Diel shifts in the structure and function of nearshore estuarine fish communities

Day–night shifts in the nearshore fish fauna of a temperate microtidal estuary were assessed using a holistic suite of structural and functional community attributes. Mean fish species richness and diversity (taxonomic distinctness) were higher at night across all regions of the estuary and seasons, concurring with the findings of numerous comparable studies reviewed worldwide, while the diel period in which mean abundance was higher varied among seasons. Likewise, species and functional guild compositions (the latter based on feeding modes and habitat use) both differed significantly between day and night, with the extent of the diel shift again varying seasonally. Daytime fish communities were characterized by higher abundances of Atherinidae, Sillaginidae and Mugilidae, while Gobiidae were far more abundant at night. Marked shifts in size composition were also evident, with smaller fishes (<100 mm total length, L_T) being more prevalent during the day and larger fishes (≥200 mm L_T) proportionally more abundant at night. The above diel shifts were feasibly related to a range of predator–prey interactions and feeding‐related movements, namely a nocturnal decrease in top‐order avian piscivory coupled with an increase in invertebrate prey availability, resulting in changes in the presence and catchability of certain fish species in shallow estuarine waters.     

Warming and oligotrophication cause shifts in freshwater phytoplankton communities

While there is a lot of data on interactive effects of eutrophication and warming, to date, we lack data to generate reliable predictions concerning possible effects of nutrient decrease and temperature increase on community composition and functional responses. In recent years, a wide‐ranging trend of nutrient decrease (re‐oligotrophication) was reported for freshwater systems. Small lakes and ponds, in particular, show rapid responses to anthropogenic pressures and became model systems to investigate single as well as synergistic effects of warming and fertilization in situ and in experiments. Therefore, we set up an experiment to investigate the single as well as the interactive effects of nutrient reduction and gradual temperature increase on a natural freshwater phytoplankton community, using an experimental indoor mesocosm setup. Biomass production initially increased with warming but decreased with nutrient depletion. If nutrient supply was constant, biomass increased further, especially under warming conditions. Under low nutrient supply, we found a sharp transition from initially positive effects of warming to negative effects when resources became scarce. Warming reduced phytoplankton richness and evenness, whereas nutrient reduction at ambient temperature had positive effects on diversity. Our results indicate that temperature effects on freshwater systems will be altered by nutrient availability. These interactive effects of energy increase and resource decrease have major impacts on biodiversity and ecosystem function and thus need to be considered in environmental management plans.     

Outbreaks by canopy-feeding geometrid moth cause state-dependent shifts in understorey plant communities

The increased spread of insect outbreaks is among the most severe impacts of climate warming predicted for northern boreal forest ecosystems. Compound disturbances by insect herbivores can cause sharp transitions between vegetation states with implications for ecosystem productivity and climate feedbacks. By analysing vegetation plots prior to and immediately after a severe and widespread outbreak by geometrid moths in the birch forest-tundra ecotone, we document a shift in forest understorey community composition in response to the moth outbreak. Prior to the moth outbreak, the plots divided into two oligotrophic and one eutrophic plant community. The moth outbreak caused a vegetation state shift in the two oligotrophic communities, but only minor changes in the eutrophic community. In the spatially most widespread communities, oligotrophic dwarf shrub birch forest, dominance by the allelopathic dwarf shrub Empetrum nigrum ssp. hermaphroditum, was effectively broken and replaced by a community dominated by the graminoid Avenella flexuosa, in a manner qualitatively similar to the effect of wild fires in E. nigrum communities in coniferous boreal forest further south. As dominance by E. nigrum is associated with retrogressive succession the observed vegetation state shift has widespread implications for ecosystem productivity on a regional scale. Our findings reveal that the impact of moth outbreaks on the northern boreal birch forest system is highly initial-state dependent, and that the widespread oligotrophic communities have a low resistance to such disturbances. This provides a case for the notion that climate impacts on arctic and northern boreal vegetation may take place most abruptly when conveyed by changed dynamics of irruptive herbivores.     

The search for disease-associated compositional shifts in bowel bacterial communities of humans

The bowels of humans contain resident bacterial communities, the members of which are numerous and biodiverse. Changes in the composition of bowel communities is accepted to occur in relation to antibiotic-associated colitis of the elderly, but compositional alterations could also be relevant to allergic diseases in children and inflammatory bowel diseases (i.e. Crohn's disease and ulcerative colitis). It is timely, therefore, to reflect on current knowledge of the bacterial community of the human bowel in relation to disease. Modern analytical methods provide tools by which compositional shifts in bacterial communities can be detected, but inadequate bowel-sampling procedures and poorly designed studies hamper progress. Moreover, demonstration that population shifts cause the disease and are not just reflections of a diseased state is necessary. Therefore, important challenges remain for bacteriologists in investigations of the bowel bacterial community in relation to disease.     

Seasonal shifts in the assembly dynamics of benthic macroinvertebrate and diatom communities in a subtropical river

Identifying seasonal shifts in community assembly for multiple biological groups is important to help enhance our understanding of their ecological dynamics. However, such knowledge on lotic assemblages is still limited. In this study, we used biological traits and functional diversity indices in association with null model analyses to detect seasonal shifts in the community assembly mechanisms of lotic macroinvertebrates and diatoms in an unregulated subtropical river in China. We found that functional composition and functional diversity (FRic, FEve, FDis, MNN, and SDNN) showed seasonal variation for macroinvertebrate and diatom assemblages. Null models suggested that environmental filtering, competitive exclusion, and neutral process were all important community assembly mechanisms for both biological groups. However, environmental filtering had a stronger effect on spring macroinvertebrate assemblages than autumn assemblages, but the effect on diatom assemblages was the same in both seasons. Moreover, macroinvertebrate and diatom assemblages were shaped by different environmental factors. Macroinvertebrates were filtered mainly by substrate types, velocity, and COD_Mn, while diatoms were mainly shaped by altitude, substrate types, and water quality. Therefore, our study showed (a) that different biological assemblages in a river system presented similarities and differences in community assembly mechanisms, (b) that multiple processes play important roles in maintaining benthic community structure, and (c) that these patterns and underlying mechanisms are seasonally variable. Thus, we highlight the importance of exploring the community assembly mechanisms of multiple biological groups, especially in different seasons, as this is crucial to improve the understanding of river community changes and their responses to environmental degradation.     

Onward but not always upward: individualistic elevational shifts of tree species in subtropical montane forests

Ongoing global climate change is driving widespread shifts in species distributions. Trends show frequent upwards shifts of treelines, but information on changes in montane forest below the treeline and in the tropics and subtropics is limited, despite the importance of these areas for biodiversity and ecosystem function. Patterns of species shifts in tropical and subtropical regions are likely to be more complex and individualistic than global averages suggest due to high species diversity and strong influence of competition, alongside direct climatic limitations on distributions. To address the question of how subtropical montane tree species are likely to move as climate changes, we used an extensive national forest inventory to estimate distribution shifts of 75 tree species in Taiwan by comparing the optimum elevation and range edges of adults and juveniles within species. Overall there was a significant difference in optimum elevation of adults and juveniles. Life stage mismatches suggested upward shifts in 35% of species but downward shifts of over half (56%), while 8% appeared stable. Upward elevation shifts were disproportionately common in high elevation species, whilst mid to low elevation species suggested greater variation in shift direction. Whilst previous research on mountain forest range shifts has been dominated by work addressing changes in treeline position, we show that although high elevation species shift up, below the treeline species may shift individualistically, heralding widespread changes in forest communities over coming decades. The wide variation of responses indicated is likely driven by individual species responses to interacting environmental factors such as competition, topography and anthropogenic influences across the broad range of forest types investigated. As global environmental changes continue, more detailed understanding of tree range shifts across a wide spectrum of forests will allow us to prepare for the implications of such changes for biodiversity, ecosystem function and dependent human populations.     

Increasing antagonistic interactions cause bacterial communities to collapse at high diversity

Biodiversity is a major determinant of ecosystem functioning. Species-rich communities often use resources more efficiently thereby improving community performance. However, high competition within diverse communities may also reduce community functioning. We manipulated the genotypic diversity of Pseudomonas fluorescens communities, a plant mutualistic species inhibiting pathogens. We measured antagonistic interactions in vitro, and related these interactions to bacterial community productivity (root colonisation) and ecosystem service (host plant protection). Antagonistic interactions increased disproportionally with species richness. Mutual poisoning between competitors lead to a 'negative complementarity effect', causing a decrease in bacterial density by up to 98% in diverse communities and a complete loss of plant protection. The results emphasize that antagonistic interactions may determine community functioning and cause negative biodiversity-ecosystem functioning relationships. Interference competition may thus be an additional key for predicting the dynamics and performance of natural assemblages and needs to be implemented in future biodiversity models.     

Method for rapid DNA extraction from bacterial communities of different soils

A method for indirect DNA extraction from various soils significantly differing in their physicochemical properties has been developed. The proposed method is based on cell desorption from soil particles using a Tris-EDTA (TE) buffer supplemented with polyvinylpolypyrrolydone (PVPP) and sodium dodecylsulfate (SDS). Methods for subsequent cell lysis and purification of DNA preparations based on alkaline lysis followed by chromatography on ion-exchange resins were described by us earlier. The purity of the DNA preparations obtained did not depend on the type of soil. It was shown that the DNA preparations can be used for the amplification of rather large fragments, e.g., sequences spanning the complete 16S rRNA gene.     

Method for rapid DNA extraction from bacterial communities of different soils

A method for indirect DNA extraction from various soils significantly differing in their physicochemical properties has been developed. The proposed method is based on cell desorption from soil particles using a Tris-EDTA (TE) buffer supplemented with polyvinylpolypyrrolydone (PVPP) and sodium dodecylsulfate (SDS). Subsequent cell lysis and purification of DNA preparations methods based on alkaline lysis followed by chromatography on ion-exchange resins were described by us earlier. The purity of the DNA preparations obtained did not depend on the type of soil. It was shown that the DNA preparations can be used for the amplification of rather large fragments, e.g., sequences spanning the complete 16S rRNA gene.     

Climate change-predicted shifts in the temperature regime of shallow groundwater produce rapid responses in ciliate communities

The ciliates living in a shallow groundwater system in southern Ontario, Canada were subjected to an in situ temperature manipulation over 14 months. Ciliates were collected from the bed surface of a small springbrook and from interstitial water collected at five depths beneath its surface. Mean temperature elevations established at each depth (?20, ?40, ?60, ?80, and ?100 cm) between the experiment's control and treatment blocks were 1.9, 3.5, 3.9, 3.8, and 3.6 °C, respectively, and were based on global warming projections for the region. In total, 160 species of ciliate belonging to 85 genera were identified. Overall, the treatment block had a higher density (6510±342 cells L^?1; ±1 SE) than the control (5797±237 cells L^?1), but densities were both vertically and longitudinally variable. Control densities decreased with depth, whereas treatment densities were more equal among depths. Total species richness showed no significant difference between blocks when combining all sampling dates and depths, although species composition changed. The ciliate community was dominated by small (15–50 μm), followed by medium (50–200 μm), and only a few large‐sized (>200 μm) species. Small ciliates contributed 82–97% of the total density. Small ciliates also contributed more to the treatment (94%) than the control block (88%). The most common ciliate feeding groups were bacterivores, omnivores, predators, and algae‐diatom feeders, with bacterivores being most dominant (83–99% of the total numbers collected). Ordination analyses revealed that ciliate distribution was strongly correlated with groundwater temperature, although dissolved oxygen level, concentrations of ammonia and nitrate, and depth also appeared to be influential. Peak densities of many species occurred in either the control or treatment blocks, but not in both. The benefits of using ciliates as a proxy for higher, much longer‐lived, eukaryotes in climate change studies are discussed.     

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.     

Responses of bacterial and fungal communities to an elevation gradient in a subtropical montane forest of China

Bacteria and fungi are ecologically important contributors to various functioning of forest ecosystems. In this study, we examined simultaneously the bacterial and fungal distributions in response to elevation changes of a forest. By using clone library analysis from genomic DNA extracted from forest humic clay soils, the composition and diversity of bacterial and fungal communities were determined across an elevation gradient from low via medium to high, in a subtropical forest in the Mountain Lushan, China. Our results showed that soil water content and nutrient availability, specifically total carbon, differed significantly with elevation changes. Although the soil acidity did not differ significantly among the three sites, low pH (around 4) could be an important selection factor selecting for acidophilic Acidobacteria and Alphaproteobacteria, which were the most abundant bacterial clones. As the majority of the fungi recovered, both Basidiomycota and Ascomycota, and their relative abundance were most closely associated with the total carbon. Based on the Shannon–Weaver diversity index and ∫-libshuff analysis, the soil at medium elevation contained the highest diversity of bacteria compared with those at high and low elevations. However, it is difficult to predict overall fungal diversity along elevation. The extreme high soil moisture content which may lead to the formation of anaerobic microhabitats in the forest soils potentially reduces the overall bacterial and fungal diversity.     

Some short-lived ruderal plant communities of non-trampled habitats in North Korea

Short-lived plant communities of ruderal habitats in North Korea were studied using the Zürich-Montpellier approach. TheBeckmannio eruciformis-Potentilletum costatae, theDaturo tatulae-Siegesbeckietum pubescentis, theHumulo japonicae-Chenopodietum albi and theCosmo-Humulion japonicae were described as new.     

Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan

The spatial and temporal variability of bacterial communities were determined for the nearshore waters of Lake Michigan, an oligotrophic freshwater inland sea. A freshwater estuary and nearshore sites were compared six times during 2006 using denaturing gradient gel electrophoresis (DGGE). Bacterial composition clustered by individual site and date rather than by depth. Seven 16S rRNA gene clone libraries were constructed, yielding 2717 bacterial sequences. Spatial variability was detected among the DGGE banding patterns and supported by clone library composition. The clone libraries from deep waters and the estuary environment revealed highest overall bacterial diversity. Betaproteobacteria sequence types were the most dominant taxa, comprising 40.2–67.7% of the clone libraries. BAL 47 was the most abundant freshwater cluster of Betaproteobacteria , indicating widespread distribution of this cluster in the nearshore waters of Lake Michigan. Incertae sedis 5 and Oxalobacteraceae sequence types were prevalent in each clone library, displaying more diversity than previously described in other freshwater environments. Among the Oxalobacteraceae sequences, a globally distributed freshwater cluster was determined. The nearshore waters of Lake Michigan are a dynamic environment that experience forces similar to the coastal ocean environment and share common bacterial diversity with other freshwater habitats.     

Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age

The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1–4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease.     

Functional shifts in lake zooplankton communities with hypereutrophication

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Associations between fish assemblages and environmental factors in nearshore habitats of a subtropical estuary

Salinity and inlet distance were the most consistent indicators of species groupings among the 40 most abundant fish species in the Indian River Lagoon (IRL), Florida. In contrast to findings of other studies conducted on small juveniles and forage fishes in the IRL, this study suggested that distributions of the more mobile organisms are influenced more by physical conditions than by biological interactions. Consequently, environmentally-corrected single-species models will be more effective in assessing changes in stock abundance and habitat preferences of mobile species in the IRL. Because of the fluctuations in physical conditions in the IRL and other estuaries, it may be inappropriate to use biologically based methods that rely solely on species interactions to assess fish stocks in those systems.     

The rapid degradation of bisphenol A induced by the response of indigenous bacterial communities in sediment

In the present study, sediment was spiked with bisphenol A (BPA) solution to explore the interaction between indigenous bacterial communities and BPA biodegradation in sediment. Results showed that BPA could be adsorbed to the sediment and then biodegraded rapidly. Biodegradation efficiency of BPA in treatments with 10 and 50 mg/L BPA reached 64.3 and 61.8% on the first day, respectively. Quantitative polymerase chain reaction and denaturing gradient gel electrophoresis analysis indicated that BPA affected the densities, species, and diversities of bacteria significantly. The response of bacterial community to BPA favored BPA biodegradation by promoting the growth of BPA-reducing bacteria and inhibiting other competitors. According to the results of sequencing, Pseudomonas and Sphingomonas played vital roles in the degradation of BPA. They presented over 73% of the original bacterial community, and both of them were promoted by BPA comparing with controls. Laccase and polyphenol oxidase contributed to the degradation of BPA and metabolic intermediates, respectively. This paper illustrates the rapid biodegradation of BPA induced by the response of indigenous bacterial communities to the BPA stress, which will improve the understandings of BPA degradation in sediment.