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.     

人工和天然湿地芦苇根际土壤细菌群落结构多样性的比较

为认识人工湿地运行初期根际土壤细菌群落的结构多样性,本研究采用聚合酶链式反应-变性梯度凝胶电泳（PCR-DGGE）的方法,比较了嘉兴石臼漾人工构筑生态湿地和白洋淀天然湿地府河河口区域芦苇根际土壤的细菌群落结构多样性。研究结果显示,嘉兴石臼漾湿地在运行初期（1~1.5年）,根际土壤细菌的物种丰富度已与白洋淀湿地相近,但香农指数和均匀度指数均显著低于白洋淀湿地;随着污染物浓度的降低,土壤细菌群落基因型多样性指数增大。     

Effects of experimental warming and nitrogen enrichment on leaf and litter chemistry of a wetland grass,Phragmites australis

As global climate is warming and the nitrogen cycle accelerates, plants are likely to respond not only by shifting community composition, but also by adjusting traits such as tissue chemistry. We subjected a widespread wetland plant, Phragmites australis, to increased nitrate supply and elevated temperature in enclosures that were established in a littoral permanently submerged freshwater marsh. The nitrogen (N) and phosphorus (P) concentrations in green leaves ranged from 11.4 to 13.8 mg N and from 1.5 to 2.0 mg P g⁻¹ dry mass. While the N concentration changed little in brown litter, the P concentration decreased to 0.53–0.65 mg P g⁻¹ litter dry mass. Neither experimental warming of the water and sediment surface, nor nitrate enrichment during the growing season affected nitrogen or phosphorus concentrations in green leaves. Concentrations of the two major structural carbon compounds in plant litter, cellulose and lignin, were also unaffected, ranging from 32.1 to 34.2% of dry mass for cellulose and from 16.3 to 17.7% of dry mass for lignin. Warming, however, significantly increased the nitrogen concentration of fully brown leaf litter. Thus, temperature appears to be more important than the supply of dissolved N in the water, especially in affecting leaf litter N concentrations in P. australis, even when only water but not air temperature is increased. This result may have implications for decomposition processes and decomposer food webs, which both depend on the quality of plant litter.     

Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer

Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductase-encoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 muM. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program integral-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site.     

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,...     

Shifts in fine root traits within and among species along a fine-scale hydrological gradient

Background and AimsLessons from above-ground trait ecology and resource economics theory may not be directly translatable to below-ground traits due to differences in function, trade-offs and environmental constraints. Here we examine root functional traits within and across species along a fine-scale hydrological gradient. We ask two related questions: (1) What is the relative magnitude of trait variation across the gradient for within- versus among-species variation? (2) Do correlations among below-ground plant traits conform with predictions from resource-economic spectrum theory?MethodsWe sampled four below-ground fine-root traits (specific root length, branching intensity, root tissue density and root dry matter content) and four above-ground traits (specific leaf area, leaf size, plant height and leaf dry matter content) in vascular plants along a fine-scale hydrological gradient within a wet heathland community in south-eastern Australia. Below-ground and above-ground traits were sampled both within and among species.Key ResultsRoot traits shifted both within and among species across the hydrological gradient. Within- and among-species patterns for root tissue density showed similar declines towards the wetter end of the gradient. Other root traits showed a variety of patterns with respect to within- and among-species variation. Filtering of species has a stronger effect compared with the average within-species shift: the slopes of the relationships between soil moisture and traits were steeper across species than slopes of within species. Between species, below-ground traits were only weakly linked to each other and to above-ground traits, but these weak links did in some cases correspond with predictions from economic theory.ConclusionsOne of the challenges of research on root traits has been considerable intraspecific variation. Here we show that part of intraspecific root trait variation is structured by a fine-scale hydrological gradient, and that the variation aligns with among-species trends in some cases. Patterns in root tissue density are especially intriguing and may play an important role in species and individual response to moisture conditions. Given the importance of roots in the uptake of resources, and in carbon and nutrient turnover, it is vital that we establish patterns of root trait variation across environmental gradients.     

Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary

Submarine groundwater discharge to coastal waters can be a significant source of both contaminants and biologically limiting nutrients. Nitrogen cycling across steep gradients in salinity, oxygen and dissolved inorganic nitrogen in sandy 'subterranean estuaries' controls both the amount and form of nitrogen discharged to the coastal ocean. We determined the effect of these gradients on betaproteobacterial ammonia-oxidizing bacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in a subterranean estuary using the functional gene encoding ammonia monooxygenase subunit A ( amoA ). The abundance of β-AOB was dramatically lower in the freshwater stations compared with saline stations, while AOA abundance remained nearly constant across the study site. This differing response to salinity altered the ratio of β-AOB to AOA such that bacterial amoA was 30 times more abundant than crenarchaeal amoA at the oxic marine station, but nearly 10 times less abundant at the low-oxygen fresh and brackish stations. As the location of the brackish mixing zone within the aquifer shifted from landward in winter to oceanward in summer, the location of the transition from a β-AOB-dominated to an AOA-dominated community also shifted, demonstrating the intimate link between microbial communities and coastal hydrology. Analysis of ammonia-oxidizing enrichment cultures at a range of salinities revealed that AOA persisted solely in the freshwater enrichments where they actively express amoA . Diversity (as measured by total richness) of crenarchaeal amoA was high at all stations and time points, in sharp contrast to betaproteobacterial amoA for which only two sequence types were found. These results offer new insights into the ecology of AOA and β-AOB by elucidating conditions that may favour the numerical dominance of β-AOB over AOA in coastal sediments.     

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.     

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.     

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.     

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.     

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...