Patterns of fungal diversity and composition along a salinity gradient

Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes—a salt, brackish and freshwater marsh—in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution.     

Virioplankton community structure along a salinity gradient in a solar saltern

The virioplankton community structure along a salinity gradient from near seawater (40 per thousand ) to saturated sodium chloride brine (370 per thousand ) in a solar saltern was investigated by pulsed-field gel electrophoresis. Viral populations with genome sizes varying from 10 kb to 533 kb were detected. The viral community structure changed along the salinity gradient. Cluster analysis of the viral genome-banding pattern resulted in two main clusters. The virioplankton diversity within the samples with salinity from 40 per thousand to 150 per thousand was on the same cluster of a cladogram. The other group consisted of virioplankton from samples with salinity above 220 per thousand. The virioplankton diversity in the different samples was calculated using the Shannon index. The diversity index demonstrated an increase in diversity in the samples along the gradient from 40 per thousand to 150 per thousand salinity, followed by a decrease in the diversity index along the rest of the salinity gradient. These results demonstrate how viral diversity changes from habitats that are considered one of the most common (seawater) to habitats that are extreme in salt concentrations (saturated sodium brine). The diversity index was highest in the environments that lie in between the most extreme and the most common.     

The importance of facilitation in the zonation of shrubs along a coastal salinity gradient

Question: What are the interactive roles of abiotic stress and plant interactions in mediating the zonation of the shrub Tamarix chinensis along a salinity gradient? Location: Yellow River estuary (37°46′N, 119°09′E), northeast China. Methods: We surveyed the zonation of T. chinensis along a salinity gradient and quantified its salt tolerance using a pot experiment. In two field experiments, we transplanted T. chinensis seedlings into salt marsh, transitional zone and upland habitats, manipulated neighbours and quantified survivorship and biomass to examine neighbour effects. We also quantified vegetation effects on abiotic conditions in each zone. Results: Tamarix chinensis dominated the transitional zone, but was absent in upland and salt marsh habitats. In the pot experiment, T. chinensis grew well in freshwater treatments, but was inhibited by increasing salinity. Field experiments revealed that competition from neighbours limited T. chinensis growth in the uplands, while T. chinensis transplants were limited, with or without neighbours, in the salt marsh by high soil salinity. In the transitional zone, however, T. chinensis transplants performed better with than without neighbours. Vegetation removal significantly elevated soil salinity in the transitional zone, but not in other zones. Conclusions: Competition, facilitation and abiotic stress are all important in mediating the zonation of T. chinensis. Within its physiological stress tolerance range, or fundamental niche, it is limited by plant competition in low salinity habitats, and facilitated by neighbours in high salt stress habitats, but cannot survive in salt marshes having salinities above its salt stress tolerance limit. Our results have implications for understanding the relationships between facilitation and stress gradients.     

Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China

The influence of altitude and salinity on bacterioplankton community composition (BCC) in 16 high-mountain lakes located at altitudes of 2,817 to 5,134 m on the Eastern Qinghai-Xizang (Tibetan) Plateau, China, spanning a salinity gradient from 0.02% (freshwater) to 22.3% (hypersaline), was investigated. Three different methods, fluorescent in situ hybridization, denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing, and reverse line blot hybridization (RLB) with probes targeting 17 freshwater bacterial groups, were used for analysis of BCC. Furthermore, the salt tolerances of 47 strains affiliated with groups detected in or isolated from the Tibetan habitats were investigated. Altitude was not found to influence BCC significantly within the investigated range. Several groups of typical freshwater bacteria, e.g., the ACK-M1 cluster and the Polynucleobacter group, were detected in habitats located above 4,400 m. Salinity was found to be the dominating environmental factor controlling BCC in the investigated lakes, resulting in only small overlaps in the BCCs of freshwater and hypersaline lakes. The relative abundances of different classes of Proteobacteria showed a sharp succession along the salinity gradient. Both DGGE and RLB demonstrated that a few freshwater bacterial groups, e.g., GKS98 and LD2, appeared over wide salinity ranges. Six freshwater isolates affiliated with the GKS98 cluster grew in ecophysiological experiments at maximum salinities of 0.3% to 0.7% (oligosaline), while this group was detected in habitats with salinities up to 6.7% (hypersaline). This observation indicated ecologically significant differences in ecophysiological adaptations among members of this narrow phylogenetic group and suggested ecological significance of microdiversity.     

Microbial community composition and trophic role along a marked salinity gradient in Laguna Puilar,Salar de Atacama,Chile

The geological, hydrological and microbiological features of the Salar de Atacama, the most extensive evaporitic sedimentary basin in the Atacama Desert of northern Chile, have been extensively studied. In contrast, relatively little attention has been paid to the composition and roles of microbial communities in hypersaline lakes which are a unique feature in the Salar. In the present study biochemical, chemical and molecular biological tools were used to determine the composition and roles of microbial communities in water, microbial mats and sediments along a marked salinity gradient in Laguna Puilar which is located in the “Los Flamencos” National Reserve. The bacterial communities at the sampling sites were dominated by members of the phyla Bacteroidetes, Chloroflexi, Cyanobacteria and Proteobacteria. Stable isotope and fatty acid analyses revealed marked variability in the composition of microbial mats at different sampling sites both horizontally (at different sites) and vertically (in the different layers). The Laguna Puilar was shown to be a microbially dominated ecosystem in which more than 60% of the fatty acids at particular sites are of bacterial origin. Our pioneering studies also suggest that the energy budgets of avian consumers (three flamingo species) and dominant invertebrates (amphipods and gastropods) use minerals as a source of energy and nutrients. Overall, the results of this study support the view that the Salar de Atacama is a heterogeneous and fragile ecosystem where small changes in environmental conditions may alter the balance of microbial communities with possible consequences at different trophic levels.     

Plasma homeostasis and cloacal urine composition inCrocodylus porosus caught along a salinity gradient

Summary Juveniles of the Estuarine or Saltwater Crocodile,Crocodylus porosus, maintain both osmotic pressure and plasma electrolyte homeostasis along a salinity gradient from fresh water to the sea. In fresh water (FW) the cloacal urine is a clear solution rich in ammonium and bicarbonate and containing small amounts of white precipitated solids with high concentrations of calcium and magnesium. In salt water (SW) the cloacal urine has a much higher proportion of solids, cream rather than white in colour, which are the major route for excretion of potassium in addition to calcium and magnesium. Neither liquid nor solid fractions of the cloacal urine represent a major route for excretion of sodium chloride. The solids are urates and uric acid, and their production probably constitutes an important strategy for water conservation byC. porosus in SW. These data, coupled with natural history observations and the recent identification of lingual salt glands, contribute to the conclusion thatC. porosus is able to live and breed in either fresh or salt water and may be as euryhaline as any reptile.     

Fungal community composition shifts along a leaf degradation gradient in a European beech forest

Aims

The fungal communities in living and decomposed leaves of European Beech (Fagus sylvatica) were compared to identify the phyllosphere fungi involved in litter decomposition at a site in Bavaria, Germany.

Methods

New primers were designed to cover a broad range of fungal ribosomal DNA sequence diversity. Following ‘environmental PCR’, clone libraries from each of five samples of living leaves (surface-sterilized and untreated), freshly fallen, initially and highly decomposed leaves, were screened using RFLP fingerprinting.

Results

Statistical analysis (ANOSIM) revealed that the fungal communities colonizing living (a) and initially decomposed leaves (c) significantly differed between each other and from freshly fallen (b) and highly decomposed leaves (d). Fungal assemblages of a and d were statistically indistinguishable from each other and from the endophyllous fungal community in living leaves.

Conclusions

The results showed that endophyllous fungi play a role throughout the whole decomposition process of beech leaf litter. Therefore, clarification of the life cycle of certain endophytic and/or soil fungi may only be achieved by considering both phyllosphere and soil habitats.     

Methane emissions along a salt marsh salinity gradient

The seasonal flux of methane to the atmosphere was measured at three salt marsh sites along a tidal creek. Average soil salinities at the sites ranged from 5 to 17 ppt and fluxes ranged from below detection limits (less than 0.3 mgCH₄ m^-2 d^-1) to 259 mgCH₄ m^-2 d^-1. Annual flux to the atmosphere was 5.6 gCH₄ m^-2 from the most saline site, 22.4 gCH₄ m^-2 from the intermediate site, and 18.2 gCH₄ m^-2 from the freshest of the three sites. Regression of the amount of methane in the soil with flux indicates that changes in this soil methane can account for 64% of the observed variation in flux. Data on pore water distributions of sulfate suggests that the activity of sulfate reducing bacteria is a primary control on methane flux in these transitional environments. Results indicate that relatively high emissions of methane from salt marshes can occur at soil salinities up to approximately 13 ppt. When these data are combined with other tidal marsh studies, annual CH₄ flux to the atmosphere shows a strong negative correlation with the long term average soil salinity over a range from essentially fresh water to 26 ppt.     

Aboveground plant community and seed bank composition along an invasion gradient

Invasive plants can reduce plant diversity and abundance in native grassland communities; however, the effect on the native seed bank is less clear. The objective of this study was to assess the effects of invasion by the exotic grass old world bluestem (OWB; Bothriochloa spp.) on native aboveground plant species composition and seed bank diversity and abundance (i.e., cover, density). In this central Great Plains grassland, OWB invasion had differential effects on native diversity and abundance of both aboveground and seed bank plant communities. Native plant species diversity and cover showed a steep decline as OWB cover increased. No change in native seed density or richness was observed in response to OWB invasion, however, OWB seed density increased with increasing invasion, thus increasing total seed density. Our results indicate that as OWB invasion increases, the native plant community decreases in diversity and abundance. Although, no effect on native seed bank diversity and density was observed in this study, as native seeds are lost through a loss of native species in the plant communities, native seed bank diversity and density is expected to decline.     

Land use impacts on stream community composition and concordance along a natural stress gradient

Most ecosystems are subjected to multiple stressors derived from natural and anthropogenic sources and community responses to human disturbance in naturally stressful habitats may differ from those in more benign habitats. We examined the influence of a natural (geology-driven acidity) vs. human-induced stress (land drainage) and their interaction on the composition and concordance of stream diatom, bryophyte and invertebrate communities. To account for differing drainage impacts in circumneutral (sedimentation) and naturally acid (reduced pH and increased metal concentrations) streams we investigated concordance in three groups of streams: reference (circumneutral and naturally acidic reference), circumneutral (reference and drained) and naturally acidic (reference and drained) streams. We expected diatoms to respond more strongly to anthropogenic acidification and more weakly to sedimentation compared to bryophytes and invertebrates. We expected overall strong concordance among the three taxonomic groups, but especially so in reference streams. All three organism groups had distinct species composition in naturally acidic vs. circumneutral streams. Concordance between communities was overall strong, especially so in the reference streams. All groups responded to drainage disturbance in both types of streams. Invertebrates were slightly less responsive to increased acidification in the naturally acidic streams but were more affected by sedimentation in the circumneutral streams than were the other two groups. The natural stressor affected communities more than the anthropogenic stressors. Naturally stressed communities were affected by an anthropogenic stressor as much as those in more benign habitats, although the additional stressor was similar to the initial stress (further reduction of stream pH). Naturally acid streams may need special concern in bioassessment because models based on circumneutral reference sites will likely produce biased predictions for these streams.     

Assessing avian diversity and community composition along a successional gradient in traditional Lacandon Maya agroforests

Evidence regarding the ability of agroforests to conserve biological diversity has been mixed; they tend to maintain avian communities with species richness similar to that of undisturbed forest ecosystems but generally do not completely preserve community composition. Using a combination of occupancy modeling and non-metric multidimensional scaling on point-count data, we assessed changes in avian community diversity and composition along a successional gradient in traditional Lacandon Maya agroforests and compared them to protected areas in the region. Bird species richness and diversity in Lacandon agroforests peaked in early secondary forest stages. These agroforests' mean Shannon–Weiner diversity was 5% higher than that of nearby protected areas, but their species richness was similar. Community composition in Lacandon agroforests changed throughout succession, with earlier stages supporting communities distinctly characterized by generalist species, while subsequent, less-intensively managed stages tended to support more forest-dwellers. The bird community observed in even the most mature secondary forest stages in Lacandon agroforests differed from that of undisturbed rain forest ecosystems. These results demonstrate the potential of traditional Lacandon agroforestry management to conserve avian biodiversity while ensuring food sovereignty for farmers. However, because the community composition of early-successional stages was different than later stages, shortening fallow cycles and reducing forest cover to increase agricultural production will limit the species this system can support. This study illustrates the value of incorporating traditional agroecosystems into conservation planning as well as maintaining protected areas, because the latter serve as refugia for species that require undisturbed forest habitat in an agroecological matrix.     

Microbial genetic diversity and ciliate community structure along an environmental gradient in coastal soil

We investigated the microbial genetic diversity and ciliate community in coastal soil from five sites with an environmental gradient using denaturing gradient gel electrophoresis (DGGE), gene sequencing and the Ludox–QPS method. The analyses of both the 16S ribosomal RNA (rRNA) gene and 18S rRNA gene DGGE resulted in equal or even a higher number of bands found in the samples taken from the high-salinity sites IV and V than in those taken from the low-to-moderate-salinity sites I–III. Cluster analysis of both DGGE profiles classified the five sites into three main groups (sites I, II and III and IV and V), which corresponded well to the analysis of environmental factors. There were 13 species observed at site I, three species at site II and nine species at site III, while no active ciliates were observed at the high-salinity sites IV and V. By contrast, the ciliate-specific DGGE revealed a higher number of bands in the samples taken from the high-salinity soil. Furthermore, gene sequencing suggested that the ciliates in the high-salinity soil comprised forms originating not only from soil but also from marine environments. The data indicate that saline soil may maintain a high diversity of ciliates and soil salinity might be the most influential factor regulating the community structure of ciliates.     

Bacterial diversity,community structure and potential growth rates along an estuarine salinity gradient

Very little is known about growth rates of individual bacterial taxa and how they respond to environmental flux. Here, we characterized bacterial community diversity, structure and the relative abundance of 16S rRNA and 16S rRNA genes (rDNA) using pyrosequencing along the salinity gradient in the Delaware Bay. Indices of diversity, evenness, structure and growth rates of the surface bacterial community significantly varied along the transect, reflecting active mixing between the freshwater and marine ends of the estuary. There was no positive correlation between relative abundances of 16S rRNA and rDNA for the entire bacterial community, suggesting that abundance of bacteria does not necessarily reflect potential growth rate or activity. However, for almost half of the individual taxa, 16S rRNA positively correlated with rDNA, suggesting that activity did follow abundance in these cases. The positive relationship between 16S rRNA and rDNA was less in the whole water community than for free-living taxa, indicating that the two communities differed in activity. The 16S rRNA:rDNA ratios of some typically marine taxa reflected differences in light, nutrient concentrations and other environmental factors along the estuarine gradient. The ratios of individual freshwater taxa declined as salinity increased, whereas the 16S rRNA:rDNA ratios of only some typical marine bacteria increased as salinity increased. These data suggest that physical and other bottom-up factors differentially affect growth rates, but not necessarily abundance of individual taxa in this highly variable environment.     

Experimental insights into the importance of ecologically dissimilar bacteria to community assembly along a salinity gradient

The response of local communities to marine–freshwater transitions and the processes that underlie community assembly are unclear, particularly with respect to bacteria that differ in their life strategies. Here, we implemented a transplant experiment where bacterioplankton from three regions of the Baltic Sea with differing salinities (～3, 7 and 28 psu) were exposed to each other's environmental conditions. We found that habitat specialists were more abundant than generalists after exposure to salinity changes, irrespective of their origins. Most specialists that were selected following a salinity change were rare in the starting communities. Selection for generalists, however, was not specifically driven by the recruitment of either rare or abundant members, suggesting that taxon's initial abundance is minor relevant to the growth of generalists. Patterns in phylogenetic relatedness indicated that environmental filtering was the most influential assembly mechanism for specialists, whereas competitive interaction was more important for the assembly of generalists. Altogether, this study shows that large salinity changes promote the establishment of habitat specialists and that deterministic processes vary during community assembly for ecologically dissimilar taxa. We, therefore, propose that distinguishing assembly mechanisms of different community members helps understand and predict community dynamics in response to environmental change.     

Species composition of an ectomycorrhizal fungal community along a local nutrient gradient in a boreal forest

Soil abiotic factors are considered to be important in determining the distribution of ectomycorrhizal (ECM) fungal species; however, there are few field data to support this. Here, we relate ECM species distributions to changes in soil chemistry along a short (90-m), natural nutrient gradient. The ECM community was characterized, using morphological and molecular techniques, in soil samples collected at 10-m intervals. There were pronounced changes in ECM fungal community structure along the transect, with many taxa showing discrete distributions. Although there was a change of host from Pinus to Picea along the gradient, host-specific fungi did not account for the observed change in community structure. Ordination analyses showed that community structure was strongly correlated with soil characteristics, in particular extractable ammonium and base saturation. However, autocorrelation among soil parameters makes it difficult to isolate the effects of individual parameters. The distinctive changes in soil and vegetation along the transect used in this study provided an exceptional opportunity to examine the local-scale impact of natural spatial heterogeneity on an ECM fungal community.     

Nitrification and nitrate reductase activity along a secondary successional gradient

The control of nitrification was studied in a secondary successional gradient on Nantucket Island, MA. It was hypothesized that 1) variability in nitrification along the gradient is controlled by litter primary and secondary chemistry, and 2) differences in nitrate availability along the gradient are reflected in potential nitrate assimilation rates in plant tissue. Nitrification varied significantly (p<0.05) by successional stage in all study sites, generally increasing with successional age. The ratio of nitrification to total N mineralization did not vary significantly between successional stages, suggesting substrate limitation of nitrification. Litter terpenoid resin concentration was a significant predictor (p<0.05) of nitrification rate, but soil %C, %N, and water content also contributed significantly to a stepwise regression model predicting nitrification. Nitrate reductase activity (NRA), an index of potential nitrate assimilation, was measured in an assay species (Schizachyrium scoparium). Although there was no significant correlation with nitrification, NRA was significantly (p<0.05) negatively correlated with soil ammonium concentration along the successional gradient at one site, suggesting that plants preferentially utilized ammonium in this system.     

Arbuscular mycorrhizal fungi alter plant community composition along a grazing gradient in Inner Mongolia Steppe

Arbuscular mycorrhizal fungi (AMF) have a significant influence on plant productivity and diversity in non-grazing grassland. However, the interactive effects between grazing intensity and AMF on plant community composition in natural grassland communities are not well known. We conducted a field experiment that manipulated AMF colonization and grazing intensity to study the impact of AMF suppression on plant community composition and nutrient status over 2 years (2015–2016) with contrasting rainfall levels. We found that AMF root colonization was significantly reduced by the application of the fungicide benomyl as a soil drench. Grazing intensity regulated plant community composition and aboveground biomass mainly by reducing the growth of Leymus chinensis over 2 years. AMF suppression increased the growth of Chenopodium glaucum, but it did not alter other plant species across all grazing intensities. The effects of AMF suppression on plant community composition changed along a grazing gradient considerably between years: AMF suppression increased the biomass of C. glaucum across all grazing intensities in 2015, but slightly increased it in 2016. Interactions between AMF suppression and grazing intensity altered the phosphorus concentration of Stipa grandis and Cleistogenes squarrosa in 2015 but not in 2016. AMF suppression decreased the shoot phosphorus content of L. chinensis but increased that of C. glaucum across all grazing intensities. Our results indicate that grazing intensity substantially alters aboveground community biomass and affects growth of dominant species; AMF by itself have limited effects on plant communities along a grazing gradient in typical steppe.     

Functional traits composition predict macrophytes community productivity along a water depth gradient in a freshwater lake

Functional trait composition of plant communities has been proposed as a helpful key for understanding the mechanisms of biodiversity effects on ecosystem functioning. In this study, we applied a step‐wise modeling procedure to test the relative effects of taxonomic diversity, functional identity, and functional diversity on macrophytes community productivity along water depth gradient. We sampled 42 plots and 1513 individual plants and measured 16 functional traits and abundance of 17 macrophyte species. Results showed that there was a significant decrease in taxonomic diversity, functional identity (i.e., stem dry mass content, leaf [C] and leaf [N]), and functional diversity (i.e., floating leaf, mean Julian flowering date and rooting depth) with increasing water depth. For the multiple‐trait functional diversity (FD) indices, functional richness decreased, while functional divergence increased with water depth gradient. Macrophyte community productivity was strongly determined by functional trait composition within community, but not significantly affected by taxonomic diversity. Community‐weighted means (CWM) showed a two times higher explanatory power relative to FD indices in determining variations in community productivity. For nine of sixteen traits, CWM and FD showed significant correlations with community productivity, although the strength and direction of those relations depended on selected trait. Furthermore, functional composition in a community affected productivity through either additive or opposite effects of CWM and FD, depending on the particular traits being considered. Our results suggested both mechanisms of mass ratio and niche complementarity can operate simultaneously on variations in community productivity, and considering both CWM and FD would lead to a more profound understanding of traits–productivity relationships.     

Prokaryotic aminopeptidase activity along a continuous salinity gradient in a hypersaline coastal lagoon (the Coorong, South Australia)

The relation between climatic parameters (relative air humidity) and the water activity of the Urmia Sea water determines the possible maximum evaporation of the lake. Using the Pitzer thermodynamic approach, the activity of the Urmia Lake water during evaporation was calculated and compared to the present relative air humidity above the water. Present climatic conditions allow the Urmia Sea water to evaporate down to water with activity of 0.55, corresponding to the lowest air humidity measured over the lake. This water activity falls in the range of halite precipitation, while carnalite precipitation starts at somewhat lower (a H₂O = 0.499) point. Our dynamic model predicts that for air humidity as low as 55% (reflecting present climate conditions), the Urmia Sea level may drop to as low as 1270 m (i. e., 1270 m above mean sea level). At that point, the lake water volume will have a volume of 11 km³. For the sake of comparison, at the beginning of 1990, the level of the lake was 1275 m, its volume was 25 km³, and its surface area was 5145 km².