A comparative study of samples of the bivalve <Emphasis Type="Italic">Ruditapes philippinarum</Emphasis> (Adams et Reeve, 1850) from populations and shell assemblages

According to the results of a comparative analysis of the size and age structures of samples from a population of the bivalve mollusk Ruditapes philippinarum (Manila clam) and from shell assemblages of this species, the possibility of data acquisition on populations using samples from shell assemblages was assessed. A considerable coincidence of these parameters after taking the losses of small individuals during formation of shell assemblage into account, which depended on the location and conditions of assemblage formation, was recorded. Due to the good level of preservation of the shells of older individuals, the sample from the assemblage gave a more comprehensive appreciation of the maximum size and life span of the species than the sample of live mollusks from the natural habitat. Samples from shell assemblages may be used for growth rate estimation of clams without catching live individuals, as the results from studying the linear growth of mollusks based on samples from live populations and from shell assemblages did not differ significantly. Samples from many-year shell accumulations can also be useful for revealing the periods of the highest death rates, the most vulnerable periods in the ontogenesis of the mollusks, and, in some cases, the causes of their death.     

Genetic Changeability by Loci <Emphasis Type="Italic">COI</Emphasis> mtDNA for Different Coloring of Shell Phenotypes of Black Sea Mussel <Emphasis Type="Italic">Mytilus galloprovincialis</Emphasis> Lam. (Mollusca: Bivalvia: Mytilidae)

The variability of the nucleotide sequences of the fragment of the COI gene of the female genome was studied in four phenotypic groups of the Black Sea mollusk Mytilus galloprovincialis. It was shown that the parameters of genomic diversity (the number of haplotypes, haplotypic and nucleotide diversity, and the number of nucleotide substitutions, including pairwise ones) in mussels with dark shell color are significantly higher than in individuals with light color phenotypes. The revealed differences are related to the peculiarities of ecological preferences of mussels with dark and light shells.     

Metagenomic characterization of oyster shell dump reveals predominance of <Emphasis Type="Italic">Firmicutes</Emphasis> bacteria

Metagenomic analyses were conducted to evaluate the biodiversity of oyster shell bacteria, under storage conditions, on the basis of 16s rDNA sequences. Temperature was recorded during a one year storage period, and the highest temperature (about 60°C) was observed after five months of storage. Bacterial diversity was greatest in the initial stage sample, with 33 different phylotypes classified under seven phyla (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Planctomycetes, Verrucomicrobia and unclassified bacteria), with 42.22% of phylotypes belonging to Proteobacteria. The lowest diversity was found in the high temperature (fermentation) stage sample, with 10 different phylotypes belonging to Firmicutes (78.57%) and Bacteroidetes. In the final stage sample, bacteria were found belonging to Proteobacteria, Bacteroidetes, and Firmicutes, and some were unclassified bacteria. Of the bacteria constituting the final stage metagenome, 69.70% belonged to Firmicutes. Our results show that bacteria belonging to phylum Firmicutes were predominant during fermentation, and during the final stages of oyster shell storage, which suggests that these bacteria supposed to be the key players for oyster shell biodegradation.     

Ecotype variability of the gastropodCeratostoma burnetti from Pos’eta bay (Sea of Japan)

This paper deals with the ecology, settlement age structure, and shell variability of the gastropodCeratostoma burnetti (Adams et Reeve) (Muricidae) from Pos’eta Bay (Sea of Japan). A change in the shell structure occurs between the open and inner bights of the bay: the shell sculpture smoothes, the ratio of body whorl diameter to height grows, the mass and degree of borer invasion of the shell increase, and lastly, the relative mollusk size decreases. The given changes are hypothesized to result from borer influence as well as from differences in salinity and oxygen concentration in the studied regions.     

Generation and reshaping of sequences in neural systems

The generation of informational sequences and their reorganization or reshaping is one of the most intriguing subjects for both neuroscience and the theory of autonomous intelligent systems. In spite of the diversity of sequential activities of sensory, motor, and cognitive neural systems, they have many similarities from the dynamical point of view. In this review we discus the ideas, models, and mathematical image of sequence generation and reshaping on different levels of the neural hierarchy, i.e., the role of a sensory network dynamics in the generation of a motor program (hunting swimming of marine mollusk Clione), olfactory dynamical coding, and sequential learning and decision making. Analysis of these phenomena is based on the winnerless competition principle. The considered models can be a basis for the design of biologically inspired autonomous intelligent systems.     

The Biomineralization Proteome: Protein Complexity for a Complex Bioceramic Assembly Process

There are over 62 different biominerals on Earth and a diverse array of organisms that generate these biominerals for survival. This review will introduce the process of biomineralization and the current understanding of the molecular mechanisms of mineral formation, and then comparatively explore the representative secretomes of two well‐documented skeletal systems: vertebrate bone (calcium phosphate) and invertebrate mollusk shell (calcium carbonate). It is found that both skeletal secretomes have gross similarities and possess proteins that fall into four functional categories: matrix formers, nucleation assisters, communicators, and remodelers. In many cases the mineral‐associated matrix former and nucleation assister sequences in both skeletal systems are unique and possess interactive conserved globular domains, intrinsic disorder, post‐translational modifications, sequence redundancy, and amyloid‐like aggregation‐prone sequences. Together, these molecular features create a protein‐based environment that facilitates mineral formation and organization and argue in favor of conserved features that evolve from the mollusk shell to bone. Interestingly, the mollusk shell secretome appears to be more complex compared to that of bone tissue, in that there are numerous protein subcategories that are required for the nucleation and organization of inner (nacre) and outer (prismatic) calcium carbonate regions of the shell. This may reflect the organizational and material requirements of an exoskeletal protective system.     

The phenotypic diversity of <Emphasis Type="Italic">Dreissena polymorpha</Emphasis> (Pallas) in the northeastern part of its range

A comparison was made of the phenotypic structure of Dreissena polymorpha (Pallas) populations in their initial range and northeastern periphery. Intraspecific diversity was studied in eleven mollusk populations. Biotopic and geographic aspects of polymorphism were analyzed. A high intrapopulation diversity of phenotypes was registered in the peripheral populations of the zebra mussel. It was shown that the formation of the phenotypic structure of the population is influenced as much by biotopic characteristics of the waterbody as it is by its geographic position.     

Formation of the prismatic layer in the freshwater bivalve Hyriopsis cumingii: the feedback of crystal growth on organic matrix

The squeezing hypothesis and the organic frameworks preformation hypothesis propose two different mechanisms to explain the interaction between organic frameworks and crystals during biomineralization of the prismatic layer of the mollusk shell. In this study, we began to study Hyriopsis cumingii shell formation and discover that this species seemed to follow the squeezing hypothesis. During the formation of the aragonite prismatic layer in the freshwater bivalve H. cumingii, we found that crystal growth was involved in controlling initiation of formation of the interprismatic organic membranes. First, newly formed crystals were embedded in the periostracum. Next, the interprismatic organic membranes of the prismatic layer were produced via squeezing between neighboring crystals. The organic matrix secreted by the mantle continuously self‐assembled into the interprismatic organic membranes as the crystals grew. In the mature stage, the interprismatic organic membranes were shaped by crystal growth. These findings provide evidence to support the squeezing hypothesis and add to the existing knowledge about interactions that occur at the organic–inorganic interfaces during mollusk shell biomineralization.     

Molluscan Community Recovery in a New England Back‐Barrier Salt Marsh Lagoon 10 Years after Partial Restoration

Like many Eastern U.S. salt marshes, East Harbor salt marsh lagoon on Cape Cod was isolated from tidal flow in the 1800s, resulting in near‐freshwater conditions and loss of native salt marsh species. After its partial restoration in 2002, a variety of marine and estuarine fauna recolonized East Harbor, and soft shell clam (Mya arenaria) recolonization was particularly prolific. The goal of our study was to evaluate molluscan community composition, density, and distribution at regular intervals for 10 years following restoration, and to relate molluscan community recovery to various physical properties at the site. In 2007, 2008, and 2011, we sampled mollusks at several points across East Harbor, and we also recorded water salinity and temperature, particle size distribution, and submerged aquatic vegetation density. In 2007 and 2008, we encountered 12 and 11 mollusk species, respectively; M. arenaria was the most abundant species in 2007 and the second most abundant species in 2008. In 2011, we encountered eight mollusk species and M. arenaria was the most abundant species. Mollusk species richness declined from 12 to 8 species between 2008 and 2011. Our results show that mollusk species richness and density have declined significantly since the first few years following restoration; related studies attribute this to high summer water temperatures in the Main Lagoon and severe macroalgal blooms during 2005–2006. This suggests that East Harbor is still equilibrating to baseline conditions and that full tidal restoration may be necessary to sustain a diverse mollusk community at East Harbor.     

Occurrence of partenites in mollusks and the influence that metacercaria of <Emphasis Type="Italic">Apophallus muehlingi</Emphasis> (Jagerskiold, 1898) and <Emphasis Type="Italic">Posthodiplostomum cuticola</Emphasis> (Nordmann, 1832) has on some biochemical parameters in fish

A heavy parasitic load from trematode partenites of Apophallus muehlingi (Jagerskiold, 1898) was observed in the mollusk population of Lithoglyphus naticoides (Pfeiffer) after its natural invasion into the Rybinsk Reservoir. An elevated concentration of glycogen was detected in the muscles of infected fish, both in the natural populations and under experimental conditions. Interspecific differences were found for the protein concentrations when elevated concentrations were observed in the muscles of the infected roach, and no differences were discovered for the goldfish (both infected and parasite-free). The ties between the biochemical parameters and motor activity are discussed for the infected fish.     

Patchiness of local species richness and its implication for large-scale diversity patterns: an example from the middle Miocene of the Paratethys

The best hope for understanding global diversity patterns is to compare local assemblages, which are mostly preserved in taphonomically-complex shell beds. The present study investigates the variability in faunal composition and diversity at the scale of a single outcrop. A total of 152 species (3315 shells) occurred in 25 samples from 5 tempestitic shell beds. Although sampling intensity was high, total species richness was not captured by far at the hierarchical levels present (outcrop, shell beds, samples) because the majority of species is rare. In contrast, sampling intensity was sufficient to cover the most abundant species, as indicated by stable evenness values. Four taxa dominate the assemblage, but their rank order differs strongly between individual shell beds and individual samples; significant differences between some shell beds are evident for faunal composition, and one shell bed differs from all others with respect to species accumulation curves. Within shell beds, rarefaction curves are generally characterized by strongly overlapping confidence intervals, but outliers occur in three of five shell beds. Patchiness is additionally indicated by a wide scatter of diversity indices in some shell beds and by a wide scatter of samples of one shell bed in an ordination on faunal composition. Most of the outcrop-scale variability in faunal composition and diversity can be related to differences between shell beds. This suggests that sampling a single shell bed of the outcrop is insufficient to characterize the local fauna and its diversity, even when sampling intensity (i.e. the number of samples and shells) within the shell bed was high. Similarly, a single sample from such a shell bed may not be sufficient to characterize its diversity, even when the number of counted shells was high. It is therefore confirmed that sampling strategy and sampling intensity are crucial to confidently characterize the shelly assemblages at such a small spatial scale and that dispersed sampling effort with many small replicate samples will characterize a local assemblage and its diversity better than a few large samples. Diversity comparisons of individual samples between localities must account for the high variability present at the smaller spatial scale, as observed in our study.     

Insertion Sequence-Driven Evolution of <Emphasis Type="Italic">Escherichia coli</Emphasis> in Chemostats

Insertion sequence (IS) elements are present in almost all bacterial genomes and are mobile enough to provide genomic tools to differentiate closely related isolates. They can be used to estimate genetic diversity and identify fitness-enhancing mutations during evolution experiments. Here, we determined the genomic distribution of eight IS elements in 120 genomes sampled from Escherichia coli populations that evolved in glucose- and phosphate-limited chemostats by comparison to the ancestral pattern. No significant differential transposition of the various IS types was detected across the environments. The phylogenies revealed substantial diversity amongst clones sampled from each chemostat, consistent with the phenotypic diversity within populations. Two IS-related changes were common to independent chemostats, suggesting parallel evolution. One of them corresponded to insertions of IS1 elements within rpoS encoding the master regulator of stress conditions. The other parallel event was an IS5-dependent deletion including mutY involved in DNA repair, thereby providing the molecular mechanism of generation of mutator clones in these evolving populations. These deletions occurred in different co-existing genotypes within single populations and were of various sizes. Moreover, differential locations of IS elements combined with their transpositional activity provided evolved clones with different phenotypic landscapes. Therefore, IS elements strongly influenced the evolutionary processes in continuous E. coli cultures by providing a way to modify both the global regulatory network and the mutation rates of evolving cells.     

Assessing microbial diversity using recent lake sediments and estimations of spatio‐temporal diversity

Aim Recent papers have used large palaeolimnological datasets to reveal the biodiversity patterns of aquatic microorganisms. However, scant attention has been paid to the influence of time on these patterns. Where lake surficial sediment samples are used as integrals of diversity, the time interval of each sample varies according to differences in sediment accumulation rates. This paper aims to test the reliability of using lake surface sediments to measure and to compare microbial diversity when the potential influences of the species–time relationships are taken into account. Location Alpine lakes in Europe. Methods We analysed microorganism (siliceous microalgae) assemblages in three European Alpine lakes using short sediment cores (²¹⁰Pb‐dated) and annual sediment trap samples from 12 UK lakes. The same number of individuals was pooled for each sample 500 times to avoid sampling effort effects and to standardize species diversity estimation. The influence of time on the diversity score was assessed by simulating an increase of time span for surface sediment samples by cumulatively adding in successive sediment core samples (from the most recent to the oldest). We used species richness (S) and the exponential of the bias‐corrected Shannon entropy index (exp(H_b‐c)) to estimate diversity. Results Increasing the time interval represented by a surficial sediment sample did not affect the diversity results. The estimation of diversity was similar for cumulative and non‐cumulative samples. Diversity estimation was only altered in lakes experiencing high community turnover due to strong environmental forcing during the time period spanned by the cumulative sample. Main conclusions The use of surface lake sediments is suitable for estimating the average site diversity of free‐living microorganisms. Diversity is integrated in a single sample and species assemblage composition is derived from microbial communities living in distinct lake microhabitats. Species remains, accumulated in a single sample over several years of environmental variability, represent a diversity integral that captures a spatio‐temporal component equivalent to the γ‐diversity measure.     

On Temporal Dynamics of Morphological Variations in the Black Sea Mussel Mytilus galloprovincialis Lam.

Temporal variations in morphological characters of the shells were studied in 12 samples of mussels M. galloprovincialis Lam. from the Black Sea commercial collectors that belong to different generations. The samples were shown to be diverse in every studied character and the degree of characters' variability in the samples was different. The morphological diversity of samples diminished with age. Different generations from the same habitat had specific features of age-related variability expressed as different rates of age-related changes and direction and degree of variability. This effect is considered as an index of the influence of ecological conditions on the shell growth and formation.     

The European oyster <Emphasis Type="Italic">(Ostrea edulis)</Emphasis> and its epibiotic succession

This study aimed to investigate intra- and inter-site differences in the epibiota on the European oyster Ostrea edulis of different ages and on hard substrata to assess their contribution to biodiversity. This research has shown that shells of O. edulis do show higher species diversity than non-living hard substrata and as oysters grow larger epibiotic diversity will increase. This investigation has revealed that O. edulis possesses biogenic engineering qualities and the value of O. edulis as a vehicle for increasing biodiversity should not be underestimated. Relatively few studies have examined the shell surfaces of Ostrea edulis, which, together with their associated epifauna provide a large portion of the natural hard substrata for sessile filter-feeding organisms, including oysters, in coastal and estuarine ecosystems. It can be considered a keystone species which has an influence on intertidal and subtidal community structures.     

煤矿污染土壤降解苯并(a)芘微生物多样性及降解能力研究

以苯并(a)芘(50 mg/L)为唯一碳源,对新疆芦草沟煤矿开采区土壤微生物进行3代胁迫培养(每代60 d);采用PCR-DGGE方法了解不同污染程度土样中降解苯并(a)芘的微生物类群和多样性特点;利用高效液相色谱(HPLC)测定胁迫培养每代培养物混合菌群对苯并(a)芘的降解能力。PCR-DGGE结果显示:不同污染程度原始样品与苯并(a)芘胁迫培养第3代培养物的微生物香浓指数(H)、丰度(S)和均匀度(E)有所不同,其中重度污染培养物降解苯并(a)芘的微生物类群最丰富。对优势条带进行克隆,其主要归属于变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria)。经HPLC检测发现重度污染样品中的群体微生物对苯并(a)芘的降解率明显高于轻度和中度污染样品,达到78.4%。研究表明新疆芦草沟煤矿开采区污染的土壤中可能蕴藏着降解苯并(a)芘的微生物资源。     

Mid-Neolithic Exploitation of Mollusks in the Guanzhong Basin of Northwestern China: Preliminary Results

Mollusk remains are abundant in archaeological sites in the Guanzhong Basin of Northwestern China, providing good opportunities for investigations into the use of mollusks by prehistoric humans. Here we report on freshwater gastropod and bivalve mollusks covering the time interval from about 5600 to 4500 cal. yrs BP from sites of Mid-Late Neolithic age. They are identified as Cipangopaludina chinensis and Unio douglasiae, both of which are currently food for humans. The shells are well preserved and have no signs of abrasion. They are all freshwater gastropods and bivalves found in pits without water-reworked deposits and have modern representatives which can be observed in rivers, reservoirs, and paddy fields in the studied region. Mollusk shells were frequently recovered in association with mammal bones, lithic artifacts, and pottery. These lines of evidence indicate that the mollusks are the remains of prehistoric meals. The mollusk shells were likely discarded into the pits by prehistoric humans after the flesh was eaten. However, these mollusk remains may not have been staple food since they are not found in large quantities. Mollusk shell tools and ornaments are also observed. Shell tools include shell knives, shell reaphooks and arrowheads, whereas shell ornaments are composed of pendants and loops. All the shell tools and ornaments are made of bivalve mollusks and do not occur in large numbers. The finding of these freshwater mollusk remains supports the view that the middle Holocene climate in the Guanzhong Basin may have been warm and moist, which was probably favorable to freshwater mollusks growing and developing in the region.     

Two new trochids of the genus <Emphasis Type="Italic">Antimargarita</Emphasis> (Gastropoda: Vetigastropoda: Trochidae) from the Bellingshausen Sea and South Shetland Islands,Antarctica

Two new trochids of the genus Antimargarita, A. powelli and A. bentarti, from the Antarctic waters are described here. A. powelli, from the Bellingshausen Sea, is distinguished by its rounded whorls, numerous spiral cords, a radula with seven lateral teeth at each side of the rachidian, and an epipodium with eight pairs of tentacles. A. bentarti, from the South Shetland Islands, is characterized by having a shell outline gradated by prominent primary spiral cords, a radula with five lateral teeth at each side of the rachidian and an epipodium with six tentacles on the left side. The diagnostic features for Antimargarita are redefined considering both shell and anatomical features and its suprageneric placement is discussed.     

Habitat predictors of genetic diversity for two sympatric wetland‐breeding amphibian species

Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond‐breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata; and Southern Leopard frogs, Lithobates sphenocephalus) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond‐breeding amphibian species.