Surface and Hyporheic Oligochaete Assemblages in a French Suburban Stream

The Chaudanne stream received urban inputs discharged through combined sewer overflows (CSOs). The water quality was not severely impaired, with pollution mainly of organic origin. Oligochaete assemblages were studied in the coarse surface sediments and the hyporheic zone and sampled at four sites on seven occasions during 2000 and 2001. The seasonal distribution of oligochaete assemblages was analyzed by a PCA, the oligochaete species being assigned to functional traits (FTrs). Site 1, located upstream of the CSOs, was characterized by FTrs 1 and 2 (species indicating permeability and those intolerant to water pollution). Below the CSOs, high densities of oligochaetes occurred in the benthic layer of sites 3 and 4, with a predominance of FTr3 (species with tolerance to water pollution). At site 4, FTr4 species (indicative of sludge conditions) constantly predominated in the hyporheic system, but predominated in the benthos only during low stream discharges associated with peaks in CSOs. FTr3 was related to amounts of the oxidized forms of nitrogen, high stream discharges and probably to groundwater upwellings and the sludge tolerant species group (FTr4) was associated with high NH₊⁴ contents. We are now testing the relevance and generalization of this new approach.     

The Effects of an Environmental Flow Release on Water Quality in the Hyporheic Zone of the Hunter River,Australia

Environmental flow releases have been advocated as a useful rehabilitation strategy for improving river condition but assessments of their success have typically focused on surface water quality and biota. In this study, we investigated the impacts of an environmental flow release on water temperature, conductivity, dissolved oxygen, and nitrate concentrations in surface and subsurface (hyporheic) water at upwelling and downwelling zones in three sites along the Hunter River, New South Wales, Australia. We hypothesised that the flow pulse would ‘flush’ the sediments with oxygenated water, stimulating hyporheic microbial activity and nitrification, enhancing nitrate concentrations over time. Surface and subsurface samples were collected before, 7 days after, and 49 days after an environmental flow release of 5000 Ml for a period of 3 days. No lasting effects on dissolved oxygen or conductivity were evident at most sites although dissolved oxygen declined over time at the downwelling site at Bowmans Crossing. At the downwelling zones at all sites, hyporheic nitrate concentrations declined initially following the release, but then rose or leveled off by Day 49. This initial drop in concentration was attributed to flushing of nitrate from the sediments. At two sites, nitrate concentrations had increased by Day 49 in the upwelling zones while at the third site, it fell significantly, associated with very low dissolved oxygen and likely reductive loss of nitrate. Electrical conductivity data indicate that potential inputs of agriculturally enriched groundwater may contribute to the nitrogen dynamics of the Hunter River. This study highlights the spatial heterogeneity that occurs in the hyporheic zone within and among sites of a regulated river, and emphasises the need for multiple-site surveys and an understanding of groundwater dynamics to assess physicochemical responses of the hyporheic zone to environmental flow releases.     

Hyporheic zone hydrology and nitrogen dynamics in relation to the streambed topography of a N-rich stream

The influence of riffle-pool units on hyporheic zone hydrology and nitrogen dynamics was investigated in Brougham Creek, a N-rich agricultural stream in Ontario, Canada. Subsurface hydraulic gradients, differences in background stream and groundwater concentrations of conservative ions, and the movement of a bromide tracer indicated the downwelling of stream water at the head of riffles and upwelling in riffle-pool transitions under base flow conditions. Channel water also flowed laterally into the floodplain at the upstream end of riffles and followed a subsurface concentric flow path for distances of up to 20 m before returning to the stream at the transition from riffles to pools. Differences in observed vs predicted concentrations based on background chloride patterns indicated that the hyporheic zone was a sink for nitrate and a source for ammonium. The removal of nitrate in the streambed was confirmed by the loss of nitrate in relation to co-injected bromide in areas of downwelling stream water in two riffles. Average stream water nitrate-N concentrations of 1.0 mg/L were often depleted to <0.005 mg/L near the sediment-water interface. Consequently, an extensive volume of the hyporheic zone in the streambed and floodplain had a large unused potential for nitrate removal. Conceptual models based mainly on studies of streams with low nutrient concentrations have emphasized the extent of surface-subsurface exchanges and water residence times in the hyporheic zone as important controls on stream nutrient retention. In contrast, we suggest that nitrate retention in N-rich streams is influenced more by the size of surface water storage zones which increase the residence time of channel water in contact with the major sites of rapid nitrate depletion adjacent to the sediment-water interface.     

Importance of transient storage zones for ammonium and phosphate retention in a sandy-bottom Mediterranean stream

1. The ability of hyporheic sediments to exchange water and retain ammonium and phosphate in the Riera Major stream ,North-East Spain, under different discharge conditions was measured by conducting short-term nutrient and chloride additions. 2. The mean exchange coefficients from free-flowing water to the storage zone (k₁) and vice versa (k₂) were 0.82 × 10–4 s^??1 and 7 × 10^??3 s^??1, respectively. The ratio of storage zone cross-sectional area to stream cross-sectional area (A_S/A) averaged 2.8 × 10–2 and was negatively correlated with discharge (r = –0.85, d.f. = 13, P < 0.001). 3. The percentage of hyporheic zone water which came from surface water varied as a function of discharge and hyporheic depth, ranging between 33% and 95% at 25 cm depth, and between 78% and 100% at 10 cm depth. 4. The nutrient retention efficiency in the hyporheic zone at 10 cm depth measured as uptake length (S_wh) was less than 3.3 cm for ammonium and 37 cm for phosphate. Higher nutrient retentions were measured in the sediments at 10 cm depth than at 25 cm, indicating that near-surface sediments were involved more actively in phosphate retention than the deeper hyporheic sediments. The lack of ammonium at any depth of the hyporheic zone showed that ammonium was very rapidly taken up in the surfacial sediments.     

Benthic insects and fish of the Doubs River system: typological traits and the development of a species continuum in a theoretically extrapolated watercourse

Using the distribution patterns of benthic insects (198 species) and fishes ( 29 species) from 11 tributaries and the main channel of the Doubs River drainage basin (French Jura), the authors have tried to establish whether there is an organization of species into discrete, identifiable communities. Principal Component Analysis (PCA) was used to identify whether a continuum existed, and also used to select 50 least-disturbed sites, which were used to define a theoretical watercourse. The density classes of each species were projected on this longitudinal gradient and each species response was characterised by two typological traits: its typological preferendum (tp) and its typological amplitude (ta),thus creating a synthesis of ecological characteristics. In the typological index given in the appendix, the 210 species which form a biological templet are listed in alphabetical order with their tp and ta values. These typological species traits are useful contributions to a database for running waters biomonitoring.     

A Survey of Escherichia coli and Salmonella in the Hyporheic Zone of a Subtropical Stream: Their Bacteriological,Physicochemical and Environmental Relationships

The Hyporheic Zone is among the most important interstitial freshwater habitats, but the relationship between biotic and abiotic factors in this zone remains under-explored. Enterobacteria were expected to be present, but no specific studies had ever confirmed this prediction. The aim of this study was, therefore, to evaluate the total coliforms, Escherichia coli and Salmonella spp. in hyporheic water and to determine the relationship of the physical, chemical and environmental factors at different depths in a rainforest stream. To this end, thirty-six water samples were collected at three depths in sites located in the first, second and third orders in diverse substrates. The total coliforms, Escherichia coli and Salmonella sp. were evaluated in terms of their CFU/ml. In the interstitial samples, coliforms were detected in 100% of the samples. The total coliform counts had higher values at intermediate depths, while E. coli and Salmonella spp. instead had higher values at intermediate and large depths, often reaching or exceeding the values of the surface samples. Our results revealed that Salmonella spp. and the coliforms have different microhabitat preferences. Salmonella spp. and coliform species prefer deposition areas, such as lateral sides of pools, curves and bars, but they have a tendency to distribute into different depths, likely due to temperature differences. Salmonella spp. prefer compact substrata, with fewer fluids passing through and with upwelling areas with lower oxygen inflow. The coliform species showed the opposite preference. Our results suggest that bacterial variation is related to environmental factors and physical-chemical parameters within the HZ and may play a key role in the microbial diversity and distribution in these ecosystems.     

Evaluation of Phosphorus Species in the Bed Sediments of an Atlantic Basin: Bioavailability and Relation with Surface Active Components of the Sediment

In this study, total phosphorus (P) concentrations and P fractions in the bed sediments of the Anllóns River (NW Spain) have been examined. The Lowest Effect Level of the Ontario Sediment Quality Guidelines was trespassed for total phosphorus (600 mg kg^?1) at three out of the five sampling sites which, in addition, showed an average of 43% of bioavailable phosphate. The inorganic P fractions (loosely bound P, redox-sensitive P, metal oxide-bound P, carbonate and apatite P, and residual P) showed that inorganic P was mostly found as metal oxide bound P. The difference between total phosphorus and the sum of the inorganic P forms determined in these extracts is attributed to P associated to organic compounds being solubilized in some of the extractants, and represented in average 58% of total phosphorus. With the exception of loosely bound P, all the P fractions showed significant positive correlations with each other and with total phosphorus.     

Sediments in Marsh Ponds of the Gulf Coast Chenier Plain: Effects of Structural Marsh Management and Salinity

Physical characteristics of sediments in coastal marsh ponds (flooded zones of marsh associated with little vegetation) have important ecological consequences because they determine compositions of benthic invertebrate communities, which in turn influence compositions of waterbird communities. Sediments in marsh ponds of the Gulf Coast Chenier Plain potentially are affected by (1) structural marsh management (levees, water control structures and impoundments; SMM), and (2) variation in salinity. Based on available literature concerning effects of SMM on sediments in emergent plant zones (zones of marsh occasionally flooded and associated with dense vegetation) of coastal marshes, we predicted that SMM would increase sediment carbon content and sediment hardness, and decrease oxygen penetration (O₂ depth) and the silt-clay fraction in marsh pond sediments. Assuming that freshwater marshes are more productive than are saline marshes, we also predicted that sediments of impounded freshwater marsh ponds would contain more carbon than those of impounded oligohaline and mesohaline marsh ponds, whereas C:N ratio, sediment hardness, silt-clay fraction, and O₂ depth would be similar among pond types. Accordingly, we measured sediment variables within ponds of impounded and unimpounded marshes on Rockefeller State Wildlife Refuge, near Grand Chenier, Louisiana. To test the above predictions, we compared sediment variables (1) between ponds of impounded (IM) and unimpounded mesohaline marshes (UM), and (2) among ponds of impounded freshwater (IF), oligohaline (IO), and mesohaline (IM) marshes. An a priori multivariate analysis of variance (MANOVA) contrast indicated that sediments differed between IM and UM marsh ponds. As predicted, the silt-clay fraction and O₂ depth were lower and carbon content, C:N ratio, and sediment hardness were higher in IM than in UM marsh ponds. An a priori MANOVA contrast also indicated that sediments differed among IF, IO, and IM marsh ponds. As predicted, carbon content was higher in IF marsh ponds than in ponds of other impounded marsh types. In contrast to our predictions, C:N ratio and sediment hardness were lowest and silt-clay fraction and O₂ depth were highest in IO and IM marsh ponds. Our results indicated that SMM has affected physical properties of sediments in coastal marsh ponds. Moreover, sediments in IF marsh ponds were affected more so than were those in IO and IM marsh ponds. Our results, in conjunction with those of previous studies, indicated that sediments of marsh ponds and emergent plant zones differed greatly. We predict that changes in pond sediments due to SMM will promote greater epifaunal macroinvertebrate biomass, which in turn should attract larger populations of wintering waterbirds. However, waterbirds that filter or probe soft sediments may be negatively affected by SMM because of the expected decrease in infaunal invertebrate biomass.     

北方农牧过渡带农户农业生产系统模式的生态评价和改良研究

农牧过渡带 (或农牧交错带、半农半牧区 )是指我国传统种植业区和传统畜牧业区的镶嵌结合地带。近世纪以来 ,由于人口剧增 ,垦草种粮面积不断扩大 ,滥垦、过牧、滥樵 ,使草地植被大面积消失 ,沙漠化和荒漠化日趋严重。据报道 ,目前我国北方农牧过渡带荒漠化土地面积已达 1 6 7×10 5ｈａ ,占土地总面积的 5 2 73% ,年增长率约为1 39% [3] 。赤峰市是我国北方农牧过渡带较典型、分布面积较大的地区。该地区资源类型丰富 ,互补优势明显 ,特别是农牧结合的潜力巨大。但长期以来这里区域生态环境恶化加剧 ,导致严重的贫困化。解决这一问题的关…     

Defining types of running waters in Germany using benthic algae: A prerequisite for monitoring according to the Water Framework Directive

The Water Framework Directive of the European Union (EU-WFD) requires the definition of different types of running water which are of relevance when assessing their ecological status. In Germany, 25 close to natural, pristine sampling sites in the Central Highlands and the Central Plains were selected which were considered to represent best conditions available at present. The abundance of benthic algae other than diatoms or Charales was investigated. Sampling was repeated in two different seasons (summer and winter). In total, 107 taxa from 12 classes could be found, of which 70 taxa from eight classes were used for statistical analysis. Multivariate statistical analysis showed that the distribution of the algae was influenced mainly by the acid capacity and hardness of water. Based on the species composition and the abundances of the species, three groups of sampling sites could be distinguished leading to the definition of three types of running water: a. siliceous sites in the Central Highlands, b. organic sites (influenced by peat) in the Central Plains, c. calcareous sites in the Central Highlands and the Central Plains. These types show a specific species composition under reference conditions and differ significantly in terms of species richness and diversity. The results presented here are fundamental for the development of a routine for monitoring the ecological status according to EU-WFD.     

Ecological Risk Assessment of Arsenic and Metals in Surface Sediments from Estuarine and Coastal Areas of the Southern Bohai Sea,China

Distribution and magnitude of arsenic and metals in surface sediments collected from the coastal and estuarine areas of the southern Bohai Sea, China, were investigated. Sediments from the estuarine and coastal areas of the Jie and Xiaoqing Rivers contained highest concentrations of arsenic, cadmium, copper, mercury, and zinc. Mean concentrations of Cu, Zn, Cr, Pb, and Cd were higher than background concentrations determined for the areas. The magnitude of both enrichment factors (EF) and geoaccumulation indices (I_geo) suggested that pollution with As and metals was occurring along estuarine and coastal areas of the southern Bohai Sea. Risk analysis also suggested that concentrations of As and metals were sufficiently elevated as to cause adverse biological effects in the study area. According to the ecological risk index (RI) values, the upstream of the Jie River has a very high ecological risk for the waterbody. The data provided in this study are considered crucial for controlling and remediation of As and metals’ pollution of the southern Bohai Sea.     

Sources of Nitrogen to the Riparian Zone of a Desert Stream: Implications for Riparian Vegetation and Nitrogen Retention

Riparian zones effectively remove nitrogen (N) from water flowing through riparian soils, particularly in agricultural watersheds. The mechanism of N removal is still unclear, especially the role of vegetation. Uptake and denitrification are the two most commonly studied mechanisms. Retention of groundwater N by plant uptake is often inferred from measurements of N in net incremental biomass. However, this assumes other sources of N are not contributing to the N demand of plants. The purpose of this work was to investigate the relative importance of three sources of available N to riparian trees in a desert stream—input in stream water during floods, input during baseflow, and mineralization of N from soil organic matter. Two approaches were used; a mass balance approach in which the mass of available N from each source was estimated, and a correlational approach in which indexes of each source were compared to leaf N for individual willow trees. Total N from all sources was 396 kg ha⁻¹ y⁻¹, with 172 kg ha⁻¹ y⁻¹ from mineralization, 214 kg ha⁻¹ y⁻¹ from the stream during baseflow, and 9.6 kg ha⁻¹ y⁻¹ from floods. Leaf N was significantly related to N mineralization rates and flood inputs; it was not related to baseflow inputs. We conclude that mineralization is a major source of available N for willow trees, subsidized by input of N from floods. Baseflow inputs are most likely removed by rapid denitrification at the stream–riparian edge, while higher rates of flood supply exceed the capacity of this “filter.” Received 18 January 2001; accepted 15 June 2001.     

Flux and grain size variation of eolian dust as a proxy tool for the paleo-position of the Intertropical Convergence Zone in the northeast Pacific

A 328 cm-long piston core (KODOS 02-01-02) collected from the northeast equatorial Pacific at 16°12′N, 125°59′W was investigated for eolian mass fluxes and grain sizes to test these proxies as a tool for the paleo-position of the Intertropical Convergence Zone (ITCZ). The eolian mass fluxes of the lower interval below 250 cm (15.5-7.6 Ma) are very uniform at 5 ± 1 mg/cm²/10³ yr, while those of the upper interval above 250 cm (from 7.6 Ma) are over 2 times higher than the lower interval at 12 ± 1 mg/cm²/10³ yr. The median grain size of the eolian dusts in the lower interval increases from 8.4? to 8.0? downward, while that of the upper interval varies in a narrow range from 8.8? to 8.6?. The determined values compare well in magnitude to those of central Pacific sediments for the upper interval and equatorial and southeast Pacific sediments for the lower interval. This result suggests a possibility that the study site had been under the influence of southeast trade winds at its earlier depositional period due to the northerly position of the ITCZ, and subsequently of the northeast trade winds for a later period when the upper sediments were deposited. This interpretation is consistent with a mineralogical and geochemical study published elsewhere that assigned the provenance of the study core dust to Central/South America for the lower interval and to Asia for the upper interval. This study suggests that the distinct differences in eolian mass flux and grain size observed across the ITCZ can be used to trace the paleo-latitude of the ITCZ.     

Aerobic Phototrophic Bacteria: New Evidence for the Diversity,Ecological Importance and Applied Potential of this Previously Overlooked Group

The aerobic phototrophic bacteria are a recently discovered group capable of producing a photosynthetic apparatus similar to that of purple phototrophic bacteria. However, this apparatus, in contrast to that of their anaerobic counterparts, is functional in terms of photoinduced electron transport only under aerobic conditions. Although these bacteria have been widely studied, little is yet known about their ecological importance, and why they differ from other anoxygenic phototrophs with respect to oxygen requirements. In recent years a large number of new genera and species have been described from a wide variety of habitats, and evidence has been presented to support their important ecological role. This minireview focuses on recent discoveries regarding taxonomy, ecology and physiology, as well as the latest advances in the understanding of their photosynthetic apparatus and its genetic regulation.This revised version was published online in October 2005 with corrections to the Cover Date.     

Biogenic Origin of Polymetallic Nodules from the Clarion-Clipperton Zone in the Eastern Pacific Ocean: Electron Microscopic and EDX Evidence

Polymetallic/ferromanganese nodules (Mn-nodules) have been assigned a huge economic potential since they contain considerable concentrations of manganese, copper, nickel, iron, and cobalt. It has been assumed that they are formed by, besides hydrogenous, nonbiogenic processes, biogenic processes based on metabolic processes driven by microorganisms. In the present study, we applied the techniques of digital optical microscopy and high-resolution scanning electron microscopy to search for microorganisms in Mn-nodules. They were collected from the Clarion-Clipperton Zone in the Eastern Pacific Ocean and are composed of Mn (23.9%), Cu (0.69%), Ni (1.02%), Fe (10.9%), and Co (0.29%). These Mn-nodules, between 2.3 and 4.8 cm, show a distinct lamination; they are composed of small-sized micronodules, 100 to 450 μm in size, which are bound together by an interstitial whitish material. In the micronodules, a dense accumulation of microorganisms/bacteria could be visualized. Only two morphotypes exist: (1) round-shaped cocci and (2) elongated rods. The cocci (diameter: ≈3.5 μm) are arranged in bead-like chains, while the rods (≈2 × 0.4 μm) are arranged either as palisades or in a linear row. Energy-dispersive X-ray spectroscopy analyses showed that the areas rich in microorganisms/bacteria are also rich in Mn, while in regions where no microorganisms are found, the element Si is dominant. We suggest that growth of the Mn-nodules starts with the formation of “micronodules.” The formation of micronodules is assumed to be mediated by microorganisms. After accretion of biogenic and additional nonbiogenic minerals, the micronodules assemble to large nodules on the sea floor through additional inclusion of nonbiogenic material.     

Importance of the Central Region of 130-kDa Insecticidal Proteins of Bacillus thuringiensis var. israelensis for Their Activity in Vivo and in Vitro

To delineate the mosquitocidal regions of the ISRH3 (CryIVB) and ISRH4 (CryIVA) proteins, which are two of the mosquitocidal 130-kDa proteins contained in the crystalline protein bodies (CPBs) of Bacillus thuringiensis var. israelensis (BTI), a deletion analysis of these protein genes has been done. Based on the evidence that each 130-kDa protein had two mosquitocidal regions, N-terminal and C-terminal ones, and these two regions shared a common part in the center of the 130-kDa proteins, deleted genes on this region were constructed. As the protein products which lacked the central region had reduced activities, the central region could be important for the mosquitocidal activity. The mosquitocidal and non-mosquitocidal truncated gene products of 130-kDa protein genes were also applied to a cultured lepidopteran cell line, TN-368. The mosquitocidal proteins caused the swelling and disruption of the cells in spite of the insecticidal specificity of CPBs of BTI, but the non-mosquitocidal proteins did not. Therefore, TN-368 cells were sensitive to the mosquitocidal fragments of 130-kDa proteins of BTI under the assay conditions used.     

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

The extracellular DNA pool in marine sediments is the largest reservoir of DNA of the world oceans and it potentially represents an archive of genetic information and gene sequences involved in natural transformation processes. However, no information is at present available for the gene sequences contained in the extracellular DNA and for the factors that influence their preservation. In the present study, we investigated the depurination and degradation rates of extracellular DNA in a variety of marine sediment samples characterized by different ages (up to 10 000 years) and environmental conditions according to the presence, abundance and diversity of prokaryotic gene sequences. We provide evidence that depurination of extracellular DNA in these sediments depends upon the different environmental factors that act synergistically and proceeds at much slower rates than those theoretically predicted or estimated for terrestrial ecosystems. These findings suggest that depurination in marine sediments is not the main process that limits extracellular DNA survival. Conversely, DNase activities were high suggesting a more relevant role of biologically driven processes. Amplifiable prokaryotic 16S rDNA sequences were present in most benthic systems analysed, independent of depurination and degradation rates and of the ages of the sediment samples. Additional molecular analyses revealed that the extracellular DNA pool is characterized by relatively low-copy numbers of prokaryotic 16S rDNA sequences that are highly diversified. Overall, our results suggest that the extracellular DNA pool in marine sediments represents a repository of genetic information, which can be used for improving our understanding of the biodiversity, functioning and evolution of ecosystems over different timescales.     

Integrated Source Apportionment,Screening Risk Assessment,and Risk Mapping of Heavy Metals in Surface Sediments: A Case Study of the Dongting Lake,Middle China

Surface sediment samples were collected from 10 typical locations throughout the Dongting Lake, China, in January 2009. Samples were assayed by atom absorption spectrophotometer and cold atomic fluorescent spectrophotometer for Pb, Cd, As, Hg. In order to investigate the spatial distribution characteristics, sources, and potential ecological risks of heavy metals, the geostatistics method, potential ecological risk index, and multivariate statistical analysis were applied. The results showed that except for the content of Hg, the contents of Pb, Cd, and As had similar spatial distribution characteristics. The average contents of Cd and As exceeded the second class contents of the National Standard for Soil Environment Quality (GB15618-1995), especially that for Cd. The potential ecological risk posed by these heavy metals decreased in the order of the outlet of the Dongting Lake > the East Dongting Lake > the South Dongting Lake > the West Dongting Lake spatially. From the results of multivariate statistical analysis, Pb and Cd, as the first group, were considered to be rooted in mining smelting processes for developed mining and heavy industry. And Hg, as the second group, was mainly derived from parent material weathering, while As was probably considered to originate from both sources above.     

Contaminated sediments in the Elbe estuary: Ecological and economic problems for the Port of Hamburg

The effects of food density on competition between Bosmina longirostris and Bosmina fatalis from Lake Kasumigaura were examined in the laboratory. When the animals were reared with a high concentration of Chlorella, B. fatalis, which is slightly larger than B. longirostris in body length, had larger brood sizes and a higher rate of population growth than B. longirostris. When the species were reared together at high food density, B. fatalis overcame B. longirostris. But B. longirostris won the competition at low food density.The effects of Microcystis on the competition were also examined. When the two species of Bosmina were reared in a mixture of Chlorella and Microcystis, the populations of both species hardly increased, although individual B fatalis showed slightly better individual growth and reproduction than B. longirostris. Decomposed Microcystis, however, was utilized well by both species.In Lake Kasumigaura, the decomposition of abundant Microcystis seemed to raise the food level, favouring B. fatalis over B. longirostris.     

The base of the cilium: roles for transition fibres and the transition zone in ciliary formation, maintenance and compartmentalization

Both the basal body and the microtubule-based axoneme it nucleates have evolutionarily conserved subdomains crucial for cilium biogenesis, function and maintenance. Here, we focus on two conspicuous but underappreciated regions of these structures that make membrane connections. One is the basal body distal end, which includes transition fibres of largely undefined composition that link to the base of the ciliary membrane. Transition fibres seem to serve as docking sites for intraflagellar transport particles, which move proteins within the ciliary compartment and are required for cilium biogenesis and sustained function. The other is the proximal-most region of the axoneme, termed the transition zone, which is characterized by Y-shaped linkers that span from the axoneme to the ciliary necklace on the membrane surface. The transition zone comprises a growing number of ciliopathy proteins that function as modular components of a ciliary gate. This gate, which forms early during ciliogenesis, might function in part by regulating intraflagellar transport. Together with a recently described septin ring diffusion barrier at the ciliary base, the transition fibres and transition zone deserve attention for their varied roles in forming functional ciliary compartments.