or if seasonal changes were not taken into account.     

Biofilm functional responses to the rehydration of a dry intermittent stream

Intermittent water flow regimes characterize streams in many world regions, especially those with arid and semiarid climates. During cease to flow conditions, biofilms on streambed sediments may be exposed to desiccation. Environmental conditions and resource availability change with desiccation and may influence biofilm functioning and whole stream ecosystem processes. Rainfall events during the nonflow phase can rehydrate streambed sediments, but the effect of these pulses on biofilm functioning is unclear. This study aimed to analyze the effects of a rehydration event on biofilm functional diversity during the nonflow period in a subtropical Australian stream. Biofilms from three different stream pools on the same reach; one permanently water-covered and the other two differing in their desiccation time were studied. Biofilms initially differed owing to the time they were exposed to dry conditions but rehydration events significantly increased biofilm functional diversity, producing a “reset” effect on the desiccation exposure, as after that bacterial functioning decreased again because of the new dry conditions. The observed rapid biofilm responses to rehydration during flow intermittency might be essential in sustaining biofilm functional diversity in intermittent streams.     

Effects of eutrophication, seasonality and macrofouling on the diversity of bacterial biofilms in equatorial coral reefs

Biofilms play an important role as a settlement cue for invertebrate larvae and significantly contribute to the nutrient turnover in aquatic ecosystems. Nevertheless, little is known about how biofilm community structure generally responds to environmental changes. This study aimed to identify patterns of bacterial dynamics in coral reef biofilms in response to associated macrofouling community structure, microhabitat (exposed vs. sheltered), seasonality, and eutrophication. Settlement tiles were deployed at four reefs along a cross-shelf eutrophication gradient and were exchanged every 4 months over 20 months. The fouling community composition on the tiles was recorded and the bacterial community structure was assessed with the community fingerprinting technique Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial operational taxonomic unit (OTU) number was higher on exposed tiles, where the fouling community was homogenous and algae-dominated, than in sheltered habitats, which were occupied by a variety of filter feeders. Furthermore, OTU number was also highest in eutrophied near-shore reefs, while seasonal variations in community structure were most pronounced in the oligotrophic mid-shelf reef. In contrast, the macrofouling community structure did not change significantly with seasons. Changes in bacterial community patterns were mostly affected by microhabitat, seasonal and anthropogenically derived changes in nutrient availability, and to a lesser extent by changes in the macrofouling community structure. Path analysis revealed a complex interplay of various environmental and biological factors explaining the spatial and temporal variations in bacterial biofilm communities under natural conditions.     

A comparison of bacterial,ciliate and macroinvertebrate indicators of stream ecological health

We evaluate the reliability of communities of bacteria and ciliated protozoa as indicators of freshwater ecological health. Samples of epilithic biofilm were taken from 18 freshwater streams, impacted by varying types and degrees of catchment modification. Communities of bacteria and ciliates were characterised using DNA fingerprinting techniques (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism, respectively) and macroinvertebrate data also obtained, for comparison. Similar to the macroinvertebrates, the taxa richness of ciliate communities was reduced in more developed stream catchments; significant differences in the evenness of ciliate communities were also detected. We could identify no significant relationship between the richness of bacterial taxa and the percentage catchment development. However, a significant trend was detected between bacterial community structure and the predominant catchment land use (rural vs. urban) using a Bray–Curtis measure of similarity, a relationship not detected for the ciliate and macroinvertebrate communities. These findings indicate that stream bacterial, ciliate and macroinvertebrate communities each respond differently to various catchment conditions and highlight the potential of microbial communities to provide novel, alternative indicators of stream ecosystem health.     

Persistent nitrogen limitation of stream biofilm communities along climate gradients in the Arctic

Climate change is rapidly reshaping Arctic landscapes through shifts in vegetation cover and productivity, soil resource mobilization, and hydrological regimes. The implications of these changes for stream ecosystems and food webs is unclear and will depend largely on microbial biofilm responses to concurrent shifts in temperature, light, and resource supply from land. To study those responses, we used nutrient diffusing substrates to manipulate resource supply to biofilm communities along regional gradients in stream temperature, riparian shading, and dissolved organic carbon (DOC) loading in Arctic Sweden. We found strong nitrogen (N) limitation across this gradient for gross primary production, community respiration and chlorophyll‐a accumulation. For unamended biofilms, activity and biomass accrual were not closely related to any single physical or chemical driver across this region. However, the magnitude of biofilm response to N addition was: in tundra streams, biofilm response was constrained by thermal regimes, whereas variation in light availability regulated this response in birch and coniferous forest streams. Furthermore, heterotrophic responses to experimental N addition increased across the region with greater stream water concentrations of DOC relative to inorganic N. Thus, future shifts in resource supply to these ecosystems are likely to interact with other concurrent environmental changes to regulate stream productivity. Indeed, our results suggest that in the absence of increased nutrient inputs, Arctic streams will be less sensitive to future changes in other habitat variables such as temperature and DOC loading.     

Macroinvertebrate communities in streams with contrasting water sources in the Japanese Alps

Alpine streams are typically fed from a range of water sources including glacial meltwater, snowmelt, groundwater flow, and surface rainfall runoff. These contributions are projected to shift with climate change, particularly in the Japanese Alps where snow is expected to decrease, but rainfall events increase. The overarching aim of the study was to understand the key variables driving macroinvertebrate community composition in groundwater and snowmelt‐fed streams (n = 6) in the Kamikochi region of the northern Japanese Alps (April–December 2017). Macroinvertebrate abundance, species richness, and diversity were not significantly different between the two stream types. Community structure, however, was different between groundwater and snowmelt‐fed streams with macroinvertebrate taxa specialized for the environmental conditions present in each system. Temporal variation in the abundance, species richness, and diversity of macroinvertebrate communities was also significantly different between groundwater and snowmelt streams over the study period, with snowmelt streams exhibiting far higher levels of variation. Two snowmelt streams considered perennial proved to be intermittent with periodic drying of the streambed, but the macroinvertebrates in these systems rebounded rapidly after flows resumed with no reduction in taxonomic diversity. These same streams, nevertheless, showed a major reduction in diversity and abundance following periods of high flow, indicating floods rather than periodic drying was a major driver of community structure. This conclusion was also supported from functional analyses, which showed that the more variable snowmelt streams were characterized by taxa with resistant, rather than resilient, life‐history traits. The findings demonstrate the potential for significant turnover in species composition with changing environmental conditions in Japanese alpine stream systems, with groundwater‐fed streams potentially more resilient to future changes in comparison to snowmelt‐fed streams.     

Does biofilm origin matter? Biofilm responses to non-flow period in permanent and temporary streams

1. In some regions, climate change is increasing the variability of rainfall and the frequency of extreme events such as drought. Consequently, non-flow periods have grown in length and frequency, both in temporary and in formerly permanent streams. Water abstraction for human use may further prolong these dry periods.
2. We analysed the resistance and resilience of biofilms from permanent and temporary streams to non-flow conditions. This was achieved by exposing cobbles (collected from permanent and temporary streams) with intact biofilm to 31 days of non-flow, followed by 20 days of stream flow in artificial stream channels. Biofilm resistance and resilience were assessed at a structural (algal biomass, pigment composition, and algae and cyanobacteria composition) and functional level (photosynthetic efficiency and community metabolism).
3. Algal taxa in biofilms from permanent and temporary streams differed throughout the experiment. Biofilms from permanent streams were less resistant to non-flow than those from temporary streams at structural level. Permanent stream biofilms also presented lower resilience at a structural level, but responded similarly to temporary stream biofilms at a functional level.
4. Our investigation shows how the non-flow period disturbed permanent stream biofilms, and suggests that temporary stream biofilms will have greater adaptive capacity as hydroperiod becomes shorter due to climate change.

     

Seasonal and Episodic Lake Mixing Stimulate Differential Planktonic Bacterial Dynamics

Yuan Yang Lake (YYL), Taiwan, experiences both winter and typhoon-initiated mixing, and each type of mixing event is characterized by contrasting environmental conditions. Previous work suggested that after typhoon mixing, bacterial communities in YYL reset to a pioneer composition and then follow a predictable trajectory of change until the next typhoon. Our goal was to continue this investigation by observing bacterial community change after a range of mixing intensities, including seasonal winter mixing. We fingerprinted aquatic bacterial communities in the epilimnion and hypolimnion using automated ribosomal intergenic spacer analysis and then assessed community response using multivariate statistics. We found a significant linear relationship between water column stability and the epilimnion to hypolimnion divergences. In comparison to the summer, we found the winter community had a distinct composition and less variation. We divided the bacterial community into population subsets according to abundance (rare, common, or dominant) and occurrence (transient or persistent) and further explored the contribution of these subsets to the overall community patterns. We found that transient taxa did not drive bacterial community patterns following weak typhoon mixing events, but contributed substantially to patterns observed following strong events. Common taxa generally did not follow the community trajectory after weak or strong events. Our results suggest intensity, frequency, and seasonality jointly contribute to aquatic bacterial response to mixing disturbance.