Hierarchical spatial structure in soft-bottom mussel beds

Mussels (Mytilus edulis L.) are unusual because they thrive in both rocky shore and soft-bottom habitats. Despite their ecological and economic importance, little is known about their spatial structure. Mussels do not generally recruit to bare soft substrate because larvae and postlarvae cannot attach to a bottom of small sediment particles. They attach to hard objects on the sediment surface (especially other mussels), so soft-bottom mussel beds may be spatially organized in ways that are fundamentally different from those on rocky shores. The purpose of our study was to characterize the scales of spatial variability for several mussel abundance parameters in soft-bottom, intertidal M. edulis beds in coastal Maine. We used a random factor nested-ANOVA design of 200 cm² Cores within 1 m² Quadrats within 6 m Transects within Positions within bed Sites along 70 km (euclidean distance) of the Maine coast. Based on the literature and our field observations, we hypothesized that Sites and Positions account for most of the spatial variance in soft-botttom mussel beds. We rejected this hypothesis. Sites and Positions were not important in explaining variation in total mussel density, density of new recruits, or density of larger mussels. Although most of the variance in surface silt-clay fraction did occur at these levels, most mussel variation occurred at smaller spatial scales, specifically at the Quadrat scale for new recruits and total mussels and at the Transect scale for larger mussels. Variance in mussel parameters was not closely linked to the silt-clay fraction of surface sediment or to Site rankings of wind exposure and tidal flow. Variance in total mussel density was due primarily to variance in recruitment. No single scale explained more than about half the mussel variance, and no single scale was best at explaining all the mussel parameters. Greater knowledge about mussel bed spatial variability would be useful because it can help direct scale-dependent sampling regimes, field experiments, and coastal management practices.     

Life in an unstable house: community dynamics in changing mussel beds

Mussels are ecosystem engineers, and fluctuations in their abundance and population structure could be important to the associated community. There is, however, little understanding of this connection. In the present study, based on quantitative monitoring (1997–2011) of three mussel beds in a fjord-like White Sea bay, two hypotheses were tested: (1) mussel assemblages are temporally unstable and local population fluctuates cyclically as a result of negative adult–juvenile interactions; and (2) oscillations in mussel size-structure are correlated with changes in the associated community structure. A negative correlation found between the abundance of small (length < 21 mm) and large (length > 20 mm) mussels suggests that adult mussels indeed suppress recruitment. Such interaction implies an auto-oscillatory pattern of population dynamics, with Large- and Small-dominated stages temporally replacing each other. This cyclic pattern was clearly revealed for one mussel bed only, but long-term replacement of the Large-dominated stage by the Small-dominated stage was revealed for the other two assemblages also. In general, temporal variations of mussel populations were significantly correlated with the dynamics of the associated community, although several abundant taxa (Tubificoides benedii, Littorina saxatilis, Macoma balthica, and Gammaridae) were insensitive to mussel changes. In contrast, filamentous algae and mud snails Hydrobia ulvae tended to be more abundant during the Large-dominated stage, whereas polychaetes Dipolydora quadrilobata were most abundant during the Small-dominated stage. Several other abundant “sensitive” taxa were obviously dependent on algal bloom. Thus, mussel beds are unstable systems, whose dynamics are shaped not only by the ecosystem engineer but also by the associated community.     

Applications of fractal geometry to biology

The applications of concepts derived from fractal geometry tobiological problems are described. Three major applicationsare identified: modelling of structures; investigation of theoreticalproblems; and the measurment of complexity. The review concentrateson methods and algorithms, including potential problems, whichcan be used with biological problems. These algorithms are drawnfrom a wide range of literature, including some non–biologicalsources.     

Effects ofFucus vesiculosus covering intertidal mussel beds in the Wadden Sea

The brown algaFucus vesiculosus formamytili (Nienburg) Nienhuis covered about 70% of mussel bed (Mytilus edulis) surface area in the lower intertidal zone of Königshafen, a sheltered sandy bay near the island of Sylt in the North Sea. Mean biomass in dense patches was 584 g ash-free dry weight m^?2 in summer. On experimental mussel beds, fucoid cover enhanced mud accumulation and decreased mussel density. The position of mussels underneath algal canopy was mainly endobenthic (87% of mussels with >1/3 of shell sunk into mud). In the absence of fucoids, mussels generated epibenthic garlands (81% of mussels with <1/3 of shell buried in mud). Mussel density underneath fucoid cover was 40 to 73% of mussel density without algae. On natural beds, barnacles (Balanidae), periwinkles (Littorina littorea) and crabs (particularly juveniles ofCarcinus maenas) were significantly less abundant in the presence of fucoids, presumably because most of the mussels were covered with sediment, whereas in the absence of fucoids, epibenthic mussel clumps provided substratum as well as interstitial hiding places. The endobenthic macrofauna showed little difference between covered and uncovered mussel beds. On the other hand, grazing herbivores — the flat periwinkleLittorina mariae, the isopodJaera albifrons and the amphipodsGammarus spp. — were more abundant at equivalent sites with fucoid cover. The patchy growth ofFucus vesiculosus on mussel beds in the intertidal Wadden Sea affects mussels and their epibionts negatively, but supports various herbivores and increases overall benthic diversity.     

The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures.

To characterize water binding to proteins, which is fundamental to protein folding, stability and activity, the relationships of 10,837 bound water positions to protein surface shape and residue type were analyzed in 56 high-resolution crystallographic structures. Fractal atomic density and accessibility algorithms provided an objective characterization of deep grooves in solvent-accessible protein surfaces. These deep grooves consistently had approximately the diameter of one water molecule, suggesting that deep grooves are formed by the interactions between protein atoms and bound water molecules. Protein surface topography dominates the chemistry and extent of water binding. Protein surface area within grooves bound three times as many water molecules as non-groove surface; grooves accounted for one-quarter of the total surface area yet bound half the water molecules. Moreover, only within grooves did bound water molecules discriminate between different side-chains. In grooves, main-chain surface was as hydrated as that of the most hydrophilic side-chains, Asp and Glu, whereas outside grooves all main and side-chains bound water to a similar, and much decreased, extent. This identification of the interdependence of protein surface shape and hydration has general implications for modelling and prediction of protein surface shape, recognition, local folding and solvent binding.     

Hard rock versus soft bottom: the fauna associated with intertidal mussel beds on hard bottoms along the coast of Chile,and considerations on the functional role of mussel beds

The fauna associated with hard bottom mussel beds along the exposed Pacific coast of Chile was examined. The abundance of adult (>10 mm body length) purple mussels Perumytilus purpuratus varied between 32 and 75 individuals per 50 cm², and their biomass between 4.8 and 8.6 g AFDW per 50 cm² at eight sampling sites between Arica (18°S) and Chiloé (42°S). At all sampling sites, the associated fauna was dominated by suspension-feeding organisms (cirripeds, spionid and sabellid polychaetes, a small bivalve) followed by grazing peracarids and gastropods. Predators and scavengers also reached high abundances while deposit- and detritus-feeding organisms were of minor importance. The majority of organisms associated with these hard bottom mussel beds feed on resources obtained from the water column or growing on the mussels rather than on materials deposited by the mussels. This is in contrast to the fauna associated with mussel beds on soft bottoms, which comprises many species feeding on material accumulated by mussels (faeces and pseudofaeces) and deposited within the mussel bed. Many of the organisms dwelling between mussels both on hard bottoms and on soft bottoms have direct development, but organisms with pelagic development also occur abundantly within mussel beds. We propose that species with direct development are disproportionately favoured by the structurally complex habitat with diverse interstitial spaces between the mussels, which provides ample shelter for small organisms. We conclude that mussels on hard-bottoms primarily provide substratum for associated fauna while mussels on soft bottoms provide both substratum and food resources. Electronic Publication     

Predation on barnacles of intertidal and subtidal mussel beds in the Wadden Sea

Balanids are the numerically dominant epibionts on mussel beds in the Wadden Sea. Near the island of Sylt (German Bight, North Sea), Semibalanus balanoides dominated intertidally and Balanus crenatus subtidally. Field experiments were conducted to test the effects of predation on the density of barnacle recruits. Subtidally, predator exclusion resulted in significantly increased abundances of B. crenatus, while predator exclusion had no significant effects on the density of S. balanoides intertidally. It is suggested that recruitment of B. crenatus to subtidal mussel beds is strongly affected by adult shore crabs (Carcinus maenas) and juvenile starfish (Asterias rubens), whereas recruits of S. balanoides in the intertidal zone are mainly influenced by grazing and bulldozing of the very abundant periwinkle Littorina littorea, which is rare subtidally. Thus, not only do the barnacle species differ between intertidal and subtidal mussel beds, but the biotic control factors do so as well. Electronic Publication     

Community dynamics of intertidal soft-bottom mussel beds over two decades

Macrozoobenthos communities in the North Sea showed pronounced changes over the past decade in relation to an increasing number of invasive species and climate change. We analysed data sets spanning 22 years on abundance, biomass and species composition of intertidal soft bottom mussel beds near the island of Sylt (German Bight) in the Northern Wadden Sea, based on surveys from 1983/1984, 1990, 1993 and from 1999 to 2005. Mussel bed area and blue mussel biomass decreased, and a change in the dominance structure in the associated community comparing 1984 to mid-1990s with the period from 1999 to 2005 was observed. Coverage of the mussel beds with the algae Fucus vesiculosus decreased since the end of the 1990s. Within the study period biomass and densities of the associated community increased significantly. Dominance structure changed mainly because of increasing abundances of associated epibenthic taxa. Apart from the Pacific oyster Crassostrea gigas all other alien species were already present in the area during the study period. Community changes already started before Pacific oysters became abundant. An attempt is made to evaluate effects on the observed changes of decreasing mussel biomass, ageing of mussel beds, decreasing fucoid coverage and increasing abundances of invader. All four factors are assumed to contribute to changing community structure of intertidal mussel beds.     

Basic principles and applications of fractal geometry in pathology: a review

The basic principles and prospects of fractal geometry in pathology are promising. All articles found with a PubMed search with the keywords fractal dimension (FD) and related to pathology were reviewed. All fractal objects have FDs, commonly calculated with box counting. Fractal geometry has been applied to measure the irregularities of nuclear and glandular margins to distinguish malignant lesions from benign ones, to measure the infiltrative margin of a malignant tumor, to assess tumor angiogenesis and to measure the distribution of collagen in tissue. Fractal geometry has also been applied to assess the irregular distribution of chromatin in malignant cells. Biologic model formation is possible with fractal geometry. In the future, fractal geometry may help with the diagnosis, understanding of pathogenesis and management of lesions. It may also provide new insights into disease processes.     

Recovery of intertidal mussel beds in the Waddensea: use of habitat maps in the management of the fishery

In the Waddensea, musselbed distribution and abundance has decreased. Management is aiming at increase of area of beds. Fisheries have been regulated. Mussel beds are slowly recovering, and localities where recovery occurs can be predicted reasonably well. Active restoration of beds has not been necessary, as long as newly formed beds are protected from fisheries. Potential suitable sites should be protected from bottom-disturbing activities which might influence the substrate for spatfall such as cockle beds and tube-building polycheates.     

Fasciola gigantica: surface topography of the adult tegument

Adult Fasciola gigantica are leaf-shaped with tapered anterior and posterior ends and measure about 35 mm in length and 15 mm in width across the mid section. Under the scanning electron microscope its surface appears rough due to the presence of numerous spines and surface foldings. Both oral and ventral suckers have thick rims covered with transverse folds and appear spineless. On the anterior part of the ventral surface of the body, the spines are small and closely-spaced. Each spine has a serrated edge with 16 to 20 sharp points, and measures about 20 microm in width and 30 microm in height. In the mid-region the spines increase in size (up to 54 microm in width and 58 microm in height) and number, especially towards the lateral aspect of the body. Towards the posterior end the spines progressively decrease in both size and number. The tegumental surface between the spines appears highly corrugated with transverse folds alternating with grooves. At higher magnifications the surface of each fold is further increased with a meshwork of small ridges separated by variable-sized pits or slits. There are three types of sensory papillae on the surface. Types 1 and 2 are bulbous, measuring 4-6 microm in diameter at the base with nipple-like tips, and the type 2 also have short cilia. Type 3 papillae are also bulbous and of similar size but with a smooth surface. These sensory papillae usually occur in clusters, each having between 2 and 15 units depending on the region of the body. Clusters of papillae on the lateral aspect (usually types 1 and 2) and around the suckers (type 3) tend to be more numerous and larger in size. The dorsal side of the body exhibits similar surface features, but the spines and papillae appear less numerous and are smaller. Corrugation and invaginations of the surface are also less extensive than on the ventral side of the body.     

Benthic-pelagic flux rates on mussel beds: tunnel and tidal flume methodology compared

Material flux rates in an intertidal mussel bed were measured synchronously over two tidal cycles in June 1989 with Benthic Ecosystem Tunnels and a double lane flume. The tunnels enclosed the near bottom water, whereas the flume canalized the total water column. One tunnel was set up in a mussel bed and another one in an adjacent sand bottom as a control. The flume enclosed a mussel lane and a sand lane. In the tunnel and in the flume the mussel bed revealed ammonium and phosphate discharge. At the same time, phytoplankton, dominated byPhyaeocystis globosa, was taken up intensively. These flux rates showed the same tendency but they were higher in the flume than in the tunnel. Different tendencies and flux rates for oxygen and particulate organic matter (POC, PN) were found in flume and tunnel. These differences demonstrate the importance of water column processes regarding the material exchange of a mussel bed. Tunnels enclose smaller bodies of water and are therefore expected to detect even small effects of the benthos on the passing water. In flumes, benthic influence may be diluted over the entire water column but conditions are more natural. The use of flumes is restricted to shallow waters while tunnels have the potential to be used at any depth.     

Structural complexity in ubiquitin recognition

Ubiquitinated proteins are sorted into distinct pathways via association with several classes of ubiquitin binding domain-containing proteins. A virtual explosion in the field of ubiquitin binding proteins has revealed several new classes and interactions with distinct surfaces on ubiquitin, providing a clearer understanding of how sorting of ubiquitinated proteins is achieved.     

Ontogenetic changes in the fractal geometry of the bronchial tree in Rattus norvegicus

Respiration and metabolism change dramatically over the course of the development of vertebrates. In mammals these changes may be ascribed to organogenesis and differentiation of structures involved in gas exchange and transport and the increase in size. Since young as well as mature individuals must be well-designed if the species is to survive, the physiological changes during the development should be matched with geometrical or structural adjustments of the respiratory system. The aim of this study was to evaluate changes in the fractal geometry of the bronchial tree during the postnatal development of the rat. The average fractal dimension of the bronchial tree of the rats was 1.587, but that of juveniles was larger than that of the adults. We found a significant negative correlation between age and fractal dimension. This correlation could be considered be misleading because of the difficulty of separating age/body size effects. Nevertheless, because fractal dimensions of the bronchial tree of rabbits and humans are known to be similar, 1.58 and 1.57 respectively, the body size effect may be nil. To our knowledge, this is the first report of ontogenetic changes in the fractal dimension of the bronchial tree in mammals.     

Structural and functional topography of the human ribosome

This review covers data on the structural organization of functional sites in the human ribosome, namely, the messenger RNA binding center, the binding site of the hepatitis C virus RNA internal ribosome entry site, and the peptidyl transferase center. The data summarized here have been obtained primarily by means of a site-directed cross-linking approach with application of the analogs of the respective ribosomal ligands bearing cross-linkers at the designed positions. These data are discussed taking into consideration available structural data on ribosomes from various kingdoms obtained with the use of cryo-electron microscopy, X-ray crystallography, and other approaches.     

The role of topography in promoting fractal patchiness in a carbonate shelf landscape

Satellite remote sensing has shown numerous aspects of coral reef seascapes to be fractal. That is, they display characteristics of scale-invariance and complexity. To date, an understanding of why reefscapes adopt this curious scaling has been lacking. This property was investigated using high-resolution terrain models built using bathymetric LiDAR soundings of the shallow Puerto Rico insular shelf. A computer-simulation model constructed using simple random processes was adequate to describe many of the intricacies of actual coral reef terrain. This model, based on fractional Brownian motion (fBm), produced surfaces that were visually and statistically indistinguishable from natural seabeds, at spatial scales of 0.001–25 km². The conformity between model and nature allowed us to ascertain the importance of topography as a driver for the fractal patchiness that has been shown to occur in plan-view maps of reefscapes (e.g. Purkis et al. J Sediment Res 75:861–876, 2005, J Geol 115:493–508, 2007). For the considered Puerto Rican shelf, the necessary Brownian-like seabed topography likely arose through karst erosion overprinted by several episodes of reef development. Communicated by Geology Editor Dr. Bernhard Riegl