Length–weight and length–length relationships of three Clupeonella species (Clupeidae) from the Caspian Sea

This study investigated length–weight and length–length relationships of three Clupeonella species: C. caspia, C. engrauliformis and C. grimmi captured in the southern Caspian Sea, Iran. Using a lantern net, 206 specimens were collected from July to August 2016. Presented for two of the species are the length–weight and the length–length relationships as well as the first reference on length–weight and length–length relationships for C. caspia in its distribution range.     

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

Targeted species‐specific and community‐wide molecular diagnostics tools are being used with increasing frequency to detect invasive or rare species. Few studies have compared the sensitivity and specificity of these approaches. In the present study environmental DNA from 90 filtered seawater and 120 biofouling samples was analyzed with quantitative PCR (qPCR), droplet digital PCR (ddPCR) and metabarcoding targeting the cytochrome c oxidase I (COI) and 18S rRNA genes for the Mediterranean fanworm Sabella spallanzanii. The qPCR analyses detected S. spallanzanii in 53% of water and 85% of biofouling samples. Using ddPCR S. spallanzanii was detected in 61% of water of water and 95% of biofouling samples. There were strong relationships between COI copy numbers determined via qPCR and ddPCR (water R² = 0.81, p < .001, biofouling R² = 0.68, p < .001); however, qPCR copy numbers were on average 125‐fold lower than those measured using ddPCR. Using metabarcoding there was higher detection in water samples when targeting the COI (40%) compared to 18S rRNA (5.4%). The difference was less pronounced in biofouling samples (25% COI, 29% 18S rRNA). Occupancy modelling showed that although the occupancy estimate was higher for biofouling samples (ψ = 1.0), higher probabilities of detection were derived for water samples. Detection probabilities of ddPCR (1.0) and qPCR (0.93) were nearly double metabarcoding (0.57 to 0.27 marker dependent). Studies that aim to detect specific invasive or rare species in environmental samples should consider using targeted approaches until a detailed understanding of how community and matrix complexity, and primer biases affect metabarcoding data.     

Control of biofouling by Cordylophora caspia in freshwater using one-off,pulsed and intermittent dosing of chlorine: laboratory evaluation

Cordylophora caspia is a hydrozoan which causes biofouling in power plants and is an increasing problem in UK drinking water treatment works. Thermal control is not usually feasible without a ready source of hot water so laboratory experiments were conducted to assess whether using pulsed doses of chlorine is an alternative solution. C. caspia polyps disintegrated after a single 20 min dose (the length of one backwash cycle in water treatment work filter beds) of 2.5 ppm chlorine. Without further treatment colonies regenerated within 3 days, but repeated dosing with chlorine for 20 min each day inhibited this regeneration. The resistance of surviving colonies to chlorine increased over time, although colony size and polyp regeneration continued to fall. These results suggest pulsed treatment with chlorinated backwashes at 2 ppm could be used to control C. caspia biofouling in rapid gravity filters and this may have relevance to other settings where thermal control is not feasible.     

Length–weight relationships of six species of the genera Cobitis and Sabanejewia (Cobitidae) in Iranian river systems

Length‐weight relationships (LWRs) were estimated for six spined loach species from Iran. Data were collected between 2010 and 2015. These represent the first reports of length–weight data for five of the species (Cobitis avicennae, Cobitis faridpaki, Cobitis keyvani, Sabanejewia aurata and Sabanejewia caspia) while also providing additional data on the remaining species (Cobitis linea). Five of these species are endemic and the remaining S. caspia, is native to the country. Estimated b values obtained for the studied species ranged from 2.381 for S. aurata to 3.411 for C. keyvani.     

Contrasting water sources and water‐use efficiency in coexisting desert plants in two saline‐sodic soils in northwest China

• Soil degradation resulting from various types of salinity is a major environmental problem, especially in arid and semiarid regions. Exploring the water‐related physiological traits of halophytes is useful for understanding the mechanisms of salt tolerance. This knowledge could be used to rehabilitate degraded arid lands.
• To investigate whether different types of salinity influence the water sources and water‐use efficiency of desert plants (Karelinia caspia, Tamarix hohenackeri, Nitraria sibirica, Phragmites australis, Alhagi sparsifolia, Suaeda microphylla, Kalidium foliatum) in natural environments, we measured leaf gas exchange, leaf carbon and xylem oxygen isotope composition and soil oxygen isotope composition at neutral saline‐sodic site (NSS) and alkaline saline‐sodic site (ASS) in northwest China.
• The studied plants had different xylem water oxygen isotope compositions (δ¹⁸O) and foliar carbon isotope compositions (δ¹³C), indicating that desert plants coexist through differentiation in water use patterns. Compared to that at the NSS site, the stem water in K. caspia, A. sparsifolia and S. microphylla was depleted in ¹⁸O at the ASS site, which indicates that plants can switch to obtain water from deeper soil layers when suffering environmental stress from both salinity and alkalinisation. Alhagi sparsifolia had higher δ¹³C at the ASS site than at the NSS site, while K. caspia and S. microphylla had lower δ¹³C, which may have resulted from interspecific differences in plant alkali and salt tolerance ability.
• Our results suggest that under severe salinity and alkalinity, plants may exploit deeper soil water to avoid ion toxicity resulting from high concentrations of soluble salts in the superficial soil layer. In managed lands, it is vital to select and cultivate different salt‐tolerant or alkali‐tolerant plant species in light of local conditions.

     

Effects of environmental factors on basidiospore germination of ammonia fungi <Emphasis Type="Italic">Coprinopsis</Emphasis> spp. collected from different geographical areas

Effects of pH, NH₄-N, and temperature on basidiospore germination in Coprinopsis austrophlyctidospora from New Zealand, C. phlyctidospora from Japan, C. aff. rugosobispora from Canada, and C. echinospora from Canada were investigated. The Coprinopsis spp. required the presence of ammonium-nitrogen under weak alkaline to neutral conditions for germination, regardless of their different areas of occurrence. The former two species had a wider concentration of NH₄Cl solution and pH range for germination in comparison to the latter two species. The optimum concentration of NH₄Cl solution for the germination was 0.01 M in C. austrophlyctidospora and 0.1 M in the other three species. The pH optimum for germination in the former two species was 8.0 whereas that for germination in the latter two species was 8.0–8.5. The temperature range (5.0–40.0°C) for the former two species was wider than that (5–30°C) for the latter two species. Temperature optima for the germination in the former two species, C. aff. rugosobispora and C. echinospora, were 30, 20–25 and 15°C, respectively. The germination abilities of these Coprinopsis species in a wide range of temperatures are relevant to their natural temperature regime, showing their potential ability to propagate in tropical to subarctic regions.     

Potential biocontrol agents for biofouling on artificial structures

The accumulation of biofouling on coastal structures can lead to operational impacts and may harbour problematic organisms, including non-indigenous species. Benthic predators and grazers that can supress biofouling, and which are able to be artificially enhanced, have potential value as augmentative biocontrol agents. The ability of New Zealand native invertebrates to control biofouling on marina pontoons and wharf piles was tested. Caging experiments evaluated the ability of biocontrol to mitigate established biofouling, and to prevent fouling accumulation on defouled surfaces. On pontoons, the gastropods Haliotis iris and Cookia sulcata reduced established biofouling cover by >55% and largely prevented the accumulation of new biofouling over three months. On wharf piles C. sulcata removed 65% of biofouling biomass and reduced its cover by 73%. C. sulcata also had better retention and survival rates than other agents. Augmentative biocontrol has the potential to be an effective method to mitigate biofouling on marine structures.     

Degradation of chloroform by immobilized cells of <Emphasis Type="Italic">Bacillus</Emphasis> sp. in calcium alginate beads

A Bacillus sp., capable of degrading chloroform, was immobilized in calcium alginate. The beads in 20 g alginate l⁻¹ (about 2 × 10⁸ cells/bead) could be re-used nine times for degradation of chloroform at 40 μM. The immobilized cells had a higher range of tolerance (pH 6.5–9 and 20–41°C) than free cells (pH 7–8.5 and 28–32°C). At 5 g alginate l⁻¹, leakage of the cells from the beads was 0.51 mg dry wt ml⁻¹. This species is the first reported Bacillus that can degrade chloroform as the sole carbon source.     

Past and future evolution of Abies alba forests in Europe – comparison of a dynamic vegetation model with palaeo data and observations

Information on how species distributions and ecosystem services are impacted by anthropogenic climate change is important for adaptation planning. Palaeo data suggest that Abies alba formed forests under significantly warmer‐than‐present conditions in Europe and might be a native substitute for widespread drought‐sensitive temperate and boreal tree species such as beech (Fagus sylvatica) and spruce (Picea abies) under future global warming conditions. Here, we combine pollen and macrofossil data, modern observations, and results from transient simulations with the LPX‐Bern dynamic global vegetation model to assess past and future distributions of A. alba in Europe. LPX‐Bern is forced with climate anomalies from a run over the past 21 000 years with the Community Earth System Model, modern climatology, and with 21st‐century multimodel ensemble results for the high‐emission RCP8.5 and the stringent mitigation RCP2.6 pathway. The simulated distribution for present climate encompasses the modern range of A. alba, with the model exceeding the present distribution in north‐western and southern Europe. Mid‐Holocene pollen data and model results agree for southern Europe, suggesting that at present, human impacts suppress the distribution in southern Europe. Pollen and model results both show range expansion starting during the Bølling–Allerød warm period, interrupted by the Younger Dryas cold, and resuming during the Holocene. The distribution of A. alba expands to the north‐east in all future scenarios, whereas the potential (currently unrealized) range would be substantially reduced in southern Europe under RCP8.5. A. alba maintains its current range in central Europe despite competition by other thermophilous tree species. Our combined palaeoecological and model evidence suggest that A. alba may ensure important ecosystem services including stand and slope stability, infrastructure protection, and carbon sequestration under significantly warmer‐than‐present conditions in central Europe.     

<Emphasis Type="Italic">Thermogladius shockii</Emphasis> gen. nov., sp. nov., a hyperthermophilic crenarchaeote from Yellowstone National Park,USA

A hyperthermophilic heterotrophic archaeon (strain WB1) was isolated from a thermal pool in the Washburn hot spring group of Yellowstone National Park, USA. WB1 is a coccus, 0.6–1.2 μm in diameter, with a tetragonal S-layer, vacuoles, and occasional stalk-like protrusions. Growth is optimal at 84°C (range 64–93°C), pH 5–6 (range 3.5–8.5), and <1 g/l NaCl (range 0–4.6 g/l NaCl). Tests of metabolic properties show the isolate to be a strict anaerobe that ferments complex organic substrates. Phylogenetic analysis of the 16S rRNA gene sequence places WB1 in a clade of previously uncultured Desulfurococcaceae and shows it to have ≤96% 16S rRNA sequence identity to Desulfurococcus mobilis, Staphylothermus marinus, Staphylothermus hellenicus, and Sulfophobococcus zilligii. The 16S rRNA gene contains a large insertion similar to homing endonuclease introns reported in Thermoproteus and Pyrobaculum species. Growth is unaffected by the presence of S⁰ or SO₄ ²⁻, thereby differentiating the isolate from its closest relatives. Based on phylogenetic and physiological differences, it is proposed that isolate WB1 represents the type strain of a novel genus and species within the Desulfurococcaceae, Thermogladius shockii gen. nov., sp. nov. (RIKEN = JCM-16579, ATCC = BAA-1607, Genbank 16S rRNA gene = EU183120).     

First description of the environmental niche of the epibenthic dinoflagellate species Coolia palmyrensis,C. malayensis,and C. tropicalis (Dinophyceae) from Eastern Australia

Environmental variables such as temperature, salinity, and irradiance are significant drivers of microalgal growth and distribution. Therefore, understanding how these variables influence fitness of potentially toxic microalgal species is particularly important. In this study, strains of the potentially harmful epibenthic dinoflagellate species Coolia palmyrensis, C. malayensis, and C. tropicalis were isolated from coastal shallow water habitats on the east coast of Australia and identified using the D1‐D3 region of the large subunit (LSU) ribosomal DNA (rDNA). To determine the environmental niche of each taxon, growth was measured across a gradient of temperature (15–30°C), salinity (20–38), and irradiance (10–200 μmol photons · m^?2 · s^?1). Specific growth rates of Coolia tropicalis were highest under warm temperatures (27°C), low salinities (ca. 23), and intermediate irradiance levels (150 μmol photons · m^?2 · s^?1), while C. malayensis showed the highest growth at moderate temperatures (24°C) and irradiance levels (150 μmol photons · m^?2 · s^?1) and growth rates were consistent across the range of salinity levels tested (20–38). Coolia palmyrensis had the highest growth rate of all species tested and favored moderate temperatures (24°C), oceanic salinity (35), and high irradiance (>200 μmol photons · m^?2 · s^?1). This is the first study to characterize the environmental niche of species from the benthic harmful algal bloom genus Coolia and provides important information to help define species distributions and inform risk management.     

Non‐native fishes and climate change: predicting species responses to warming temperatures in a temperate region

1. Temperate regions with fish communities dominated by cold‐water species (physiological optima <20 °C) are vulnerable to the effects of warming temperatures caused by climate change, including displacement by non‐native cool‐water (physiological optima 20–28 °C) and warm‐water fishes (physiological optima >28 °C) that are able to establish and invade as the thermal constraints on the expression of their life history traits diminish. 2. England and Wales is a temperate region into which at least 38 freshwater fishes have been introduced, although 14 of these are no longer present. Of the remaining 24 species, some have persisted but failed to establish, some have established populations without becoming invasive and some have become invasive. The aim of the study was to predict the responses of these 24 non‐native fishes to the warming temperatures of England and Wales predicted under climate change in 2050. 3. The predictive use of climate‐matching models and an air and water temperature regression model suggested that there are six non‐native fishes currently persistent but not established in England and Wales whose establishment and subsequent invasion would benefit substantially from the predicted warming temperatures. These included the common carp Cyprinus carpio and European catfish Silurus glanis, fishes that also exert a relatively high propagule pressure through stocking to support angling and whose spatial distribution is currently increasing significantly, including in open systems. 4. The potential ecological impacts of the combined effects of warming temperatures, current spatial distribution and propagule pressure on the establishment and invasion of C. carpio and S. glanis were assessed. The ecological consequences of C. carpio invasion were assessed as potentially severe in England and Wales, with impacts likely to relate to habitat destruction, macrophyte loss and increased water turbidity. However, evidence of ecological impacts of S. glanis elsewhere in their introduced range was less clear and so their potential impacts in England and Wales remain uncertain.     

Molecular identification of the economically important freshwater mussels (Mollusca–Bivalvia–Unionoida) of Thailand: developing species‐specific markers from AFLPs

Shells of certain freshwater mussel (Unionoida) species are highly demanded and serve as raw material for a range of decorative and pharmaceutical products. In Thailand, most animals for this purpose are currently harvested from wild populations, with unionoid culture still being in its infancy. Whilst reliable species identification is a prerequisite for developing a large‐scale industry, identification by morphological means is hampered by extensive phenotypic plasticity and poor knowledge of species delimitations. To facilitate alternative molecular identification, we developed species‐specific markers for the three Thai unionoids with considerable economic potential (CEP): that is, Chamberlainia hainesiana, Hyriopsis desowitzi and Hyriopsis myersiana. For this purpose, amplified fragment length polymorphism (AFLP) fingerprints using 24 specific primer pairs were generated for eight samples of each CEP species and four samples of the closely related, non‐CEP species Contradens contradens. Cloning and sequencing of 13 CEP species‐specific AFLP bands revealed fragment collision at three occasions. In total, 16 species‐specific primer pairs were designed and tested on 92 Thai specimens spanning seven species and four genera. Thereby, specificity of (1) three primers to C. hainesiana, (2) one primer to H. desowitzi + Hyriopsis bialata, (3) one primer to H. myersiana + H. bialata and (4) four primers to all three Hyriopsis species tested was confirmed. Respective multiplex PCR protocols are provided. The developed primers enable cheap, quick and reliable identification of the Thai CEP species by one to three PCRs and offer a tool for a range of additional applications within mussel culture and ecological and evolutionary research on these important organisms.     

Molecular cloning and analysis of the UDP-Glucose Pyrophosphorylase in <Emphasis Type="Italic">Streptococcus equi</Emphasis> subsp<Emphasis Type="Italic">. zooepidemicus</Emphasis>

UDP-Glucose Pyrophosphorylase (EC 2.7.7.9, UGPase) plays an important role in Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) cell envelope Hyaluronic acid (HA) biosynthesis and it is also recognized as a virulence determinant in several bacterial species. HA is valuable biopolymer used in the pharmaceutical and cosmetic industry. In addition, encapsulation by HA is considered an important virulence factor in other streptococci. Research UGPase will contribute to the vaccine development of S. zooepidemicus and the production of HA. In this study, The UGPase gene fragment (789 bp) obtained from previous research was amplified using PCR, and located by Genome walking technology (Genebank No.GQ423507). The UGPase was expressed, purified and identified using UGPase antibody. The enzyme kinetic parameters were determined, the temperature and pH of the highest activity for the cloned UGPase were 37°C, pH 7.5. The K _m and K _cat value against UTP and G-1-P was 8.5 μM, 69.05 s⁻¹ and 36.41 μM, 48.81 s⁻¹, respectively. The homology-modeling was operated. Overexpression of the UGPase in S. zooepidemicus, its virulence was slightly affected, and HA yield reduced. Real-time PCR was carried out to determine the UGPase expression levels of both SEZp and SEZugp in different grow period, the level is high in logarithmic phase and low in Decline phase.     

The oxygen-binding modulation of hemocyanin from the Southern spiny lobster <Emphasis Type="Italic">Palinurus gilchristi</Emphasis>

Arthropod hemocyanins transport and store oxygen and are composed of six subunits, or multiples thereof depending on the species. Palinurus gilchristi hemocyanin is found only as 1 × 6-mers, as normally occurs in spiny lobsters. An alkaline pH and removal of calcium ions induce a wholly reversible dissociation into monomers. The oxygen-binding properties of 1 × 6-meric hemocyanin from P. gilchristi were investigated with respect to pH and modulating effect exerted by calcium, lactate and urate. The oxygen affinity was highly affected by pH in the presence of calcium ions, while in its absence the Bohr coefficient became 60% lower. The protein is insensitive to lactate, but affected by urate which markedly increased hemocyanin–oxygen affinity, acting as the physiological major positive effector. Calcium ions decrease oxygen affinity at low concentration range (0–1 mM), while as concentration becomes higher than 100 mM, the oxygen affinity increases, indicating the presence of two independent types of calcium-binding sites with high and low affinity, respectively. The previous hypothesis, that the presence of high-affinity binding sites in addition to low affinity ones could be a characteristic feature of Palinuran hemocyanins, has been tested by analyzing, with respect to calcium–hemocyanin interaction, three other species belonging to Palinura.     

Effects of pH on the Submerged Macrophyte <Emphasis Type="Italic">Hydrilla verticillata</Emphasis>

Hydrilla verticillata (L.f.) Royle is widely distributed and protects the water environment mainly by serving as a potential heavy metal hyperaccumulator. Hydroponic experiments were performed to investigate the biochemical responses of the leaves and stems of H. verticillata at pH values of 5.5, 6.5, 7.5, 8.5, and 9.5 for 7, 14, and 21 days. The results showed that a weak alkaline environment (pH 8.5) promoted plant growth and that an acidic environment (pH 5.5, 6.5) adversely affected normal metabolism. The malondialdehyde content and three antioxidant enzyme activities changed in a similar pattern after the pH treatments: varying increases occurred following all pH treatments with the exception of pH 8.5. The activities of the three N metabolism enzymes briefly increased in an acidic environment and then sharply decreased compared to the control. The ROS-scavenging mechanisms and N metabolism mechanisms in H. verticillata worked together to respond to pH-induced effects. Based on the interplay between antioxidant enzymes and N metabolism enzymes, H. verticillata could defend against the toxicity induced by an acidic environment for approximately seven days and demonstrate stronger adaptability to the alkaline environment. Depending on the growth status and the synergistic effects of the enzymes, an optimum pH of 8.5 for H. verticillata was found in our experiment. Thus, these characteristics reveal a better understanding of this species so that it can be effectively controlled and better referenced for phytoremediation.     

Paradise lost: End‐of‐century warming and acidification under business‐as‐usual emissions have severe consequences for symbiotic corals

Despite recent efforts to curtail greenhouse gas emissions, current global emission trajectories are still following the business‐as‐usual representative concentration pathway (RCP) 8.5 emission pathway. The resulting ocean warming and acidification have transformative impacts on coral reef ecosystems, detrimentally affecting coral physiology and health, and these impacts are predicted to worsen in the near future. In this study, we kept fragments of the symbiotic corals Acropora intermedia (thermally sensitive) and Porites lobata (thermally tolerant) for 7 weeks under an orthogonal design of predicted end‐of‐century RCP8.5 conditions for temperature and pCO₂ (3.5°C and 570 ppm above present‐day, respectively) to unravel how temperature and acidification, individually or interactively, influence metabolic and physiological performance. Our results pinpoint thermal stress as the dominant driver of deteriorating health in both species because of its propensity to destabilize coral–dinoflagellate symbiosis (bleaching). Acidification had no influence on metabolism but had a significant negative effect on skeleton growth, particularly when photosynthesis was absent such as in bleached corals or under dark conditions. Total loss of photosynthesis after bleaching caused an exhaustion of protein and lipid stores and collapse of calcification that ultimately led to A. intermedia mortality. Despite complete loss of symbionts from its tissue, P. lobata maintained small amounts of photosynthesis and experienced a weaker decline in lipid and protein reserves that presumably contributed to higher survival of this species. Our results indicate that ocean warming and acidification under business‐as‐usual CO₂ emission scenarios will likely extirpate thermally sensitive coral species before the end of the century, while slowing the recovery of more thermally tolerant species from increasingly severe mass coral bleaching and mortality. This could ultimately lead to the gradual disappearance of tropical coral reefs globally, and a shift on surviving reefs to only the most resilient coral species.