Species-specific Distribution Research Articles

Disparity in elevational shifts of upper species limits in response to recent climate warming in the Qinling Mountains, North-central China

Examinations of upper elevational distribution limits of tree species can provide indications of how subalpine vegetation responds to the ongoing climate warming. Dynamics and functional mechanisms of elevational treelines are reasonably well understood, while explanations for tree species-specific upper elevational distribution limits below the treeline still remain unclear. In this study, we used a state-of-the-art dendroecological approach to reconstruct long-term changes of species-specific upper elevational distribution limits of different plant functional type (i.e., light-demanding deciduous coniferous larch at treeline, shade-tolerant evergreen coniferous fir and shade-intolerant deciduous broad-leaved birch below treeline) along elevational gradients in the Qinling Mountains of north-central China. Over the past three centuries, all the upper species limits shifted upslope as a response to climate warming. However, the warming-induced upslope migrations showed substantial differences, displaying the maximum upward shift of larch with an average elevation of 24.7 m during the past century, while only a slight advance of the non-treeline tree species. The disparity in elevational advance of upper species limits might be attributable to the presence of interspecific competition, showing that the non-treeline tree species experienced intermediate interspecific competition while the treeline tree species experienced no interspecific competition. Thus, our findings suggested that in addition to climate warming, biotic interaction may contribute much to shaping the species-specific upper limit dynamics. This study not only enhanced mechanistic understanding of long-term species-specific upper elevational distribution limit changes, but also highlighted the jointly effects of rising temperatures and species interactions on subalpine vegetation dynamics.

Characterization of the Site-Specific Acid-Base Equilibria of 3-Nitrotyrosine.

The complete macro- and microequilibrium analyses of 3-nitrotyrosine, a biomarker of oxidative stress damage, are presented for the first time. The protonation macroconstants were determined by 1 H-NMR-pH titration, while microconstants were elucidated by a combination of deductive and NMR methods, in which properties of the methyl ester derivative as an auxiliary compound were also studied. Combination of the NMR-pH characterization of the title and auxiliary compounds and the pair-interactivity parameters of 3-iodotyrosine provided the sufficient system to evaluate all the microconstants. NMR-pH profiles, macroscopic and microscopic protonation schemes, and species-specific distribution diagrams are included. The phenolate basicity of 3-nitrotyrosine is 500 times below that of tyrosine, and it is even lower than that of 3-iodotyrosine. This phenomenon can be explained by the stronger electron withdrawing and the negative mesomeric effect of the nitro group. Based on our results, 89 % of the phenolic OH groups are deprotonated in 3-NT molecules at the pH of the blood plasma.

Occurrence and Species-Specific Distribution of Plastic Debris in Wild Freshwater Fish from the Pearl River Catchment, China.

Freshwater systems are an important source and vector of plastic debris found in oceans. However, plastic debris in freshwater organisms has not been well studied. The occurrence, characterization, polymer composition, and seasonal and spatial distribution of plastic debris were investigated in 9 species of wild freshwater fish from the Pearl River catchment, south China. Approximately 50% of the total fish (n = 279) belonging to 9 species were found to ingest plastic debris with an average abundance of 7.0 ± 23.8 items/individual, indicating wide plastic contamination in the Pearl River catchment. Plastic debris were predominantly transparent or white in color, fibers or fragments in shape, and polyethylene, polypropylene, ethylene-propylene copolymer (PE-PP), and polyethylene terephthalate (PET) in polymer composition. A species-specific distribution of the plastic debris was observed in terms of abundance, shape, and polymer composition. Redbelly tilapia had the highest (27.4 ± 54.0 items/individual), whereas common carp had the lowest (0.2 ± 0.4 items/individual) abundance of the plastic debris in their gastrointestinal tracts. Fibers of PET were predominant in the freshwater species except in barbel chubs, which had mostly PE-PP fragments. Omnivores and bottom-dwellers were more likely to ingest plastic debris. Seasonal variation was observed, with generally higher abundance of plastic debris in fish collected in the dry season than in the wet season. Environ Toxicol Chem 2019;38:1504-1513. © 2019 SETAC.

Biomass and nitrogen distribution ratios reveal a reduced root investment in temperate lianas vs. self-supporting plants.

The reliance on external support by lianas has been hypothesized to imply a reduction in the biomass cost of stem construction and root anchorage, and an increased investment in leaves, relative to self-supporting plants. These evolutionary trade-offs have not been adequately tested in an ontogenetic context and on the whole-plant scale. Moreover, the hypothesis may be extended to other potentially limiting resources, such as nitrogen (N.). Plants belonging to five con-familiar pairs of temperate liana/shrub species were cultivated in 120 L barrels and sequentially harvested over up to three growing seasons. To account for the ontogenetic drift, organ biomass and nitrogen fractions were adjusted for plant biomass and N pool, respectively. Lianas invested, on average, relatively less biomass in the root fraction in comparison with shrubs. This was offset by only insignificant increases in leaf or stem investment. Even though liana stems and roots showed higher N concentration in comparison with shrubs, plant N distribution was mostly driven by, and largely matched, the pattern of biomass distribution. Lianas also showed a greater relative growth rate than shrubs. The differences between the growth forms became apparent only when ontogenetic drift was controlled for. These results were confirmed regardless of whether reproductive biomass was included in the analysis. Our results suggest that temperate lianas, in spite of their diverse, species-specific resource distribution patterns, preferentially allocate resources to above-ground organs at the expense of roots. By identifying this trade-off and demonstrating the lack of a general trend for reduction in stem investment in lianas, we significantly modify the prevailing view of liana allocation strategies and evolutionary advantages. Such a resource distribution pattern, along with the cheap unit leaf area and stem unit length construction, situates lianas as a group close to the fast acquisition/rapid growth end of the life strategy spectrum.

Species-specific distribution of intertidal seagrasses along environmental gradients in a tropical estuary (Brunei Bay, Borneo)

Seagrass diversity and distribution in Southeast Asia have been mainly studied in backreef zones but have rarely been studied on intertidal mudflats in estuaries. This research article aims to study seagrass distribution (species diversity, shoot density, and biomass) and morphology (leaf length and leaf number per shoot) on intertidal mudflats in Brunei Bay, Borneo, to understand seagrass responses to water and sediment conditions along the environmental gradient in the estuary. In total, five seagrass species (Cymodocea rotundata, Halodule pinifolia, Halophila ovalis, Halophila minor, and Thalassia hemprichii) were found at five different intertidal sites, and the diversity and biomass were highest at the most upstream site. H. pinifolia was the only species found at all five sites, indicating that this species is the most tolerant of and adaptable to varying water and sediment conditions. H. pinifolia had the highest biomass and longest leaf length at the site with the highest silt and clay percentage (SC%) and organic matter content of sediment, where no other seagrass species were found, suggesting that H. pinifolia could efficiently acquire nutrients without interspecies competition. In contrast, H. ovalis and T. hemprichii were found at the upstream sites and preferred a relatively low SC% in sediment. H. minor was found only at the most downstream site, which had the lowest SC% and is likely to experience the strongest hydrodynamics and receive the least nutrients of all the sites. Based on this study, the seagrass response to environmental gradients in estuaries is proposed to be species-specific, which would have led to the unique seagrass distribution in Brunei Bay.

Spatial distribution, seasonal abundance and exploitation status of shark species in Kenyan coastal waters

Efforts to conserve and manage shark populations are often hampered by a lack of basic data, such as species-specific landings and distribution ranges. We bridge this gap in coastal East Africa by providing data on the distributions, catch rates, morphometrics, and exploitation status of shark species in Kenyan coastal waters. Data were collected from artisanal fishers and from bycatch taken by shallow-water (10–50 m) prawn trawlers from Malindi-Ungwana Bay and demersal research trawlers (10–150-m depth) along the ∼640-km coastline, over a 12-month period (June 2012 to May 2013). A total of 1 893 individual sharks (representing 20 species and 11 families) were sampled from the artisanal fishery (n = 1 610) and the trawlers (n = 283). The demersal trawl bycatches were dominated by the African angelshark Squatina africana (2.39 kg h–1), shortnose spurdog shark Squalus megalops (1.48 kg h–1) and African spotted catshark Holohalaelurus punctatus (0.11 kg h–1). Catches of the scalloped hammerhead shark Sphyrna lewini (0.73 kg h–1), smooth hammerhead shark Sphyrna zygaena (0.60 kg h–1) and grey reef shark Carcharhinus amblyrhynchos (0.77 kg h–1) dominated in the prawn trawlers. Only a few species (S. lewini, C. amblyrhynchos, and blacktip reef shark Carcharhinus melanopterus) showed a coast-wide distribution in the artisanal fishery. Artisanal fishers harvested mostly immature specimens of S. lewini, C. melanopterus and blacktip shark Carcharhinus limbatus, suggesting that the fishery might be unsustainable in the long-term. The Endangered S. lewini is the most vulnerable to overexploitation on the Kenyan coast, with most specimens landed (>90%) being below the size at maturity. Data are also presented on morphometric relationships and observed or estimated exploitation reference points (maximum observed length Lmax, asymptotic length L∞, mean length at first maturity Lm, and optimum length Lopt) for the commonly landed species. A more comprehensive coast-wide National Plan of Action is recommended for the management of shark populations in Kenya.

Long-distance influence of the Rhône River plume on the marine benthic ecosystem: Integrating descriptive ecology and predictive modelling

The Gulf of Lions (GoL) is among the most productive areas of the Mediterranean Sea, with the Rhône River contributing with as much as 90% of the liquid and solid materials (including anthropogenic chemicals) reaching the area. In this paper, we assessed whether classical descriptive ecology and MaxEnt predictive species distribution modelling were able to provide complementary information when analysing the long-distance influence of the river discharges on the GoL benthic ecosystem. Samples were collected in August 2014 from 12 stations covering the sedimentary plain of the deep submarine delta, from the Gulf of Fos to Gruissan. Sediments were mostly muddy with a high organic carbon and low P and N contents first decreasing and then increasing from east to west. The same pattern occurred for chlorophyll-a, particulate organic carbon and sea surface temperature, and was overall correlated with metal and pollutant contents derived from agricultural, port, urban and industrial sources driven by Rhône outputs. We observed a typical deltaic succession in the benthos, showing a relatively low diversity and including polychaetes (Sternaspis scutata) and holothurians (Oestergrenia digitata) known to be indicators of high sedimentation rates. Overall, benthos showed an inversed pattern regarding environmental variables, an evident consequence of the Rhône River influence. The suitability of some species was either positively or negatively correlated with some of the environmental variables, producing species-specific predicted distribution patterns, with the highest amount of information allowing to predict distributions being mainly provided by organic pollutants. Even with a limited number of available samples, our integrated approach reveals to be a very robust tool to highlight hidden patterns and contributes to improve our knowledge on how river-mediated anthropogenic discharges may influence biodiversity distribution and functional patterns in marine benthic ecosystems.

UPLC⁻MS/MS Identification of Sterol Sulfates in Marine Diatoms.

Diatoms are unicellular eukaryotic organisms that play a key ecological and biogeochemical role in oceans as major primary producers. Recently, these microalgae have also attracted interest as a promising source of functional products with widespread relevance. Progress in the knowledge of cell and molecular biology of diatoms is envisaged as a key step to understanding regulation of their life cycle in marine environments as well as facilitating their full and profitable exploitation by biotechnological platforms. Recently, we identified sterol sulfates (StS) as regulatory molecules of cell death in the diatom Skeletonema marinoi. As these compounds may have a general role in diatom physiology and chemical signals in aquatic systems, we investigated a suitable tool for their analysis in laboratory and field samples. Herein, we describe a sensitive, fast, and efficient ultra performance liquid chromatography–mass spectrometry (UPLC–MS) method for qualitative and quantitative analysis of StS from crude extract of diatoms and other microalgae. The method was applied to 13 different strains of our collection of marine protists. This first study suggested a species-specific distribution of StS and identified the sulfated derivatives of 24-methylene cholesterol and 24-methyl cholesterol as the most common members in diatoms.

Spatial distributions, feeding ecologies, and behavioral interactions of four rabbitfish species (Siganus unimaculatus, S. virgatus, S. corallinus, and S. puellus).

Clarifying the underlying mechanisms that enable closely related species to coexist in a particular environment is a fundamental aspect of ecology. Coral reefs support a high diversity of marine organisms, among which rabbitfishes (family Siganidae) are a major component The present study aimed to reveal the mechanism that allows rabbitfishes to coexist on coral reefs in Okinawa, Japan, by investigating the spatial distributions, feeding ecologies, and behavioral interactions of four species: Siganus unimaculatus, S. virgatus, S. corallinus, and S. puellus. All four species had a size-specific spatial distribution, whereby small individuals were found in sheltered areas that were covered by branching and bottlebrush Acropora spp. and large individuals were found in both sheltered and exposed rocky areas. However, no clear species-specific spatial distribution was observed. There was some variation in the food items taken, with S. unimaculatus primarily feeding on brown foliose algae, red foliose algae, and red styloid algae, and S. virgatus and S. puellus preferring brown foliose algae and sponges, respectively. However, S. corallinus did not show any clear differences in food preferences from S. virgatus or S. unimaculatus, mainly feeding on brown foliose algae and red styloid algae. The four species exhibited differences in foraging substrate use, which was probably related to differences in their body shape characteristics: S. unimaculatus has a slender body with a remarkably protruding snout and mainly used concave substrates for feeding, whereas S. virgatus has a deeper body with a low degree of snout protrusion and mainly used convex substrates. The other two species have a low degree of snout protrusion combined with a deeper body in the case of S. corallinus and a slender body in the case of S. puellus and used concave, flat, and convex substrates to an equal degree for feeding. Behavioral interactions were categorized into “agonistic behaviors” (attack and agonistic displays) and “no interactions.” For all four species, a greater frequency of agonistic behaviors was observed when two conspecific pairs approached each other than when two heterospecific individuals encountered each other. Together, these results suggest that food item partitioning is one of the main factors enabling the coexistence of these four syntopic rabbitfish species, which is enhanced by species-specific differences in feeding substrates as a result of their different body shape and behavioral characteristics.

Application of passive-acoustic telemetry to explore the behaviour of ballan wrasse (Labrus bergylta) and lumpfish (Cyclopterus lumpus) in commercial Scottish salmon sea-pens

A passive-acoustic telemetry system was used for the first time for the fine-scale, three-dimensional tracking of individual cleaner fish in commercial Scottish salmon sea-pens in full commercial operation. The aim was to test the system performance and provide baseline data on the comparative distribution and swimming activity of individual ballan wrasse and lumpfish under standard farm practices with the long-term aim of informing stocking and husbandry strategies. In March 2015, wild ballan wrasse (Labrus bergylta) (115 ± 20 g; n = 13) and farmed lumpfish (Cyclopterus lumpus) (281 ± 42 g; n = 13) previously deployed in June–October 2014 were recaptured, implanted with acoustic tags pinging every 6–12 s and released into their original sea cage holding Atlantic salmon (Q2 2014; 2059 ± 35 g mean-weight). Control tags were deployed in cleaner fish hides to validate the system performance. Positional data from nine specimens per species were analysed from March 24th to June 1st 2015, during which time water temperature rose from 7.2 to 9.1 °C and water salinity averaged 26.8 ± 1.5 ppt at 4 m depth. The accuracy of the acoustic positions averaged 0.6 m across the three dimensions of all control tags and was <1 m in 93% of all cases. Significant differences in the distribution and activity of ballan wrasse and lumpfish were observed. Ballan wrasses spent 60 ± 2% of the day-time at or below 15 m, were positioned at significantly shallower depths at night and seldom used the hides provided despite an apparent resting behaviour at the pen bottom and corners. In comparison, lumpfish spent over 80% of the time above 10 m, used hides extensively and preferentially at night (50.1 ± 2.1% at night), but to a lesser extent when the water temperature increased. The acoustic tracking system proved to be an effective tool for visualising cleaner fish behaviour under challenging farm conditions, and the study highlights the critical role of hides in cleaner fish husbandry. Overall, the study quantified species-specific cleaner fish distribution in salmon net-pens supporting distinct interactions with the salmon stock and seasonal behaviour profiles. The results support the current commercial strategy of using two cleaner fish species against sea lice and the need for species-specific management strategies to optimise delousing activity.

Transcriptional and physiological data reveal the dehydration memory behavior in switchgrass (Panicum virgatum L.)

BackgroundSwitchgrass (Panicum virgatum L.) is a model biofuel plant because of its high biomass, cellulose-richness, easy degradation to ethanol, and the availability of extensive genomic information. However, a little is currently known about the molecular responses of switchgrass plants to dehydration stress, especially multiple dehydration stresses.ResultsStudies on the transcriptional profiles of 35-day-old tissue culture plants revealed 741 dehydration memory genes. Gene Ontology and pathway analysis showed that these genes were enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. Further analysis of specific pathways combined with physiological data suggested that switchgrass improved its dehydration resistance by changing various aspects of its responses to secondary dehydration stress (D2), including the regulation of abscisic acid (ABA) and jasmonic acid (JA) biosynthesis and signal transduction, the biosynthesis of osmolytes (l-proline, stachyose and trehalose), energy metabolism (i.e., metabolic process relating to photosynthetic systems, glycolysis, and the TCA cycle), and lignin biosynthesis. The transcriptional data and chemical substance assays showed that ABA was significantly accumulated during both primary (D1) and secondary (D2) dehydration stresses, whereas JA accumulated during D1 but became significantly less abundant during D2. This suggests the existence of a complicated signaling network of plant hormones in response to repeated dehydration stresses. A homology analysis focusing on switchgrass, maize, and Arabidopsis revealed the conservation and species-specific distribution of dehydration memory genes.ConclusionsThe molecular responses of switchgrass plants to successive dehydration stresses have been systematically characterized, revealing a previously unknown transcriptional memory behavior. These results provide new insights into the mechanisms of dehydration stress responses in plants. The genes and pathways identified in this study will be useful for the genetic improvement of switchgrass and other crops.

Genomic in situ hybridization in interspecific hybrids of scallops (Bivalvia, Pectinidae) and localization of the satellite DNA Cf303, and the vertebrate telomeric sequences (TTAGGG)n on chromosomes of scallop Chlamys farreri (Jones & Preston, 1904).

Mitotic chromosome preparations of the interspecific hybrids Chlamys farreri (Jones & Preston, 1904) × Patinopecten yessoensis (Jay, 1857), C. farreri × Argopecten irradians (Lamarck, 1819) and C. farreri × Mimachlamys nobilis (Reeve, 1852) were used to compare two different scallop genomes in a single slide. Although genomic in situ hybridization (GISH) using genomic DNA from each scallop species as probe painted mitotic chromosomes of the interspecific hybrids, the painting results were not uniform; instead it showed species-specific distribution patterns of fluorescent signals among the chromosomes. The most prominent GISH-bands were mainly located at centromeric or telomeric regions of scallop chromosomes. In order to illustrate the sequence constitution of the GISH-bands, the satellite Cf303 sequences of C. farreri and the vertebrate telomeric (TTAGGG)n sequences were used to map mitotic chromosomes of C. farreri by fluorescence in situ hybridization (FISH). The results indicated that the GISH-banding pattern presented by the chromosomes of C. farreri is mainly due to the distribution of the satellite Cf303 DNA, therefore suggesting that the GISH-banding patterns found in the other three scallops could also be the result of the chromosomal distribution of other species-specific satellite DNAs.

Correction: Predicted Shifts in Small Mammal Distributions and Biodiversity in the Altered Future Environment of Alaska: An Open Access Data and Machine Learning Perspective.

[This corrects the article DOI: 10.1371/journal.pone.0132054.].

Deciphering the repetitive DNA landscape in Phaseolus beans and Allied genera (Cajanus and Vigna) by a comparative cytogenomic approach

Several bean species (Fabaceae) have been undergoing intensive genomic research, which includes the generation of massive amount of DNA sequence data. We performed a comparative investigation of the repetitive DNA composition in some bean species (Phaseolus vulgaris - Pvu, P. acutifolius - Pac, P. coccineus - Pco, Cajanus cajan - Cca, Vigna angularis - Van and V. nakashimae - Vna). Genomic sequences were obtained from the NCBI public database Cca/SRX031567, Pac/SRX1182015), Pco/SRX1182014, Pvu-andean accession/SRX1182008 and mesoamerican accession/SRX1182013, Vna/SRX758247 and Van/SRX7575509) and run in the Repeat Explorer pipeline using an all-to-all comparison analysis. Physical mapping of the most abundant repetitive elements was performed by FISH using mitotic chromosomes. Overall, the repetitive DNA fraction makes up around 30% of the genomes, except for both Vigna species (9.7% and 14.6%, for Van and Vna, respectively). LTR-retrotransposons represented the major class, with Ogre-Tat elements showing a large variation, followed by LTR-Chromovirus, satellite DNA repeats, LINEs and DNA transposons. The composition of satellite repeats was variable and four new families were identified, together with five previously described. All satellites were genus- or species-specific. Chromosomal mapping of LTR sequences (Chromovirus and Ogre) showed a differential accumulation on the pericentromeres of most chromosomes, particularly on Phaseolus. Among the satellite repeats, five were used for FISH (four newly identified). The three satellite families from Phaseolus showed different species-specific distribution. PacSAT363 was detected in 12 pericentromeres. PcoSAT36 and PcoSAT336 were accumulated at pericentromes, but PcoSAT336 were also located in some chromosome termini co-localized with 45 rDNA, suggesting that this satellite have probably originated from ribosomal sequences. Cajanus cajan and Vigna showed only one satellite repeat each. CcaSAT100 was located in 18 centromeres, while VanSAT174 corresponded to the 45 rDNA in Vna, but appeared also as an independent centromeric satellite repeat in Van. Our analysis indicates a very dynamic landscape on the evolution of repetitive DNA among beans. Retrotransposons appeared as the main component of genomes and showed higher accumulation in the pericentromeric heterochromatin of Phaseolus species. Satellite repeats were mostly centromeric or pericentromeric and frequently species-specific, suggesting a fast evolution of this type of sequence in the bean genomes.

A comparison of the zooplankton community in the Bay of Bengal and South China Sea during April–May, 2010

This study compares the structure of the zooplankton community in the Bay of Bengal (BoB) and South China Sea (SCS) during the period of spring inter-monsoon, 2010. A total of 215 species of zooplankton were identified, of which 187 species were present in the BoB and 119 in the SCS. Of the taxonomic groups recorded, Copepoda was the most diverse group in all samples followed by pelagic Tunicata, Siphonophorae and Chaetognatha. Flaccisagitta enflata, Cosmocalanus darwinii, Euchaeta larva, Macrura larva and Candacia truncata were predominant both in the BoB and SCS. Moreover, the distribution of some dominant species differed regionally, such as Cypridina dentata, Pleuromamma robusta and Mesosagitta decipiens only in the BoB, and Pleuromamma gracilis, Neocalanus gracilis and Eudoxoides spiralis in the SCS. The average zooplankton abundance was 33.37 ± 7.19 ind. m−3 in the BoB and 35.08 ± 2.07 ind. m−3 in the SCS. Copepoda was one of the most abundant groups in the BoB and SCS. Based on multivariate analysis, it was possible to distinguish the zooplankton in the BoB and SCS communities at the similarity level of approximately 55%, and the dissimilarity was mainly due to C. dentata, P. robusta, M. decipiens, C. darwinii, N. gracilis and P. gracilis. The relationships between zooplankton and temperature, salinity and chlorophyll a were not statistically significant. Zooplankton community structure in the BoB and SCS was observed to be generally similar in terms of species composition and abundance, but the differences observed may be the result of species-specific geographical distribution and local hydrographic conditions.

Characterization of the population structure, drug resistance mechanisms and plasmids of the community-associated Enterobacter cloacae complex in China

To investigate the population structure, drug resistance mechanisms and plasmids of community-associated Enterobacter cloacae complex (CA-ECC) isolates in China. Sixty-two CA-ECC isolates collected from 31 hospitals across China were typed by hsp60 typing and MLST. ESBL and AmpC-overexpression phenotype was determined by double-disc synergy test. Replicon typing and conjugation were performed for plasmid analysis. All ESBL-positive isolates and representative conjugants were subjected to detailed characterization by WGS. Enterobacter hormaechei and Enterobacter kobei were predominant in our collections. MLST distinguished 46 STs with a polyclonal structure. ST591 was the most prevalent clone detected in northern China. Twenty-two isolates (35.5%) were ESBL positive and half of them were E. kobei. ESBL positivity was related to ESBL production (15/22) and to AmpC overexpression (18/22). Core-genome phylogenetic analysis identified intra- and inter-regional dissemination of ESBL-producing E. kobei clones. ESBL producers were exclusively classified as E. hormaechei and E. kobei, and blaCTX-M-3 was the most prevalent ESBL genotype (10/15) detected in four different environments. In the ESBL-positive population, the ESBL producers encoded more drug resistance genes (8-24 genes) by carrying more plasmids (1-3 plasmids) than the non-ESBL-producing isolates, resulting in an inter-group difference in drug susceptibilities. IncHI-type plasmids were prevalent in the ESBL producers (12/15). All IncHI2-type plasmids (n = 11) carried ESBL genes and shared a similar backbone to p09-036813-1A_261 recovered from Salmonella enterica in Canada. The species-specific distribution, species-dependent ESBL mechanism and endemic plasmids identified in our study highlight the necessity for tailored surveillance of CA-ECC in the future.

Downstream migration and mechanisms of dispersal of young fish in rivers

Downstream migration (DSM) of young fish has traditionally been considered a passive process. A review of studies of the patterns and mechanisms of DSM showed that it met the main criterion for migration: that animals move between well-defined habitats according to a predictable schedule. During DSM, fish often leave the habitat in which they reside (inshore zone) and enter a migratory habitat (main channel). DSM is manifested at a seasonal or diel scale and in species-specific spatial distribution patterns. According to our “dispersal with low dilution” hypothesis, the supposed adaptive value of DSM is due not only to dispersal but also to maintenance of aggregations and synchronization of migratory activity. Temporal and spatial peaks of migration promote efficient intraspecific interactions, such as shoaling, and the integrity of populations. We conclude that migratory behaviour is most successful in habitats with optimum complexity and that the influence of behaviour on DSM is most important at key periods and sites (twilight windows and interfaces between habitats).

Diversity and biogeography of arbuscular mycorrhizal fungi in agricultural soils

It has widely been acknowledged that the diversity of arbuscular mycorrhizal fungi (AMF) is greatly affected by climate, land use intensity, and soil parameters. The objective of this study was to investigate AMF diversity in multiple agricultural soils (154 sites; 92 grasslands and 62 croplands) distributed over all agricultural regions in Switzerland and differing in a number of soil parameters (e.g., land use type and intensity, and altitude). We highlighted the main factors responsible for major AMF community shifts and documented specific distribution patterns for each AMF species. AMF spores were morphologically identified and counted for each species. In total, 17,924 spores were classified and 106 AMF species were identified. In general, AMF species richness (SR) was higher in grasslands than in croplands. In croplands, SR increased with altitude but this trend was not observed in grasslands. Some species occurred at virtually all sites, while others were rarely detected, and for others, species-specific distribution patterns were revealed. Some species were affected by land use type or intensity, or related factors like soil organic matter, soil microbial biomass and respiration or nutrient availability. Other species were more affected by soil pH and related parameters like base saturation and carbonate contents, by soil texture, or by altitude, or by a combination of two to several of all these parameters. We conclude that a high number of AMF species may serve as indicator species for specific habitats and land use. These species might deliver certain ecosystem services at their habitats and deserve further investigation about their functional diversity.

Habitat-based species distribution modelling of the Hawaiian deepwater snapper-grouper complex

Deepwater snappers and groupers are valuable components of many subtropical and tropical fisheries globally and understanding the habitat associations of these species is important for spatial fisheries management. Habitat-based species distribution models were developed for the deepwater snapper-grouper complex in the main Hawaiian Islands (MHI). Six eteline snappers (Pristipomoides spp., Aphareus rutilans, and Etelis spp.) and one endemic grouper (Hyporthodus quernus) comprise the species complex known as the Hawaiian Deep Seven Bottomfishes. Species occurrence was recorded using baited remote underwater video stations deployed between 30 and 365m (n=2381) and was modeled with 12 geomorphological covariates using GLMs, GAMs, and BRTs. Depth was the most important predictor across species, along with ridge-like features, rugosity, and slope. In particular, ridge-like features were important habitat predictors for E. coruscans and P. filamentosus. Bottom hardness was an important predictor especially for the two Etelis species. Along with depth, rugosity and slope were the most important habitat predictors for A. rutilans and P. zonatus, respectively. Models built using GAMs and BRTs generally had the highest predictive performance. Finally, using the BRT model output, we created species-specific distribution maps and demonstrated that areas with high predicted probabilities of occurrence were positively related to fishery catch rates.

Submerged aquatic vegetation, topography and flow characteristics in the upper, tidal Hudson River: Progress toward a predictive habitat model

Submerged aquatic vegetation (SAV) plays a critical role in biogeochemical cycling, primary productivity, sediment dynamics and current flow within the systems they inhabit. SAV communities in the Upper Hudson River Estuary are comprised of species assemblages dominated by two very morphologically distinct species: the native Vallisneria americana, which has wide-strap shaped leaves that are completely submerged underwater, and the invasive Trapa natans, which produces leaf rosettes that float at the water’s surface. Using characteristics of modeled tidal/riverine flow, we examined the distribution and composition of the predominant SAV in the estuary. SAV habitat space was, on average, well described by depth and flow. From a hydrodynamic standpoint however, the two species occupied very similar niche spaces. Species-specific distribution patterns and co-occurrence rates did not appear to be strongly controlled by physical tolerances of topography or flow. Other ecological drivers such as disturbance regimes, dispersal strategies, plant-animal interactions, and sediment chemistry and composition might explain distribution patterns and T. natans expansion more accurately, rather than hydrodynamics alone. Sixty years after reaching the Hudson River Estuary, T. natans appears unable to fully displace V. americana, despite significant overlap in habitat space and spatial distribution. Future management of the exotic T. natans should consider its role as an ecosystem engineer, adding to overall habitat diversity, rather than the current focus on its perceived invasibilty.