Denitrification potential of epilithic communities in a lotic environment

Denitrification potentials of epilithic microbial populations were assessed using the acetylene inhibition method, in which acetylene is used to block the reduction of nitrous oxide (N₂O) to nitrogen (N₂). Samples of the epilithic community were incubated in filtered river water containing modified Bushnell-Haas salts, glycerol, and yeast extract—under aerobic (0.2 atm O₂) and anaerobic (0.2 atm He) acetylene atmospheres. N₂O was produced under both atmospheres only if exogenous nitrate of nitrite was added. Denitrification potentials were typically higher when nitrite was the added electron acceptor. The rates of denitrification were temperature-and carbon-dependent and the maximum rate, 8.53 g N₂O–N per cm² per day occurred at 23°C when nitrite was the electron acceptor.     

A multi-lake comparison of epilithic diatom communities on natural and artificial substrates

In a multi-season, multi-lake study of epilithic diatom communities, glass slide artificial substrate samplers provided poor representation of communities on natural substrates. Percent similarities between the two communities averaged only 37 over the course of the study. Overall, natural substrates exhibited greater species richness than artificial samplers, particularly during the summer, although this difference was slight. Patterns of selection and inhibition by artificial substrates of individual diatom species varied by both season and lake. Members of the genus Cymbella, particularly C. microcephala, appeared to be the most consistently inhibited, while Achnanthes minutissima was often selected for. In spite of the great differences between the two substrate types, replicability of artificial substrates was very high, and could prove to be a more important quality in monitoring applications than accurate representation of the natural community.     

Different methods and storage duration affect measurements of epilithic extracellular enzyme activities in lotic biofilms

Extracellular enzyme activity (EEA) is becoming increasingly common for measuring biofilm function in streams. Different methods for enzyme assays may yield results that cannot be compared among studies, and duration of sample storage may also affect EEAs, leading to erroneous conclusions. We compared two frequently used methods for measuring phosphatase (PHOS), leucine aminopeptidase (LAMP), β-glucosidase (GLU), and β-xylosidase (XYLO) by conducting assays with intact and disrupted epilithic biofilms grown on tiles in three streams. Storage duration effects on EEA were documented with intact and disrupted biofilms kept in the dark at 4°C for 3 and 5 days. Intact biofilms had significantly less EEA than disrupted biofilms for all enzymes (P < 0.01). The two methods gave conflicting EEA results among streams, and ratios of disrupted to intact EEAs for each enzyme were not consistent among the three streams. PHOS was significantly greater than day 1 measurements when stored as disrupted (Day 3 = 210%, Day 5 = 199% increases) and intact biofilms (Day 3 = 375%, Day 5 = 240% increases). LAMP activities were significantly less when stored as disrupted biofilms (Day 3 = ?49% decrease) and greater when stored as intact biofilms (Day 5 = 72% increase). GLU (Day 3 = 313% increase) and XYLO (Day 3 = 121%, Day 5 = 188% increases) were significantly greater when stored as intact biofilms. The magnitude of change for all EEAs was inconsistent among streams, indicating that a consistent correction factor cannot be used to account for variation associated with storage duration. Consistent methods must be used and storage time should be minimized, preferably to the day of sampling, for valid inter-study comparisons. Conclusions can significantly differ between the two methods, therefore having implications for inter-study comparisons, understanding of biofilm function and dynamics, and environmental management decisions.     

Persistence and stability of lotic invertebrate communities in New Zealand

1. Persistence and stability of lotic invertebrate communities were determined at an annual time scale over a 9‐year period (1990–98) at 26 river sites over the northern half of New Zealand. In addition, a number of water quality variables were measured monthly and flow information collected continuously over the same period at each site. 2. The aim of the study was to describe the levels of interannual variability in invertebrate communities, and relate community changes to variability in environmental conditions. The consequences of this temporal variability for the sensitivity of predictive models were also investigated. 3. Levels of change in environmental conditions varied significantly between years, but were relatively similar across sites. In contrast, community persistence (similarity between years in species assemblage composition), and stability (similarity between years with respect to relative abundance of species in the community) both varied significantly between sites, but changes between years were similar. Community stability was highest at sites with relatively harsh flow conditions (high coefficient of variation, high relative size of floods), and was also greater in communities dominated by Ephemeroptera. 4. Relationships between change in environmental conditions and changes in community composition and structure were relatively weak for most individual sites. However, when average levels of change for each of the 26 sites were used, communities showed greater persistence under conditions where flow conditions remained relatively constant. Water quality changes had no significant effect on community persistence when assessed for all 26 sites combined. 5. Results from this study suggest that lotic invertebrate communities fluctuate around a relatively stable state, at least over a 9‐year period. However, the extent of interannual variation in community composition and structure observed, along with the relatively low degree of cluster fidelity observed within a single region, suggests that predictive models based on reference site conditions extrapolated over several years should be applied with caution in New Zealand streams.     

Spatial and temporal heterogeneity of the bacterial communities in stream epilithic biofilms

The spatial and temporal variability in bacterial communities within freshwater systems is poorly understood. The bacterial composition of stream epilithic biofilms across a range of different spatial and temporal scales both within and between streams and across the profile of individual stream rocks was characterised using a community DNA-fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA). The differences in bacterial community structure between two different streams were found to be greater than the spatial variability within each stream site, and were larger than the weekly temporal variation measured over a 10-week study period. Greater variations in bacterial community profiles were detected on different faces of individual stream rocks than between whole rocks sampled within a 9-m stream section. Stream temperature was found to be the most important determinant of bacterial community variability using distance-based redundancy analysis (dbRDA) of ARISA data, which may have broad implications for riparian zone management and ecological change as a consequence of global warming. The combination of ARISA with multivariate statistical methods and ordination, such as multidimensional scaling (MDS), permutational manova and RDA, provided rapid and effective methods for quantifying and visualising variation in bacterial community structure, and to identify potential drivers of ecological change.     

Presence and sources of fecal coliform bacteria in epilithic periphyton communities of Lake Superior

Epilithic periphyton communities were sampled at three sites on the Minnesota shoreline of Lake Superior from June 2004 to August 2005 to determine if fecal coliforms and Escherichia coli were present throughout the ice-free season. Fecal coliform densities increased up to 4 orders of magnitude in early summer, reached peaks of up to 1.4x10(5) CFU cm-2 by late July, and decreased during autumn. Horizontal, fluorophore-enhanced repetitive-PCR DNA fingerprint analyses indicated that the source for 2% to 44% of the E. coli bacteria isolated from these periphyton communities could be identified when compared with a library of E. coli fingerprints from animal hosts and sewage. Waterfowl were the major source (68 to 99%) of periphyton E. coli strains that could be identified. Several periphyton E. coli isolates were genotypically identical (>or=92% similarity), repeatedly isolated over time, and unidentified when compared to the source library, suggesting that these strains were naturalized members of periphyton communities. If the unidentified E. coli strains from periphyton were added to the known source library, then 57% to 81% of E. coli strains from overlying waters could be identified, with waterfowl (15 to 67%), periphyton (6 to 28%), and sewage effluent (8 to 28%) being the major potential sources. Inoculated E. coli rapidly colonized natural periphyton in laboratory microcosms and persisted for several weeks, and some cells were released to the overlying water. Our results indicate that E. coli from periphyton released into waterways confounds the use of this bacterium as a reliable indicator of recent fecal pollution.     

Colonization rates and community structure of diatoms on three different rock substrata in a lotic system

Diatom assemblages were monitored at weekly intervals over a 5 week period on Verde limestone, Supai sandstone, and Andesitic basalt substrata in a mountain stream in northern Arizona, U.S.A. Density, Shannon-Weiner diversity, evenness, and community similarity (SIMI) were used to compare colonization patterns and community structure between individual substratum types. Average standing crop values were nearly two-fold higher on sandstone than on either basalt or limestone substrata after the first week of the study. It is proposed that differences in micro-surface features between substrata and possibly the rate of substratum solubilization may cause these differences in density early in the colonization period. Following the initial week, standing crop and community structure were significantly similar on all substrata for the remainder of the study period. Maximum densities were attained by the third week and remained relatively constant on all substrata for the remainder of the study.

SEM micrographs demonstrated that surfaces of submerged substrata in streams are modified after the first week by the accumulation of organic aggregates. The establishment of an “organic matrix” early in the colonization process may provide relatively similar attachment surfaces for microbial invasion. This appears to reduce the initial microtopographic differences displayed by substrata and allows for a more uniform colonization pattern.     

Composition dynamics of epilithic intertidal bacterial communities exposed to high copper levels

Copper has a dual role for organisms, both as micronutrient and toxic element. Copper mining activities have an enormous ecological impact because of the extraction process and the consequent release of copper-containing waste materials to the environment. In northern Chile, mainly in the Cha?aral coastal area, this phenomenon is clearly evident. The released waste material has caused a strong modification of the area, and copper enrichment of beaches and rocky shores has provoked a decrease in the richness and diversity of many species of macroorganisms. However, the effects that copper enrichment has on microbial (e.g. bacterial epilithic) communities associated with the rocky shore environment are poorly understood. Using a culture-independent molecular approach, field sampling and laboratory microcosm experiments, we determined the effects of copper enrichment on bacterial communities inhabiting the rocky shore environment. Field samples showed a strong effect of copper on the structure of the natural bacterial epilithic communities, and microcosm experiments demonstrated rapid changes in bacterial community when copper is added, and reversibility of this effect within 48?h after copper is removed.     

Enzymic and molecular analysis of microbial communities associated with lotic particulate organic matter

1. Most allochthonous plant detritus moves through stream ecosystems as fine particulate organic matter (FPOM), whose associated microbial communities, unlike those of coarse detritus, have received little scrutiny. 2. Benthic POM was collected from a fourth-order boreal river and two first-order tributaries in northern New York during July 1991, sorted it into eight size fractions ranging from 38 to >4000 μm, and assayed each fraction for ergosterol, DNA, and the activity of nine extracellular enzymes: β-1, 4-glucosidase, endocellulase, cellobiohydrolase, phenol oxidase, peroxidase, β-N-acetylglucosaminidase, acid phosphatase, alkaline phosphatase, and aryl sulphatase. In addition, DNA-DNA hybridization was used to investigate the structural similarity of the microbial communities associated with the FPOM fractions. 3. Various enzymes showed distinct activity patterns in relation to particle size as well as among sites. Half of the possible pairwise correlations among enzyme variables were statistically significant, but no enzyme activities were correlated with biomass indices (DNA and ergosterol concentration). DNA-DNA dot-blot hybridizations suggested extensive structural similarity among the microbial communities associated with FPOM fractions. 4. Cluster analysis was used to compare microbial functional similarity, measured by enzyme assays, and structural similarity, measured by DNA—DNA hybridization. Comparison of cluster coefficients showed a weak correlation between community structural similarity and functional similarity (r= 0.51) with fifteen of eighteen fractions grouped within a narrow range of distance. 5. The results suggest a convergence in microbially mediated FPOM processing despite system-level differences in litter and water quality.     

Convergent photophysiology and prokaryotic assemblage structure in epilithic cyanobacterial tufts and algal turf communities

As global change spurs shifts in benthic community composition on coral reefs globally, a better understanding of the defining taxonomic and functional features that differentiate proliferating benthic taxa is needed to predict functional trajectories of reef degradation better. This is especially critical for algal groups, which feature dramatically on changing reefs. Limited attention has been given to characterizing the features that differentiate tufting epilithic cyanobacterial communities from ubiquitous turf algal assemblages. Here, we integrated an in situ assessment of photosynthetic yield with metabarcoding and shotgun metagenomic sequencing to explore photophysiology and prokaryotic assemblage structure within epilithic tufting benthic cyanobacterial communities and epilithic algal turf communities. Significant differences were not detected in the average quantum yield. However, variability in yield was significantly higher in cyanobacterial tufts. Neither prokaryotic assemblage diversity nor structure significantly differed between these functional groups. The sampled cyanobacterial tufts, predominantly built by Okeania sp., were co-dominated by members of the Proteobacteria, Firmicutes, and Bacteroidota, as were turf algal communities. Few detected ASVs were significantly differentially abundant between functional groups and consisted exclusively of taxa belonging to the phyla Proteobacteria and Firmicutes. Assessment of the distribution of recovered cyanobacterial amplicons demonstrated that alongside sample-specific cyanobacterial diversification, the dominant cyanobacterial members were conserved across tufting cyanobacterial and turf algal communities. Overall, these data suggest a convergence in taxonomic identity and mean photosynthetic potential between tufting epilithic cyanobacterial communities and algal turf communities, with numerous implications for consumer-resource dynamics on future reefs and trajectories of reef functional ecology.     

Community concordance in lotic ecosystems: How to establish unbiased congruence between macroinvertebrate and fish communities

Community concordance within aquatic biota could provide useful information for improving the methods used in bioassessment and biodiversity conservation management. The main goal of the study was to investigate the mechanism of community concordance between macroinvertebrates and fish in a single river basin (South Morava river Basin, Serbia). In order to achieve this, a Self organizing map (SOM) ordinated and classified sampling sites based on the community structures of five different taxa groups (macroinveretbrates (MIB), fish (FSH), Chironomidae (CHI), Macroinvertebrates without Chironomidae (MWC) and the Ephemeroptera Plecoptera Trichioptera group (EPT)). SOM also revealed 6 environmental gradients along the groups tested that significantly changed their community structures. Using the results of the SOM analysis as the input, the Mantel test quantified the highest community concordance between FSH and MIB (r = 0.42) followed by FSH and CHI (r = 0.29). The lowest concordance was recorded between FSH and EPT (r = 0.14). The indicator species analysis (IndVal) revealed 39 species to be responsible for the community patterns obtained. The Geo-SOM visualized the spatial distribution of the IndVal taxa, revealing the generators of community concordance. The strength of community concordance depends on the variability of the data on the aquatic biota. Thus, having an appropriate sampling and statistical design as well as high taxonomic resolution, as some of the factors which increase the variability in the data set, could present community concordance between fish and macroinvertebrates in an unbiased way.     

Colonization and extinction of ant communities in a fragmented landscape

Abstract In this paper we tested the assumption that smaller and more isolated remnants receive fewer ant colonizers and lose more species. We also tested hypotheses to explain such a pattern. We sampled ants in Brazil for 3 years in 18 forest remnants and in 10 grasslands between them. We tested the influence of remnant area and isolation on colonization rate, as well as the effect of remnant area on extinction rate. We tested the correlation between remnant area and isolation to verify the landscape design. Colonization rate was not affected by remnant area or isolation. Extinction rate, however, was smaller in larger remnants. Remnant area and isolation were negatively correlated. We tested two hypotheses related to the decrease in ant species extinction rate with increased remnant area: (i) small remnants support smaller and more extinction‐prone populations; and (ii) small remnants are more often invaded by generalist species, which suffer higher extinction inside remnants. The density of ant populations significantly increased with area. Generalist species presented a lower colonization rate in larger remnants, contrary to the pattern observed in forest species. Generalist species suffered more extinction than expected inside remnants. The lack of response of colonization rate to remnant area can be explained by the differential colonization by generalist and forest species. The decrease of ant population density in smaller remnants could be related to loss of habitat quality or quantity. The higher colonization by generalist ant species in the smaller remnants could be related to landscape design, because smaller remnants are more similar to the matrix than larger ones. Our results have important implications for conservation strategies because small remnants seem to be more affected by secondary effects of fragmentation, losing more forest species and being invaded more often by generalist species. Studies that compare only species richness between remnants cannot detect such patterns in species composition.     

Spatial and temporal variability in epilithic biofilm bacterial communities along an upland river gradient

Riverine biofilms remain one of the least-studied habitats despite the significant increase in the examination of aquatic microbial communities in recent years. In this study, the dynamics of epilithic biofilm communities native on rocks from a low-order upland stream were examined over a period of 3 years. Spatial and temporal variations in bacterial communities were assessed using terminal restriction fragment length polymorphism, based on analysis of the 16S rRNA gene. In total, 108 epilithic biofilm samples were analysed and 170 different ribotypes were detected. A strong temporal gradient in ribotype composition was noticed, especially between samples collected in 2001 and those collected in 2002 and 2003, most likely reflecting interannual differences in weather conditions, such as temperature. A spatial gradient in ribotype composition, from upstream sites to the low-lying sites, was also evident and interpreted as an environmental variation gradient along the river course. Distinct biofilm communities consistently occurred at the first site along the river, which was significantly correlated to low pH. Temporal factors explained the highest degree of variation within the epilithic biofilms. Recurrent blooms of certain bacteria were noted within the system. Phylogenetic relationships of bacteria at one point in the river were determined using a cloning and sequencing approach, with Alphaproteobacteria dominating the community, followed by Cyanobacteria, Bacteroidetes and Betaproteobacteria.     

Effects of live coral,epilithic algal communities and substrate type on algal recruitment

The recruitment of algae is a critical process during algal colonization and invasions, including coral-to-algal phase shifts. Although algae are widely assumed to colonize and kill corals, there is very little known about the recruitment dynamics of coral reef algae. This study tested the ability of two dominant macroalgae (Fucales including Sargassum spp. and Lobophora variegata) to settle and grow on healthy coral tissue. The study also explored the effects of interactions with prior occupants, and of abiotic substrate properties (texture, and ceramic and carbonate material). The results indicate that healthy corals were able to prevent attachment or survival of recruits of these macroalgae. This is a significant point, since it suggests that the replacement of corals by algae may often require prior stress or death in the coral tissue. Pre-conditioning of plates at different sites had some effects, but these were relatively minor, whereas there was considerable variation within sites. Some of this variation appeared to be related to the amount of turf algae or crustose coralline algae on the plates. Recruitment was generally, but not always, higher on plates with rougher texture. Overall, this preliminary exploration indicates considerable potential for variability in outcomes of algal colonization, with implications for the dynamics of algal invasions. In particular, the results do not support suggestions that planktonic algal propagules can directly settle on and colonize healthy coral tissue.Communicated by Topic Editor D. Barnes     

水质对东江流域附生硅藻群落的影响

运用相关分析(CA),典型对应分析(CCA),加权平均分析(WA)研究了影响东江流域附生硅藻的主要水质因子及对应的最适生态范围。CA显示,13项水质指标中溶解氧(Dissolved Oxygen,DO)、氨氮(NH4-N)、亚硝氮(NO2-N)、氯化物(Cl)、五日生化需氧量(BOD5)、磷酸盐(PO4-P)与其它指标间的相关性较强(P0.05),其余指标间相关性较低(P0.05)。以相关性较弱的p H、电导率(Cond.)、硅酸盐(Si O2)、总磷(TP)、总氮(TN)、硝氮(NO3-N)、化学需氧量(CODKMn O4)进行CCA分析,排序显示影响附生硅藻的水质因子依次为Cond.、NO3-N、CODKMn O4、TP、TN,对应的生态最适范围分别为39.20—642.00μs/cm、0.46—2.77mg/L、1.0—5.5mg/L、0.02—0.64mg/L、0.48—3.43mg/L。研究表明,Cond、NO3-N、CODKMn O4、TP、TN是影响东江附生硅藻分布的主要水质因子,Cyclostephanos invisitatus、Gomphonema olivaceum、Nitzschia acicularis、N.capitellata、N.intermedia可以指示东江较高的电导率,Aulacoseira ambigua、A.lirata、Cyclotella meneghiniana、Cyclostephanos invisitatus、Eunotia minor、Nitzschia acicularis、N.Clausii、Pinnularia subcapitata是东江TN、TP污染的指示种。Nitzschia acicularis对TN、TP的耐受性最高,Navicula eidrigiana对TN、TP敏感性最强。     

Response of epilithic diatom communities to environmental gradients along an Ecuadorian Andean River

Epilithic diatom communities are particularly suitable for the evaluation of freshwater quality. In Ecuador, however, no water quality index includes this biotic parameter. This work is the first attempt in the country to determine the composition of epilithic diatom communities associated with different degrees of eutrophication. This was accomplished by measuring physical, chemical and microbiological variables at five sampling sites along the Pita River, Ecuador, from August to December 2016. The results indicate a clear gradient of eutrophication from sampling sites P1 (good water) in the upper reaches to P5 (bad water) located in the lower reaches. Concerning diatom analyses, the results indicated a high diversity for tropical areas in terms of species richness, varying from S = 34 in headwaters to S = 42 downstream. Moreover, the results obtained suggest a lack of concordance with the trophic values given to some of the epilithic diatoms in the literature. There were also species that seem to be sensitive to downstream nutrient increases that were not considered as bioindicators in previous studies. We concluded that the trophic values of diatom species available in the scientific literature are not directly applicable to their sites in the Pita River. Hence, it is necessary to establish a trophic diatom index for the Andean region of Ecuador.     

Viability of differentiated epilithic bacterial communities in the River Garonne (SW France)

Epilithic bacterial community viability was assessed on natural biofilm assemblages from environmentally contrasting locations over a 17-months period to determine if it reflects environmental conditions or conditions within the biofilm assemblage. Vital state was assessed by membrane integrity using LIVE/DEAD^® BacLight? staining kit. Samples were regularly collected in a large river, up and downstream of a large urban centre. Epilithic biomasses were similar between sites irrespective of the distinct water quality but varied temporarily, peaking up to 48 g AFDM m^?2. Bacterial community composition assessed by 16S rDNA based PCR-DGGE significantly differed between sites. Bacterial densities (median of 2.5 × 10¹¹ cell g AFDM^?1) were stable whatever the sample origin or biomass. Viable bacterial fractions ranged between 13 and 83% of the total bacterial densities and were correlated with hydrological stability indicators (average of 41.9% during stable water periods, 62.4% during intermediate flow regimes and 50.0% during flow instability) and seasonal parameters. At the river section and epilithic community scales, consistent bacterial densities per unit of biomass could reflect a biofilm assemblage carrying capacity while variable membrane integrity likely integrates changes in the vital state of the community under changing environmental conditions.