A novel bacterial community index to assess stream ecological health

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

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Local factors control the community composition of cyanobacteria in lakes while heterotrophic bacteria follow a neutral model

1. Neutral community models are derived from the proposition that basic probabilities of species loss (extinction, emigration) and gain (immigration, speciation) explain biological community structure, such that species with many individuals are very likely to be widespread. Niche models on the other hand assume that interactions between species and differential resource use mediate species coexistence, thus invoking environmental factors to explain community patterns. 2. In this study, we compared neutral and niche models to test how much of the spatial variability of assemblages of heterotrophic bacteria and phytoplankton in 13 lakes they could explain. Analysis of phytoplankton was restricted to cyanobacteria, so that they could be studied with the same molecular fingerprinting method, automated ribosomal intergenic spaces analysis (ARISA), as heterotrophic bacteria. We determined local biotic and abiotic lake variables as well as lake age, glacial history and distance between sites. 3. The neutral community model had a good fit to the community composition of heterotrophic bacteria (R² = 0.69), whereas it could not produce a significant model for the community composition of cyanobacteria. 4. The community composition of cyanobacteria was instead correlated to environmental variables. The best model, a combination of total organic carbon, biomass of eukaryotic phytoplankton, pH and conductivity, could explain 8% of the variation. In contrast, variation in the community composition of heterotrophic bacteria was not predicted by any of the environmental variables. Historical and spatial variables were not correlated to the community composition of either group. 5. The pattern found for heterotrophic bacteria suggests that stochastic processes are important. The correlation of cyanobacteria with local environmental variables alone is consistent with the niche model. We suggest that cyanobacteria, a group of organisms containing bloom‐forming species, may be less likely to fit a neutral community model, since these blooms are usually triggered by a particular combination of environmental conditions.     

城市溪流中径流式低坝对底栖动物群落结构的影响

调查了浙江省安吉县内具径流式低坝的城市溪流(6个样点)和参照溪流(3个样点)的底栖动物群落,目的是了解城市溪流底栖动物群落结构退化规律和径流式低坝(2—3 m)对城市溪流底栖动物群落组成与结构的影响。结果表明,参照样点的底质组成以大石块(35.92%)和卵石(33.66%)为主,城市溪流以砾石为主(57.97%)。城市溪流水温和电导率显著高于参照溪流,TN和TP高于参照溪流。底栖动物总分类单元数和EPT分类单元数显著低于参照溪流。城市溪流河道内水坝上下游之间的流速(P=0.273)和宽深比(P=3.92)无显著差异。坝下游水体中的TP高于坝上游,电导率、溶解氧、pH值和水温在坝上下游之间几乎一致。除BI指数坝下游高于坝上游外,坝上下游间底栖动物总分类单元数、EPT分类单元数以及多样性指数、优势度和均匀度指数没有显著差异。但坝下游的耐污类群比例显著高于坝上游,敏感类群比例则显著低于坝上游。与坝上游相比,坝下游捕食者比例上升和集食者比例下降。NMDS结果进一步表明,城市溪流内水坝的建设导致坝上下游底栖动物群落物种组成明显改变。     

Differences in intestinal microbiota between avian brood parasites and their hosts

The intestinal microbiota determines the effectiveness of digestion in vertebrates, and is influenced by the external environment (mainly the diet), gut characteristics, and phylogeny. Avian brood-parasitic nestlings of the sub-family Cuculinae develop in nests of phylogenetically distant passerines and can be fed with the host diet. If the shaping of bacterial communities is dominated by phylogenetic constraints, and therefore the microbiota of parasitic nestlings differs from that of host nestlings, the energy and micronutrients that parasites and hosts obtain from a similar amount of food would be different. In this case, the bacterial communities of parasitic and host nestlings would have important consequences with respect to brood parasite development. By experimentally creating mixed broods of magpies ( Pica pica ) and great spotted cuckoos ( Clamator glandarius ), we investigated their cloacal microbiota using ribosomal intergenic spacer analysis. We found significant differences in bacterial assemblages of the parasitic and host nestlings, although none of the phylotypes were specific in either great spotted cuckoos or magpies. Cuckoos presented more complex communities, which could help the brood parasitic life style and allow the digestion of food provided by different potential hosts. Moreover, the intestinal morphology is different between the two species due to phylogenetic differences in the two taxa, which would influence the dissimilar bacterial assemblages. The detected differences in microbiota of great spotted cuckoo and magpie nestlings, which might occur in other brood parasite–host systems, may imply a lower digestion efficiency in parasites. Thus, the higher level requirements of cuckoo nestlings may be explained, at least in part, by cuckoos having a suboptimal bacterial community for processing the host diet.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 406–414.     

Effect of sediment quality on benthic macroinvertebrate communities in streams in the north of France

The Nord/Pas-de-Calais region located in the North of France has been submitted, for several decades, to important pollution due to intensive industrialization. The present study reports on the effects of the metal and organic content of sediments in different streams on the benthic fauna, using multivariate analyses (PCA, CA, co-inertia analysis). Benthic macroinvertebrate communities present different assemblages along the Canal à Grand Gabarit and the river Aa, both in its natural and in its canalized stretches. These differences are more specifically due to anthropic factors such as the regulation of waterways and urban and industrial contamination. Co-inertia analysis enables to bring to the light the existence of a significant co-structure between environmental and faunistic data. This revised version was published online in September 2006 with corrections to the Cover Date.     

Seasonal and management influences on bacterial community structure in an upland grassland soil

Floristically diverse Nardo-Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement.     

Combined monitoring of changes in δ13CH4 and archaeal community structure during mesophilic methanization of municipal solid waste

Reconstituted municipal solid waste (MSW) with varying contents of putrescible and cellulosic waste was incubated anaerobically under mesophilic conditions. Standard physicochemical parameters were monitored, together with stable isotopic signatures of produced CH₄ and CO₂. δ¹³C values for CH₄ indicated a change of methanogenic metabolism with time. CH₄ was predominantly produced from H₂/CO₂ at the beginning of the incubations. This period was associated with important shifts in archaeal communities monitored by automated ribosomal intergenic spacer analysis (ARISA) and FISH of oligonucleotidic probes targeting specifically 16S rRNA gene of various methanogenic groups. The onset of the active methane generation phase was characterized by an increase of CH₄δ¹³C, indicating a progressive shift toward an aceticlastic metabolism. When the methane production levelled off, a decrease in the isotopic signature was observed toward values characteristics of hydrogenotrophic metabolism. ARISA profiles were, however, found to be stable from the beginning of the active methane generation phase until the end of the experiment. FISH observation indicated that members of the family Methanosarcinaceae were predominant in the archaeal community during this period, suggesting that these methanogens might exhibit a high metabolic versatility during methanization of waste.     

Physiological indicators of fitness in benthic invertebrates: a useful measure for ecological health assessment and experimental ecology

Physiological indicators of fitness present a measure of an organism’s response to a changing environment. An analysis of how these organisms allocate and store their energy resources provides an understanding of how they cope with such environmental changes. Each individual has to balance the investment necessary to acquire a certain resource with the energy gained by it. This trade-off can be monitored by measuring several physiological indicators of fitness such as energy storage components, metabolic state or RNA/DNA ratio. Because environmental adaptations and ecological strategies of survival are best examined within the natural environment, our research has to rely on the physiological indicators that are easily accessible in the field. The physiological indicators presented here are significant for an individual’s fitness and in turn lead to reliable values in field-collected samples. Based on our own expertise and on a literature survey, the physiological relevance of the presented indicators is explained. Furthermore, some consideration to the analytical methods used to obtain the physiological indicators is given, and possible errors introduced at the sampling site and during the laboratory procedures are discussed. This work demonstrates that the integration of ecological and physiological expertise facilitates the identification of future ecological problems much earlier than separate approaches of both disciplines alone.     

Herbs and grasses as an allochthonous resource in open-canopy headwater streams

1. The organic matter dynamics of streams dominated by herbs and grass on their banks are poorly understood, despite the fact that such streams are common worldwide. Further, herbs and grasses can provide large quantities of detritus to stream food webs, and particularly small streams can be heavily shaded by overhanging vegetation, perhaps limiting in‐stream primary production. 2. We quantified the standing crop of edge vegetation and associated macroinvertebrate communities along three headwater streams with herbaceous and grass riparian vegetation on agricultural land in the Piedmont of Maryland, U.S.A., measured the decomposition of four common species of herbs and grasses using experimental leaf packs, and removed edge vegetation experimentally to determine the effect of shading on benthic algal production. 3. Large standing crops of plant material (average range: 68–276 g ash‐free dry mass per m⁻²), composed largely of monocotyledons, were found at all three study streams. These values are similar to those for coarse particulate organic matter in deciduous forested streams in the eastern U.S.A. In addition, diverse assemblages of shredding macroinvertebrates were observed at all three study sites. 4. Decomposition of the herbs was faster than that of the grasses, and both decomposed faster than most deciduous tree leaf litter. The decomposition rates of the herbs and grasses were significantly related to leaf quality as measured by leaf nitrogen content. Macroinvertebrate shredders colonized all experimental leaf packs, and the colonization of the herbs was faster than that of the grasses. 5. The accrual of chlorophyll‐a after the removal of shading vegetation was faster than that measured prior to removal as well as that in an unmanipulated control reach. 6. Given that the standing crop of organic matter in streams with herbs and grass along their banks was similar to that in forested streams, that the organic matter was rich in nitrogen and used by detritivores, and riparian shading limited algal growth, we suggest that herbaceous and grass plant material may be an important allochthonous food resource in such systems.     

ARISA方法研究产甲烷菌共存及去除条件下瘤胃真菌多样性变化

摘要：【目的】建立厌氧真菌多样性分析方法,并研究厌氧真菌与产甲烷菌共培养液在传代过程中厌氧真菌的区系变化及共培养液中去除产甲烷菌条件下厌氧真菌多样性的变化。【方法】根据厌氧真菌ITS1序列长度多态性,设计厌氧真菌特异性引物,然后PCR扩增样品中厌氧真菌ITS1序列,在基因分析仪中分析PCR产物序列长度多态性,分析共培养液在传代过程中及共培养液中去除产甲烷菌后厌氧真菌多样性的变化。【结果】对瘤胃厌氧真菌Caecomyces属YC301菌株、Neocallimastix属菌株（YC501与YC502）的ARI     

Hindcasting cyanobacterial communities in Lake Okaro with germination experiments and genetic analyses

Cyanobacterial blooms are becoming increasingly prevalent worldwide. Sparse historic phytoplankton records often result in uncertainty as to whether bloom-forming species have always been present and are proliferating in response to eutrophication or climate change, or if there has been a succession of new arrivals through recent history. This study evaluated the relative efficacies of germination experiments and automated rRNA intergenic spacer analysis (ARISA) assays in identifying cyanobacteria in a sediment core and thus reconstructing the historical composition of cyanobacterial communities. A core (360 mm in depth) was taken in the central, undisturbed basin of Lake Okaro, New Zealand, a lake with a rapid advance of eutrophication and increasing cyanobacteria populations. The core incorporated a tephra from an 1886 volcanic eruption that served to delineate recent sediment deposition. ARISA and germination experiments successfully detected akinete-forming nostocaleans in sediment dating 120 bp and showed little change in Nostocales species structure over this time scale. Species that had not previously been documented in the lake were identified including Aphanizomenon issatschenkoi , a potent anatoxin-a producer. The historic composition of Chrococcales and Oscillatoriales was more difficult to reconstruct, potentially due to the relatively rapid degradation of vegetative cells within sediment.     

Conservation and variation of ribosomal DNA in eukaryotes

The organization of ribosomal DNA clusters, repetitive units, and their conserved and variable elements in eukaryotes is considered with special emphasis on the structure and function of the ribosomal intergenic spacer (rIGS). Data on rDNA variation, evolution, and possible role in various biological processes are reviewed.     

Relationships between stream acidity and bacteria,macroinvertebrates, and fish: a comparison of north temperate and south temperate mountain streams,USA

A comparative study of relationships between stream acidity and bacteria, macroinvertebrates, and fish in the Adirondack Mountains of upper New York state and in the Southern Blue Ridge Mountains of eastern Tennessee, USA, was conducted. Although the study sites in both regions spanned a pH range from approximately 4.5 to 6.4, considerably greater seasonal variability in pH and higher monomeric Al concentrations characterized the Adirondack sites. Relationships between several biological characteristics and stream water acidity were similar in both regions, including lower production of epilithic bacteria and bacteria on decomposing leaves, lower leaf decomposition rates, lower density and generic richness of scraper/grazer macroinvertebrates, particularly Ephemeroptera, and lower fish abundance and survival in more acidic streams. Densities of total macroinvertebrates and densities of macroinvertebrates and bacteria inhabiting or closely associated with stream sediments were generally not related to stream water acidity.Regional differences occur in some of the relationships between biological characteristics and stream water acidity. Negative correlations between bacterial production on rocks and pH, between bacterial production on decomposing leaves and pH, and between densities of Ephemeroptera and scrapers and pH were stronger in the Adirondacks than in the Southern Blue Ridge. Higher Al concentrations in the Adirondacks may be responsible for the stronger relationships with pH there. The steeper slopes of the relationships between Ephemeroptera density and all forms of Al in the Adirondacks compared with the Southern Blue Ridge suggests that there may be some adaptation among a few acid/aluminum-tolerant species in the seasonally more constant acidic Southern Blue Ridge streams. Fish bioassays indicated longer survival times in acidic streams in the Adirondacks compared with the Southern Blue Ridge, but these results may be an artifact associated with the use in the Southern Blue Ridge of rainbow trout as the test species which is known to be more acid sensitive compared with brook trout, the test species used in the Adirondacks.     

2,4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic spacer analysis. The 2,4-D degrading genetic potential was estimated by real-time PCR targeted on tfdA sequences coding an enzyme specifically involved in 2,4-D mineralization. The genetic structure of bacterial communities was significantly modified in response to 2,4-D application, but only during the intense phase of 2,4-D biodegradation. This effect disappeared 7 days after the treatment. The 2,4-D degrading genetic potential increased rapidly following 2,4-D application. There was a concomitant increase between the tfdA copy number and the 14C microbial biomass. The maximum of tfdA sequences corresponded to the maximum rate of 2,4-D mineralization. In this soil, 2,4-D degrading microbial communities seem preferentially to use the tfd pathway to degrade 2,4-D.     

A comparison of clustering methods for river benthic community analysis

Four commonly used clustering methods (UPGMA, Ward Linkage,Complete Linkage and TWINSPAN) were compared in their abilitytorecognise the structure of three river macroinvertebratesdatasetswhich were pre-determined based on habitat and biologicalcharacteristics or chemical water quality of sampling sites.DCA,NMDS and ANOSIM were applied to the same datasets to providefurther information about data structure, and nonparametrictestswere also undertaken on major chemical variables to justifythepredeterminations. The modified Rand Index was used to measuretheagreement between a particular solution and the pre-determinedclassification. The results showed that Ward Linkage performedbestwhen its use was broadened and used with the CY DissimilarityMeasure, followed by TWINSPAN and Complete Linkage with UPGMAbeingleast successful. There was evidence to suggest that theeffectiveness of some clustering methods (e.g. UPGMA) may varyatdifferent clustering levels, and simulation techniques whichhavebeen used to assess clustering methods could leave somepropertiesof clustering methods unexamined.     

A truce with neutral theory: local deterministic factors, species traits and dispersal limitation together determine patterns of diversity in stream invertebrates

1. Studies seeking to explain local patterns of diversity have typically relied on niche explanations, reflected in correlations with local environmental conditions, or neutral theory, invoking dispersal processes and speciation. 2. We used macroinvertebrate community data from 10 streams that varied independently in local ecological conditions and spatial proximity. Neutral theory predicts that similarity in communities will be negatively associated with distance between sites, while niche theory suggests that community similarity will be positively associated with similarity in local ecological conditions. 3. Similarity in total invertebrate, grazer and predator assemblages showed negative relationships with distance and, for grazers and predators, positive relationships with local ecological conditions. However, the best model predicting community similarity in all three cases included aspects of both local ecological conditions and distance between sites. 4. When assemblages were analysed according to dispersal ability, high-dispersal species were shown to be freely accessing all sites and community similarity was not well predicted by either local ecology or spatial separation. Assemblages of species with low and moderate dispersal ability were best predicted by combined models, including distance between sites and local ecological factors. 5. The results suggest that the perceived dichotomy between neutral and local environmental processes in determining local patterns of diversity may not be useful. Neutral and niche processes structured these communities differentially depending on trophic level and species traits. 6. We emphasize the potential for both dispersal processes and local environmental conditions to explain local patterns of diversity.     

Predictability of streamflow and particulate organic matter concentration as indicators of stability in prairie streams

Predictability of stream discharge and particulate organic matter (POM) in the water column was estimated, using Colwell's indices of constancy and contingency, for 6 Texas prairie streams (1 each of 2nd, 3rd, and 4th order with intermittent or perennial discharge). Stream discharge in these 6 prairie streams varied between 0 and 36000 1 s^–1, depending on the stream and season. Predictability (P) of discharge in these streams ranged from 0.45 to 0.62, within the range of values expected for North American streams. Predictability of stream discharge was not significantly different between streams. Particulate organic matter concentrations in these prairie streams are relatively low, ranging from 0.25 to 4.00 mg AFDM 1^–1. Predictability of POM concentration in these streams was high, ranging from 0.75 to 0.85, and was largely the result of constancy of POM concentrations. Within the different POM size classes, Fine POM (FPOM) had the highest predictability (P = 0.89–0.96). In spite of relatively unpredictable stream discharge, POM remained fairly constant providing a measure of habitat predictability and stability.     

Hyporheic invertebrates as bioindicators of ecological health in temporary rivers: A meta-analysis

Worldwide, many rivers cease flow and dry either naturally or owing to human activities such as water extraction. However, even when surface water is absent, diverse assemblages of aquatic invertebrates inhabit the saturated sediments below the river bed (hyporheic zone). In the absence of surface water or flow, biota of this zone may be sampled as an alternative to surface water-based ecological assessments. The potential of hyporheic invertebrates as ecological indicators of river health, however, is largely unexplored. We analysed hyporheic taxa lists from the international literature on temporary rivers to assess compositional similarity among broad-scale regions and sampling conditions, including the presence or absence of surface waters and flow, and the regional effect of hydrological phase (dry channel, non-flowing waters, surface flow) on richness. We hypothesised that if consistent patterns were found, then effects of human disturbances in temporary rivers may be assessable using hyporheic bioindicators. Assemblages differed geographically and by climate, but hydrological phase did not have a strong effect at the global scale. However, hyporheic assemblage composition within regions varied along a gradient of higher richness during wetter phases. This indicates that within geographic regions, hyporheic responses to surface drying are predictable and, by extension, hyporheic invertebrates are potentially useful ecological indicators of temporary river health. With many rivers now experiencing, or predicted to experience, lower flows and longer dry phases owing to climate change, the development of ecological assessment methods specific to flow intermittency is a priority. We advocate expanded monitoring of hyporheic zones in temporary rivers and recommend hyporheic invertebrates as potential bioindicators to complement surface water assessments.