5S rRNA fingerprints of marine bacteria, halophilic archaea and natural prokaryotic assemblages along a salinity gradient

Natural prokaryotic assemblages from two multi-pond solar salterns and pure cultures of both marine bacteria and halophilic archaea were analyzed and compared by electrophoretic analysis of 5S rRNAs. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied. The culture-independent, PCR-free, fingerprinting analysis covered two objectives: (i) to compare natural assemblages among them and with results previously obtained through a PCR-dependent approach and (ii) to estimate the in situ relevance of those prokaryotic groups obtained with classical culture methodologies. Natural assemblages were analyzed through cluster analysis of quantitative 5S rRNA band patterns. The resulting groups were in accordance with environmental parameters (i.e., NaCl concentration) and with the clustering obtained after a PCR-dependent approach, showing the formation of three salinity-based groups of samples (<10%, 10-25% and >25% salinity). Similarities between the laboratory strains tested and dominant community members were studied by comparing 5S rRNA band patterns. The lack of match obtained after cluster analysis indicated that the prokaryotic populations relevant in the ponds below 25% salinity were neither Flavobacteria nor haloarchaeal strains belonging to the genera Halococcus, Haloarcula and Halobacterium. Members of Proteobacteria and Gram-positive bacteria were found to match bands in these samples. The 5S rRNA fingerprint from the dominant community members in the ponds above 30% salinity did not fit any of the cultured halophilic archaea studied, in agreement with earlier PCR results. This is consistent with a greater bias introduced by culture-dependent methods than by those based on PCR, especially for archaeal populations.     

Effects of cutting Phragmites australis along an inundation gradient, with implications for managing reed encroachment in a South African estuarine lake system

Substantive encroachment of Phragmites australis (common reed) occurred since the 1970s in the Wilderness estuarine lakes, a National Park and Ramsar site. Cutting of reeds in late summer as a means of controlling reed encroachment was investigated under three different inundation regimes, termed ‘wet zone’ (permanently inundated), ‘moist zone’ (infrequently inundated) and ‘dry zone’ (rarely inundated). The effects of a single annual cut were furthermore compared to those of two successive annual cuts. Without cutting, wet zones had thinner and shorter, but more abundant reeds than drier zones. Cutting in dry and moist zones resulted after one year in more, but shorter and thinner reeds, whereas in wet zones reeds were almost eliminated. After two years, reeds in wet zones had not recovered from the first annual cut. In moist and dry zones, a second annual cut did not result in amplified detrimental effects on reeds. Throughout the experiment, moisture zone was the factor with the largest effect, cutting had the second largest impact, and inter-annual variation was relatively unimportant. We have demonstrated that cutting alone has minimal long-term effect on above-ground reed biomass, whereas reed growth and survivorship can be strongly suppressed through cutting in late-summer in conjunction with inundation with moderately saline water (5.0–7.5 g kg⁻¹). Cut reeds must remain completely inundated for at least a four-week period, or else emerging shoots should be re-cut below the water level. Cut material should be removed from the treatment site. Whenever possible, cutting and inundation should be undertaken to coincide with periods when salinity levels of surface waters are higher. It is foreseen that reed management in the Wilderness Lakes would have positive effects on other biota by countering progression towards single species domination of wetland plant communities and reinstating exposed sandbanks which are extensively utilised by resident and migratory waterbirds.     

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.     

Mapping changes in tidal wetland vegetation composition and pattern across a salinity gradient using high spatial resolution imagery

Detailed vegetation mapping of wetlands, both natural and restored, can offer valuable information about vegetation diversity and community structure and provides the means for examining vegetation change over time. We mapped vegetation at six tidal marshes (two natural, four restored) in the San Francisco Estuary, CA, USA, between 2003 and 2004 using detailed vegetation field surveys and high spatial-resolution color-infrared aerial photography. Vegetation classes were determined by performing hierarchical agglomerative clustering on the field data collected from each tidal marsh. Supervised classification of the CIR photography resulted in vegetation class mapping accuracies ranging from 70 to 92%; 10 out of 12 classification accuracies were above 80%, demonstrating the potential to map emergent wetland vegetation. The number of vegetation classes decreased with salinity, and increased with size and age. In general, landscape diversity, as measured by the Shannon’s diversity index, also decreased with salinity, with an exception for the most saline site, a newly restored marsh. Vegetation change between years is evident, but the differences across sites in composition and pattern were larger than change within sites over two growing seasons.     

Comparative study of periphyton colonisation on common reed (Phragmites australis) and artificial substrate in a shallow lake,Manyas, Turkey

Hydrobiologia - Colonisation of epiphytic algae on the common reed (Phragmites australis) and on glass slides were studied during a twenty-four week exposure period in a shallow, turbid lake,...     

Temporal and spatial macrofaunal community changes along a salinity gradient in seagrass meadows of Akkeshi-ko estuary and Akkeshi Bay,northern Japan

Changes in water clarity (secchi disc transparency) in relation to the presence/absence of introduced, exotic fish, including rudd (Scardinius erythrophthalmus), tench (Tinca tinca), perch (Perca fluviatilis), brown bullhead catfish (Ameiurus nebulosus), goldfish (Carassius auratus), and koi carp (Cyprinus carpio) were determined for 49 small, North Island, New Zealand lakes. There was a negative association between water clarity and the presence of exotic fish independent of lake depth. Moreover, a ‘before-and-after’ comparison and examination of case-studies indicated that introductions of exotic fish reduce water clarity. The number of species introduced affected the relationship between lake depth and water clarity but the specific role of each species could not be distinguished because most of the lakes (83%) contained more than one exotic fish species. A model incorporating the known mechanisms by which planktivorous, benthivorous and herbivorous fish can influence water clarity in lakes showed that control over just one species or feeding guild may not result in an improvement in water clarity because of the additive and synergistic effects of different species on lake trophic processes. Handling editor J. Cambray     

Macroinvertebrate community structure across a wetland hydroperiod gradient in southern New Hampshire,USA

We conducted a field study to examine the influence of hydroperiod and concomitant changes in abiotic (wetland size, pH, conductivity, dissolved oxygen and water temperature) and biotic (predatory fish presence) characteristics on macroinvertebrate communities in isolated wetlands in southern New Hampshire. Invertebrates were sampled using dipnet sweeps in 42 wetlands with short (<4 months), intermediate (4–11 months) or long (permanent) hydroperiods in 1998 and 1999. We found that invertebrate genera richness, and to a lesser degree abundance, increased linearly along the hydrological gradient, and in response to temperature and dissolved oxygen. Relative abundance of genera also differed markedly with respect to hydroperiod. Most notably, invertebrate communities changed from Acilius-dominated communities to Notonecta-dominated communities. Invertebrate relative abundances in permanent wetlands also differed with respect to the occurrence of predatory fish. Some genera (e.g., Libellula, and Dytiscus) were more likely to occur in permanent wetlands without fish, whereas other genera (e.g., Buena, and Basiaeshna) were more likely to occur in wetlands with predatory fish. Because aquatic invertebrate communities differed markedly with respect to wetland hydroperiod, and in relation to the occurrence of predatory fish, it is essential to retain a diversity of wetlands in the landscape to ensure the long-term persistence of aquatic invertebrate biodiversity.     

Pressure gradients along whole culms and leaf sheaths, and other aspects of humidity-induced gas transport in Phragmites australis

Emergent aquatic macrophytes growing in waterlogged anaerobic sediments overlain by deep water require particularly efficient ventilating systems. In Phragmites australis (Cav.) Trin. ex Steud, pressurized gas flows, generated by humidity-induced diffusion of air into leaf sheaths, enhance oxygen transport to below-ground parts and aid in the removal of respiratory CO2 and sediment-generated CO2 and methane. Although modelling and flow measurements have pointed to the probable involvement of all leaf sheaths in the flow process and the development of pressure gradients along the whole lengths of living culm and leaf sheaths, direct measurements of pressure gradients have never been reported. The aim of this study was to search for pressure gradient development in Phragmites culms and leaf sheaths and to determine their magnitudes and distribution. In addition, dynamic (with gas flow) and static pressures (no flow condition) and their relationship to flows, leaf sheath areas, and living-to-dead culm ratios were further investigated. Dynamic pressures (DeltaPd) recorded in the pith cavities of intact (non-excised) leafy culms, pneumatically isolated from the below-ground parts and venting through an artificial bore-hole near the base, revealed a curvilinear gradient of pressure 'asymptoting' towards the tips of the culms. Similarly, DeltaPd in upper and lower parts of leaf sheaths increased with distance from the base of the culm, with values in the upper parts always being greater. Curvilinear gradients of pressure were also found along pneumatically isolated individual leaf sheaths, but radial channels linking the leaf sheath aerenchyma with the pith cavity of the culm appeared to offer little resistance to flow. In keeping with predictions, static pressure differentials (DeltaPs) achieved in intact and excised culms and single leaf sheaths on intact culms proved to be relatively independent of leaf sheath area, whereas the potential for developing convective flows (pressure-driven flows) increased with increasing leaf sheath area. As measured by the ventilating coefficient [1-(DeltaPd/(DeltaPs)] the old dead (efflux) to living (influx) culm ratio of 1:12 compared with 1:25 raised ventilating efficiency from 31% to 71%, giving flows per tall culm into the rhizome system of c. 2.8 cm3 and 6.5 cm3 min-1, respectively. It was concluded that dynamic pressure gradients probably extend along the whole length of the leafy culms and leaf sheaths of Phragmites and that all leaf sheaths and all exposed points along the leaf sheaths can contribute convective gas-flow to the rhizome system.     

Salt tolerance and osmotic adjustment of Spartina alterniflora (Poaceae) and the invasive M haplotype of Phragmites australis (Poaceae) along a salinity gradient

An invasive variety of Phragmites australis (Poaceae, common reed), the M haplotype, has been implicated in the spread of this species into North American salt marshes that are normally dominated by the salt marsh grass Spartina alterniflora (Poaceae, smooth cordgrass). In some European marshes, on the other hand, Spartina spp. derived from S. alterniflora have spread into brackish P. australis marshes. In both cases, the non-native grass is thought to degrade the habitat value of the marsh for wildlife, and it is important to understand the physiological processes that lead to these species replacements. We compared the growth, salt tolerance, and osmotic adjustment of M haplotype P. australis and S. alterniflora along a salinity gradient in greenhouse experiments. Spartina alterniflora produced new biomass up to 0.6 M NaCl, whereas P. australis did not grow well above 0.2 M NaCl. The greater salt tolerance of S. alterniflora compared with P. australis was due to its ability to use Na(+) for osmotic adjustment in the shoots. On the other hand, at low salinities P. australis produced more shoots per gram of rhizome tissue than did S. alterniflora. This study illustrates how ecophysiological differences can shift the competitive advantage from one species to another along a stress gradient. Phragmites australis is spreading into North American coastal marshes that are experiencing reduced salinities, while Spartina spp. are spreading into northern European brackish marshes that are experiencing increased salinities as land use patterns change on the two continents.     

Microcystin-LR, a cyanobacterial toxin, induces growth inhibition and histological alterations in common reed (Phragmites australis) plants regenerated from embryogenic calli

The aim of this study was to establish the histological effects of exposure to microcystin-LR (MC-LR), a cyanotoxin, on axenic Phragmites australis plantlets. Plantlets were regenerated from embryogenic reed calli by tissue culture methods. Microcystin-LR inhibited the growth and development of embryogenic calli and the growth of reed plantlets. The 50% plantlet growth inhibitory concentration value (IC50) of MC-LR was 12 microg ml(-1) (12.07 microM) on mineral medium and 36 microg ml(-1) (36.22 microM) on Murashige-Skoog medium. In the case of roots, the IC50 value was 4.1 microg ml(-1) (4.12 microM) on both media. Microcystin-LR induced aerenchyma obturation, altered lignification of cell walls in the axial organs, root necrosis and the capture of lateral or adventitious roots in the tissues of axial organs of reed plantlets. Cyanotoxin induced the premature development of lateral roots, root coalescence and early aerenchyma formation. Our data suggest that microcystin-LR, a cyanotoxin, induced developmental and histological alterations leading to growth inhibition of reed, and the induced harms have an impact on understanding reed decay in eutrophic fresh waters.     

The endophytic fungal communities associated with the leaves and roots of the common reed (Phragmites australis) in Lake Trasimeno (Perugia,Italy) in declining and healthy stands

We surveyed the fungal endophytes in the leaves and roots of Phragmites australis plants along a gradient of reed decline at Lake Trasimeno (central Italy) in Oct. 2010. An integrated approach consisting of cultivation and molecular identification was used. Endophytes were recovered from 61.59 % of the samples, with a total of 1 541 isolates. On the basis of a molecular analysis of the rDNA Internal Transcribed Spacer (ITS) region, 25 operational taxonomic units (OTUs) were identified. Fusarium sp. (OTU 21) and Gibberella moniliformis (OTU 1) were the most frequently isolated fungi. Comparisons of the leaf and root samples demonstrated spatial heterogeneity in the endophyte assemblages among the plant parts and sites. In this study, we have shown that reed plants in different states of decline harbour different endophytic communities. This finding may help to understand the very complex scenario of reed die-back.     

Soil microbial diversity and community structure across a climatic gradient in western Canada

Soil microbial functional diversity was assessed along a climatic gradient in Western Canada. Mineral soil samples were collected from jack pine (Pinus banksiana Lamb.) stands along an 800km transect between Prince Albert, Saskatchewan and Gillam, Manitoba. Microbial communities were isolated from the soil samples, washed and inoculated into wells of Gram-negative Biolog microplates. Optical density values were used to calculate Shannon diversity indices and to perform principal component analysis. Colour development rank plots (CDR) were created by expressing optical density values as a percentage of total colour development and plotting the wells in descending order. Soil microbial functional diversity decreased with increasing latitude and correlated positively with measures of atmospheric temperature and pH. Soil microbial diversity may be lower in northern sites due to decreased productivity, nutrient limitation and higher acidity. CDR plots are consistent with a trend of increasing environmental harshness moving north along the transect.     

Evidence of elemental homeostasis in fine root and leaf tissues of saplings across a fertility gradient in tropical montane forest in Hainan,China

Plant and Soil - For plants, elemental nutrients are important belowground resources that sustain growth and survival. To understand how tropical plant nutrient status responds to environmental...     

Matching molecular diversity and ecophysiology of benthic cyanobacteria and diatoms in communities along a salinity gradient

The phylogenetic diversity of oxygenic phototrophic microorganisms in hypersaline microbial mats and their distribution along a salinity gradient were investigated and compared with the halotolerances of closely related cultivated strains. Segments of 16S rRNA genes from cyanobacteria and diatom plastids were retrieved from mat samples by DNA extraction and polymerase chain reaction (PCR), and subsequently analysed by denaturing gradient gel electrophoresis (DGGE). Sequence analyses of DNA from individual DGGE bands suggested that the majority of these organisms was related to cultivated strains at levels that had previously been demonstrated to correlate with characteristic salinity responses. Proportional abundances of amplified 16S rRNA gene segments from phylogenetic groupings of cyanobacteria and diatoms were estimated by image analysis of DGGE gels and were generally found to correspond to abundances of the respective morphotypes determined by microscopic analyses. The results indicated that diatoms accounted for low proportions of cells throughout, that the cyanobacterium Microcoleus chthonoplastes and close relatives dominated the communities up to a salinity of 11% and that, at a salinity of 14%, the most abundant cyanobacteria were related to highly halotolerant cultivated cyanobacteria, such as the recently established phylogenetic clusters of Euhalothece and Halospirulina . Although these organisms in cultures had previously demonstrated their ability to grow with close to optimal rates over a wide range of salinities, their occurrence in the field was restricted to the highest salinities investigated.     

Fish assemblages across a vegetation gradient in a restoring tidal freshwater wetland: diets and potential for resource competition

Marsh habitats have been the focus of recent worldwide restoration efforts due to their degradation and destruction as a result of human development. We assessed fish resource use at a naturally restoring marsh (Liberty Island, California, USA) by comparing diet composition, stomach fullness, normalized stomach weight, and diet overlap across a vegetation gradient. Fish were collected using gill nets and fyke nets at six sites during spring 2010, summer 2011 and winter 2012. We analyzed 392 stomachs from the eleven most abundant species collected. Prey composition and biomass varied seasonally for all fish species, but there were no notable differences across sites or seasons for stomach fullness or normalized stomach weight for most fish species. Results from non-metric multidimensional scaling (NMDS) and two-way analysis of similarities (ANOSIM) indicated minimal diet overlap between species (R?=?0.633, p?=?0.001) and seasons (R?=?0.413, p?=?0.001). Seasonal habitat and resource use across the vegetation gradient was species-specific. Small but significant spatial diet differences were detected for inland silverside, striped bass and bigscale logperch. Delta smelt exhibited seasonal diet differences by shifting from chironomids and zooplankton during spring, to amphipods and zooplankton during winter. More generally, fish maintained stomach fullness across all sites and seasons while maintaining minimal dietary overlap. Our study emphasizes the importance of tidal marshes as feeding habitat for several fish species, including the endangered delta smelt.     

Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient

To determine whether the distribution of estuarine ammonia-oxidizing bacteria (AOB) was influenced by salinity, the community structure of betaproteobacterial ammonia oxidizers (AOB) was characterized along a salinity gradient in sediments of the Ythan estuary, on the east coast of Scotland, UK, by denaturant gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rRNA gene fragments. Ammonia-oxidizing bacteria communities at sampling sites with strongest marine influence were dominated by Nitrosospira cluster 1-like sequences and those with strongest freshwater influence were dominated by Nitrosomonas oligotropha-like sequences. Nitrosomonas sp. Nm143 was the prevailing sequence type in communities at intermediate brackish sites. Diversity indices of AOB communities were similar at marine- and freshwater-influenced sites and did not indicate lower species diversity at intermediate brackish sites. The presence of sequences highly similar to the halophilic Nitrosomonas marina and the freshwater strain Nitrosomonas oligotropha at identical sampling sites indicates that AOB communities in the estuary are adapted to a range of salinities, while individual strains may be active at different salinities. Ammonia-oxidizing bacteria communities that were dominated by Nitrosospira cluster 1 sequence types, for which no cultured representative exists, were subjected to stable isotope probing (SIP) with 13C-HCO3-, to label the nucleic acids of active autotrophic nitrifiers. Analysis of 13C-associated 16S rRNA gene fragments, following CsCl density centrifugation, by cloning and DGGE indicated sequences highly similar to the AOB Nitrosomonas sp. Nm143 and Nitrosomonas cryotolerans and to the nitrite oxidizer Nitrospira marina. No sequence with similarity to the Nitrosospira cluster 1 clade was recovered during SIP analysis. The potential role of Nitrosospira cluster 1 in autotrophic ammonia oxidation therefore remains uncertain.     

Regional and local patterns of ectomycorrhizal fungal diversity and community structure along an altitudinal gradient in the Hyrcanian forests of northern Iran

? Altitudinal gradients strongly affect the diversity of plants and animals, yet little is known about the altitudinal effects on the distribution of microorganisms, including ectomycorrhizal fungi. ? By combining morphological and molecular identification methods, we addressed the relative effects of altitude, temperature, precipitation, host community and soil nutrient concentrations on species richness and community composition of ectomycorrhizal fungi in one of the last remaining temperate old-growth forests in Eurasia. ? Molecular analyses revealed 367 species of ectomycorrhizal fungi along three altitudinal transects. Species richness declined monotonically with increasing altitude. Host species and altitude were the main drivers of the ectomycorrhizal fungal community composition at both the local and regional scales. The mean annual temperature and precipitation were strongly correlated with altitude and accounted for the observed patterns of richness and community. ? The decline of ectomycorrhizal fungal richness with increasing altitude is consistent with the general altitudinal richness patterns of macroorganisms. Low environmental energy reduces the competitive ability of rare species and thus has a negative effect on the richness of ectomycorrhizal fungi. Because of multicollinearity with altitude, the direct effects of climatic variables and their seasonality warrant further investigation at the regional and continental scales.     

Dramatic changes in ectomycorrhizal community composition, root tip abundance and mycelial production along a stand-scale nitrogen deposition gradient

? Nitrogen (N) availability is known to influence ectomycorrhizal fungal components, such as fungal community composition, biomass of root tips and production of mycelia, but effects have never been demonstrated within the same forest. ? We measured concurrently the abundance of ectomycorrhizal root tips and the production of external mycelia, and explored the changes in the ectomycorrhizal community composition, across a stand-scale N deposition gradient (from 27 to 43 kg N ha?1 yr?1) at the edge of a spruce forest. The N status was affected along the gradient as shown by a range of N availability indices. ? Ectomycorrhizal root tip abundance and mycelial production decreased five and 10-fold, respectively, with increasing N deposition. In addition, the ectomycorrhizal fungal community changed and the species richness decreased. The changes were correlated with the measured indices of N status, in particular N deposition and N leaching. ? The relationship between the altered ectomycorrhizal community, root tip abundance and mycelial production is discussed in the context of the N parameters. We suggest that increased N deposition to forests will cause large changes in ectomycorrhizal fungal community structure and functioning, which, in turn, may result in reduced N uptake by roots and fungi, and increased losses of N by leaching.