Interactions between the grass shrimp <Emphasis Type="Italic">Palaemonetes pugio</Emphasis> and the salt marsh grasses <Emphasis Type="Italic">Phragmites australis</Emphasis> and <Emphasis Type="Italic">Spartina alterniflora</Emphasis>

The grass shrimp Palaemonetes pugio, a species common to Spartina alterniflora-dominated marshes, may be sensitive to the invasion of the common reed Phragmites australis in northeastern US salt marshes. We examined two questions: (1) Do grass shrimp have a preference for the native plant over the non-native plant? (2) Are grass shrimp more effective foragers on P. australis? We tested the first hypothesis by comparing the amount of time shrimp spend in physical contact with the plant types over a 1-h period. Shrimp were observed under different arrangements of vegetation to control for differences in conspicuous structural features. Additionally, the amount of time shrimp spent foraging on S. alterniflora and P. australis shoots was compared to determine if shrimp graze more often on S. alterniflora. Shrimp spent significantly more time in contact with S. alterniflora only when plant types were grouped at opposite ends of aquaria, but did not exhibit a foraging preference for this plant type. To address our second question, we investigated the effects of shrimp foraging on stem epifauna, an assemblage of semi-aquatic invertebrates associated with macrophyte shoots. Previous research showed that P. australis supports a lower density of stem-dwelling epifauna relative to S. alterniflora. We hypothesized that the primary grazer of this community, P. pugio, can forage on P. australis stems more effectively due to structural differences between the two plants, causing the lower abundance of epifauna through top-down effects. We exposed individual shoots inhabited by epifauna to shrimp and compared faunal densities on exposed shoots to densities on control shoots after 18 h. The reduction of epifauna by predation was proportional on the two plant types. Therefore, top-down effects can be ruled out as an explanation for the patchy distribution of epifauna observed in P. australis–S. alterniflora marshes.     

Incidence of <Emphasis Type="Italic">Fusarium</Emphasis> spp. on the invasive <Emphasis Type="Italic">Spartina alterniflora</Emphasis> on Chongming Island,Shanghai, China

Fusarium palustre is an endophyte/pathogen of Spartina alterniflora, a saltmarsh grass native to North America that has been associated in the USA with a saltmarsh decline known as Sudden Vegetation Dieback (SVD). Since the intentional introduction of S. alterniflora to stabilize mud flats on Chongming Island, Shanghai, China, S. alterniflora has become invasive, but shows no symptoms of dieback even though F. palustre can be isolated from the plant. When declining S. alterniflora from SVD sites in the northeastern USA were assayed for Fusarium species, an average of 8 % of tissues sampled gave rise to a species of Fusarium of these, 64 % were F. palustre and 16 % were F. incarnatum, a nonpathogenic species. To determine if low densities of F. palustre could explain the lack of dieback symptoms on S. alterniflora from Chongming Island, we assessed the incidence and distribution of Fusarium spp. on S. alterniflora from 12 sites on Chongming Island. On average, 26 % of the stem and root tissues sampled were colonized by a Fusarium species. Of 196 isolates recovered from S. alterniflora, 44 % were F. incarnatum and 41 % were F. palustre. Species determinations were confirmed for a subset of these isolates using a phylogenetic analysis of partial sequences of the translation elongation factor (tef) gene. The observation that Fusarium incidence on S. alterniflora was much greater on Chongming Island than in the USA survey raises the question as to why S. alterniflora on Chongming Island is showing no dieback. Other factors, such as predator release, enhanced nutritional, edaphic and/or other unidentified environmental constraints on Chongming Island may afford S. alterniflora protection from dieback.     

The Impacts of Above- and Belowground Plant Input on Soil Microbiota: Invasive <Emphasis Type="Italic">Spartina alterniflora</Emphasis> Versus Native <Emphasis Type="Italic">Phragmites australis</Emphasis>

Invasive plants affect soil food webs through various resource inputs including shoot litter, root litter and living root input. The net impact of invasive plants on soil biota has been recognized; however, the relative contributions of different resource input pathways have not been quantified. Through a 2 × 2 × 2 factorial field experiment, a pair of invasive and native plant species (Spartina alterniflora vs. Phragmites australis) was compared to determine the relative impacts of their living roots or shoots and root litter on soil microbial and nematode communities. Living root identity affected bacteria-to-fungi PLFA ratios, abundance of total nematodes, plant-feeding nematodes and omnivorous nematodes. Specifically, the plant-feeding nematodes were 627% less abundant when living roots of invasive S. alterniflora were present than those of native P. australis. Likewise, shoot and root biomass (within soil at 0–10 cm depth) of S. alterniflora was, respectively, 300 and 100% greater than those of P. australis. These findings support the enemy release hypothesis of plant invasion. Root litter identity affected other components of soil microbiota (that is, bacterial-feeding nematodes), which were 34% more abundant in the presence of root litter of P. australis than S. alterniflora. Overall, more variation associated with nematode community structure and function was explained by differences in living roots than root or shoot litter for this pair of plant species sharing a common habitat but contrasting invasion degrees. We conclude that belowground resource input is an important mechanism used by invasive plants to affect ecosystem structure and function.     

Field assessment of environmental factors constraining the development and expansion of <Emphasis Type="Italic">Schoenoplectus californicus</Emphasis> marsh at a California tidal freshwater restoration site

The effective restoration of wetland habitats requires understanding the establishment requirements, growth responses, and expansion dynamics of targeted plant species. This is particularly true when restoring areas that have been previously managed for other activities, such as agriculture, which can have legacy effects on the local environment. We investigated environmental factors (specifically hydrology and soil physicochemical conditions) that may influence the establishment, growth and expansion of Schoenoplectus californicus in a tidal freshwater marsh restoration site in the Sacramento–San Joaquin Delta, California, USA. This study site was previously leveed, drained, and utilized for agricultural production. A 1997 levee breach restored tidal connectivity and wetland vegetation has re-established in portions of the area. Our approach coupled an intensively-sampled transect study in S. californicus-dominated marshes with a spatially-extensive survey of S. californicus lateral expansion rates and elevation. Lateral expansion of S. californicus marsh edge was significantly less in lower elevation areas (0.61 ± 0.04 m NAVD88), whereas the marsh edge at higher elevations (0.84 ± 0.03 m NAVD88) exhibited greater expansion, often at rates greater than 1.0 m year^?1. These elevation means correspond to percentages of time that the marsh surface was flooded of 100 and 94 %, respectively. Although marsh edge expansion was influenced by elevation and the resultant hydrology, other factors, such as physical exposure of marsh shorelines and compacted agricultural soils also appear to be important. However, once established, S. californicus appears to be able to ameliorate high soil bulk densities over time as the advancing marsh platform develops.     

Temporal and spatial impact of <Emphasis Type="Italic">Spartina alterniflora</Emphasis> invasion on methanogens community in Chongming Island,China

Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China’s wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.     

Role of Arabidopsis <Emphasis Type="Italic">ABF1</Emphasis>/<Emphasis Type="Italic">3</Emphasis>/<Emphasis Type="Italic">4</Emphasis> during <Emphasis Type="Italic">det1</Emphasis> germination in salt and osmotic stress conditions

Key message

Arabidopsis det1 mutants exhibit salt and osmotic stress resistant germination. This phenotype requires HY5, ABF1, ABF3, and ABF4.

Abstract

While DE-ETIOLATED 1 (DET1) is well known as a negative regulator of light development, here we describe how det1 mutants also exhibit altered responses to salt and osmotic stress, specifically salt and mannitol resistant germination. LONG HYPOCOTYL 5 (HY5) positively regulates both light and abscisic acid (ABA) signalling. We found that hy5 suppressed the det1 salt and mannitol resistant germination phenotype, thus, det1 stress resistant germination requires HY5. We then queried publically available microarray datasets to identify genes downstream of HY5 that were differentially expressed in det1 mutants. Our analysis revealed that ABA regulated genes, including ABA RESPONSIVE ELEMENT BINDING FACTOR 3 (ABF3), are downregulated in det1 seedlings. We found that ABF3 is induced by salt in wildtype seeds, while homologues ABF4 and ABF1 are repressed, and all three genes are underexpressed in det1 seeds. We then investigated the role of ABF3, ABF4, and ABF1 in det1 phenotypes. Double mutant analysis showed that abf3, abf4, and abf1 all suppress the det1 salt/osmotic stress resistant germination phenotype. In addition, abf1 suppressed det1 rapid water loss and open stomata phenotypes. Thus interactions between ABF genes contribute to det1 salt/osmotic stress response phenotypes.

     

Association between <Emphasis Type="Italic">cagA</Emphasis>, <Emphasis Type="Italic">vacAi</Emphasis>, and <Emphasis Type="Italic">dupA</Emphasis> genes of <Emphasis Type="Italic">Helicobacter pylori</Emphasis> and gastroduodenal pathologies in Chilean patients

In addition to the already known cagA gene, novel genetic markers have been associated with Helicobacter pylori (H. pylori) virulence: the dupA and vacAi genes. These genes might play an important role as specific markers to determine the clinical outcome of the disease, especially the vacAi gene, which has been expected to be a good marker of severe pathologies like gastric adenocarcinoma. In the present study, the association of cagA, dupA, and vacAi genes with gastroduodenal pathologies in Chilean patients was studied. One hundred and thirty-two patients positive for H. pylori were divided into two groups—non-severe and severe gastric pathologies—and investigated for the presence of cagA, dupA, and vacAi H. pylori virulence genes by PCR. The cagA gene was detected in 20/132 patients (15.2%), the vacAi1 gene was detected in 54/132 patients (40.9%), the vacAi2 gene was detected in 26/132 patients (19.7%), and the dupA gene was detected in 50/132 (37.9%) patients. Logistic regression model analysis showed that the vacAi1 isoform gene in the infected strains and the severity of the diseases outcome were highly associated, causing severe gastric damage that may lead to gastric cancer (p < 0.0001; OR = 8.75; 95% CI 3.54–21.64). Conversely, cagA (p = 0.3507; OR = 1.62; 95% CI 0.59–4.45) and vacAi2 (p = 0.0114; OR = 3.09; 95% CI 1.26–7.60) genes were not associated with damage, while the dupA gene was associated significantly with non-severe clinical outcome (p = 0.0032; OR = 0.25; 95% CI 0.09–0.65). In addition, dupA gene exerts protection against severe gastric pathologies induced by vacAi1 by delaying the outcome of the disease by approximately 20 years.     

First record of <Emphasis Type="Italic">Spartina alterniflora</Emphasis> in southern Africa indicates adaptive potential of this saline grass

Spartina alterniflora was recorded in 2004 in the Great Brak Estuary, a system along the southern coast of South Africa that closes to the sea. This is alarming as this is a species with a known history as an aggressive invasive plant which has now been found 8000 km from its nearest known location and furthermore it is spreading under atypical conditions of submergence. This first recorded population in Africa indicates the adaptive potential of this invasive grass which survives inundation and non-tidal conditions for months at a time. Spartina alterniflora spread from 2566 m² in 2006 to a maximum area covered of 10,221 m² in 2011. There was an increase in silt, sediment organic matter and a significant reduction in sediment redox potential at sites invaded by S. alterniflora. When the estuary closes to the sea the water level rises and S. alterniflora is flooded, limiting opportunities for mechanical and chemical control. Application of a glyphosate-based herbicide in 2012 showed that chemical control was more effective in reducing the stands than mechanical removal. The additional use of imazapyr in 2014 significantly reduced stem density and the proportion of live stems. Spread of this invasive plant to the intertidal marshes in adjacent estuaries is a potential biodiversity threat although, fortunately, this population does not seem to produce viable seed. There is also the concern that hybridization with the resident S. maritima may occur. Important research and management questions remain i.e. how quickly will the natural marsh re-establish following eradication and how can we prevent movement of the grass to other estuaries?     

<Emphasis Type="Italic">Talaromyces heiheensis</Emphasis> and <Emphasis Type="Italic">T. mangshanicus</Emphasis>, two new species from China

Two new species, Talaromyces heiheensis from rotten wood and T. mangshanicus isolated from soil, are illustrated and described as new to science in sections Trachyspermi and Talaromyces. The phylogenetic positions of the two new species inferred from the internal transcribed spacer, beta-tubulin, calmodulin and RNA polymerase II second largest subunit regions were carried out. Talaromyces heiheensis is phylogenetically closely related to T. albobiverticillius, T. rubrifaciens, T. solicola and T. erythromellis, and characterised by slow growth on Czapek yeast autolysate agar at 25 °C, orange conidia en masse on malt extract agar at 25 °C, biverticillate and terverticillate conidiophores, acerose phialides and subglobose to ellipsoidal, smooth-walled conidia. Talaromyces mangshanicus is related to T. kendrickii, T. qii and T. thailandensis, and characterised by slow-growing colonies with absent or sparse sporulation on CYA agar at 25 °C, conidia en masse greyish purple, purplish red soluble pigment on yeast extract agar (YES) at 25 °C, biverticillate conidiophores, ampulliform phialides and subglobose to ellipsoidal conidia with echinulate walls. They are distinguished from the known species in culture characteristics on four standard media, microscopic features and sequence data.     

The <Emphasis Type="Italic">yajC</Emphasis> gene from <Emphasis Type="Italic">Lactobacillus buchneri</Emphasis> and <Emphasis Type="Italic">Escherichia coli</Emphasis> and its role in ethanol tolerance

The yajC gene (Lbuc_0921) from Lactobacillus buchneri NRRL B-30929 was identified from previous proteomics analyses in response to ethanol treatment. The YajC protein expression was increased by 15-fold in response to 10 % ethanol vs 0 % ethanol. The yajC gene encodes the smaller subunit of the preprotein translocase complex, which interacts with membrane protein SecD and SecF to coordinate protein transport and secretion across cytoplasmic membrane in Escherichia coli. The YajC protein was linked to sensitivity to growth temperatures in E. coli, involved in translocation of virulence factors during Listeria infection, and stimulating a T cell-mediated response of Brucella abortus. In this study, the L. buchneri yajC gene was over-expressed in E. coli. The strain carrying pET28byajC that produces YajC after isopropyl β-d-1-thiogalactopyranoside induction showed tolerance to 4 % ethanol in growth media, compared to the control carrying pET28b. This is the first report linking YajC to ethanol stress and tolerance.     

Ectopic expression of cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) <Emphasis Type="Italic">CsTIR</Emphasis>/<Emphasis Type="Italic">AFB</Emphasis> genes enhance salt tolerance in transgenic <Emphasis Type="Italic">Arabidopsis</Emphasis>

Auxin receptors TIR1/AFBs play an essential role in a series of signaling network cascades. These F-box proteins have also been identified to participate in different stress responses via the auxin signaling pathway in Arabidopsis. Cucumber (Cucumis sativus L.) is one of the most important crops worldwide, which is also a model plant for research. In the study herein, two cucumber homologous auxin receptor F-box genes CsTIR and CsAFB were cloned and studied for the first time. The deduced amino acid sequences showed a 78% identity between CsTIR and AtTIR1 and 76% between CsAFB and AtAFB2. All these proteins share similar characteristics of an F-box domain near the N-terminus, and several Leucine-rich repeat regions in the middle. Arabidopsis plants ectopically overexpressing CsTIR or CsAFB were obtained and verified. Shorter primary roots and more lateral roots were found in these transgenic lines with auxin signaling amplified. Results showed that expression of CsTIR/AFB genes in Arabidopsis could lead to higher seeds germination rates and plant survival rates than wild-type under salt stress. The enhanced salt tolerance in transgenic plants is probably caused by maintaining root growth and controlling water loss in seedlings, and by stabilizing life-sustaining substances as well as accumulating endogenous osmoregulation substances. We proposed that CsTIR/AFB-involved auxin signal regulation might trigger auxin mediated stress adaptation response and enhance the plant salt stress resistance by osmoregulation.     

Molecular evidence for hybridization between invasive <Emphasis Type="Italic">Solidago canadensis</Emphasis> and native <Emphasis Type="Italic">S</Emphasis>. <Emphasis Type="Italic">virgaurea</Emphasis>

Hybridization between alien and native species is biologically very important and could lead to genetic erosion of native taxa. Solidago × niederederi was discovered over a century ago in Austria and described by Khek as a natural hybrid between the alien (nowadays regarded also as invasive) S. canadensis and native S. virgaurea. Although interspecific hybridization in the genus Solidago is considered to be relatively common, hybrid nature of S. × niederederi has not been independently proven using molecular tools, to date. Because proper identification of the parentage for the hybrid Solidago individuals solely based on morphological features can be misleading, in this paper we report an additive polymorphism pattern expressed in the ITS sequences obtained from individuals representing S. × niederederi, and confirm the previous hypothesis that the parental species of this hybrid are S. canadensis and S. virgaurea. Additionally, based on variability at the cpDNA rpl32-trnL locus, we showed that in natural populations hybridization occurs in both directions.     

Effect of <Emphasis Type="Italic">Pinus ponderosa</Emphasis> afforestation on soilborne <Emphasis Type="Italic">Frankia</Emphasis> and saprophytic Actinobacteria in Northwest Patagonia,Argentina

Large areas in the extra-Andean region in the forest - steppe ecotone in “Northwestern Argentinean Patagonia” have been replaced by plantations of the exotic conifer Pinus ponderosa which modify soils physical and chemical factors and alter the biodiversity. Considering that in the region occur saprophytic soilborne actinobacteria that play important role as the fixation of atmospheric nitrogen (N₂) in symbiosis with native plant species and the production of bioactive molecules in plants rhizosphere, we aimed to study the effect of the plantation on the abundance of the N₂ fixer Frankia and on the genus diversity of cultivable rhizospheric actinobacteria. The study was performed with soils of six paired sites with pine plantations and natural neighbor areas (including steppes or shrublands). Abundance of infective Frankia was estimated by evaluating the nodulation capacity of soils, through a plant bioassay using Ochetophila trinervis as trap plant. Isolation trials for saprophytic actinobacteria were performed by applying chemotactic and successive soils dilutions methods. We concluded that P. ponderosa afforestation affect soil actinobacteria. This was mainly evidenced by a decrease in the Frankia nodulation capacity in O. trinervis, which was related to plantation age, to lower soil carbon and nitrogen content, higher available phosphorus, and to a slight decrease in soils pH. Pine plantation influence on the cultivable saprophytic actinobacteria was less clear. The study highlights the importance of soils as source of Frankia and rhizospheric actinobacteria in relation to disturbance caused by pine plantation in natural environments with native actinorhizal plant species.     

The diversity of rhizobia nodulating the <Emphasis Type="Italic">Medicago</Emphasis>, <Emphasis Type="Italic">Melilotus</Emphasis> and <Emphasis Type="Italic">Trigonella</Emphasis> inoculation group in Egypt is marked by the dominance of two genetic types

Twenty four rhizobial strains were isolated from root nodules of Melilotus, Medicago and Trigonella plants growing wild in soils throughout Egypt. The nearly complete 16S rRNA gene sequence from each strain showed that 12 strains (50 %) were closely related to the Ensifer meliloti LMG6133^T type strain with identity values higher than 99.0 %, that 9 (37.5 %) strains were more than 99 % identical to the E. medicae WSM419^T type strain, and that 3 (12.5 %) strains showed 100 % identity with the type strain of N. huautlense S02^T. Accordingly, the diversity of rhizobial strains nodulating wild Melilotus, Medicago and Trigonella species in Egypt is marked by predominance of two genetic types, E. meliloti and E. medicae, although the frequency of isolation was slightly higher in E. meliloti. Sequencing of the symbiotic nodC gene from selected Medicago and Melilotus strains revealed that they were all similar to those of the E. meliloti LMG6133^T and E. medicae WSM419^T type strains, respectively. Similarly, nodC sequences of strains identified as members of the genus Neorhizobium were more than 99 % identical to that of N. galegae symbiovar officinalis HAMBI 114.     

<Emphasis Type="Italic">SnRK2</Emphasis> Homologs in <Emphasis Type="Italic">Gossypium</Emphasis> and <Emphasis Type="Italic">GhSnRK2.6</Emphasis> Improved Salt Tolerance in Transgenic Upland Cotton and <Emphasis Type="Italic">Arabidopsis</Emphasis>

SnRK2s are a large family of plant-specific protein kinases, which play important roles in multiple abiotic stress responses in various plant species. But the family in Gossypium has not been well studied. Here, we identified 13, 10, and 13 members of the SnRK2 family from Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum, respectively, and analyzed the locations of SnRK2 homologs in chromosomes based on genome data of cotton species. Phylogenetic tree analysis of SnRK2 proteins showed that these families were classified into three groups. All SnRK2 genes were comprised of nine exons and eight introns, and the exon distributions and the intron phase of homolog genes among different cotton species were analogous. Moreover, GhSnRK2.6 was overexpressed in Arabidopsis and upland cotton, respectively. Under salt treatment, overexpressed Arabidopsis could maintain higher biomass accumulation than wild-type plants, and GhSnRK2.6 overexpression in cotton exhibited higher germination rate than the control. So, the gene GhSnRK2.6 could be utilized in cotton breeding for salt tolerance.     

<Emphasis Type="Italic">R</Emphasis>-acetoin accumulation and dissimilation in <Emphasis Type="Italic">Klebsiella pneumoniae</Emphasis>

Klebsiella pneumoniae is a 2,3-butanediol producer, and R-acetoin is an intermediate of 2,3-butanediol production. R-acetoin accumulation and dissimilation in K. pneumoniae was studied here. A budC mutant, which has lost 2,3-butanediol dehydrogenase activity, accumulated high levels of R-acetoin in culture broth. However, after glucose was exhausted, the accumulated R-acetoin could be reused by the cells as a carbon source. Acetoin dehydrogenase enzyme system, encoded by acoABCD, was responsible for R-acetoin dissimilation. acoABCD mutants lost the ability to grow on acetoin as the sole carbon source, and the acetoin accumulated could not be dissimilated. However, in the presence of another carbon source, the acetoin accumulated in broth of acoABCD mutants was converted to 2,3-butanediol. Parameters of R-acetoin production by budC mutants were optimized in batch culture. Aerobic culture and mildly acidic conditions (pH 6–6.5) favored R-acetoin accumulation. At the optimized conditions, in fed-batch fermentation, 62.3 g/L R-acetoin was produced by budC and acoABCD double mutant in 57 h culture, with an optical purity of 98.0 %, and a substrate conversion ratio of 28.7 %.