Seed Release in Lodgepole Pine Forests After Mountain Pine Beetle Outbreak

Serotinous lodgepole pine (Pinus contorta var. latifolia) usually regenerates after fire or harvesting provided conditions that are warm enough to open the cones. There are concerns that large-scale stand mortality due to mountain pine beetle (MPB) outbreak could greatly reduce natural regeneration of lodgepole pine because the closed cones are held in place in the tree canopy without any seed release. We selected 15 stands (five gray-attacked, five red-attacked, and five green) in the Sub-Boreal Spruce biogeoclimatic zone of British Columbia to determine loss of canopy seed via breakage of twig-bearing cones and cone opening (i.e., loss of serotiny) throughout the 2008 growing season. We also quantified seed loss of fallen cones via predation and cone opening. Red-attacked stands lost an estimated 175 000 seed-bearing canopy cones ha-1 yr -1 due to crown friction resulting in twig breakage, representing an over three-fold increase compared to green stands. This result was considered ecologically important since it equated to over 25 % of canopy cones lost to the forest floor. Red- and gray-attacked stands also had 15 % of canopy seed lost due to cone weathering resulting in cone opening. Additional seed losses occurred in the gray-attacked stands due to additional cone opening (58 % yr-1) on the forest floor and predation (12 000 fallen seed-bearing cones ha-1 yr-1). MPB-killed stands released some canopy seed through breakage of twig-bearing cones, partial loss of serotiny, and forest floor cone opening. The implications are: i) seed supply is gradually lost in the first years after attack; ii) if adequate levels of regeneration are to occur, either anthropogenic or fire disturbances must happen shortly after tree mortality. We conclude that lodgepole pine is poorly-adapted to disturbances such as MPB because seed is slowly released onto an unfavorable seed bed

Patterns of plant naturalization show that facultative mycorrhizal plants are more likely to succeed outside their native Eurasian ranges

The naturalization of an introduced species is a key stage during the invasion process. Therefore, identifying the traits that favor the naturalization of non-native species can help understand why some species are more successful when introduced to new regions. The ability and the requirement of a plant species to form a mutualism with mycorrhizal fungi, together with the types of associations formed may play a central role in the naturalization success of different plant species. To test the relationship between plant naturalization success and their mycorrhizal associations we analysed a database composed of mycorrhizal status and type for 1981 species, covering 155 families and 822 genera of plants from Europe and Asia, and matched it with the most comprehensive database of naturalized alien species across the world (GloNAF). In mainland regions, we found that the number of naturalized regions was highest for facultative mycorrhizal, followed by obligate mycorrhizal and lowest for non-mycorrhizal plants, suggesting that the ability of forming mycorrhizas is an advantage for introduced plants. We considered the following mycorrhizal types: arbuscular, ectomycorrhizal, ericoid and orchid mycorrhizal plants. Further, dual mycorrhizal species were those that included observations of arbuscular mycorrhizas as well as observations of ectomycorrhizas. Naturalization success (based on the number of naturalized regions) was highest for arbuscular mycorrhizal and dual mycorrhizal plants, which may be related to the low host specificity of arbuscular mycorrhizal fungi and the consequent high availability of arbuscular mycorrhizal fungal partners. However, these patterns of naturalization success were erased in islands, suggesting that the ability to form mycorrhizas may not be an advantage for establishing self-sustaining populations in isolated regions. Taken together our results show that mycorrhizal status and type play a central role in the naturalization process of introduced plants in many regions, but that their effect is modulated by other factorsFil: Moyano, Jaime. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Dickie, Ian. University of Canterbury; Nueva ZelandaFil: Rodriguez Cabal, Mariano Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Nuñez, Martin Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentin

Southern Hemisphere atmospheric history of carbon monoxide over the late Holocene reconstructed from multiple Antarctic ice archives

Carbon monoxide (CO) is a naturally occurring atmospheric trace gas, a regulated pollutant, and one of the main components determining the oxidative capacity of the atmosphere. Evaluating climate–chemistry models under different conditions than today and constraining past CO sources requires a reliable record of atmospheric CO mixing ratios ([CO]) that includes data since preindustrial times. Here, we report the first continuous record of atmospheric [CO] for Southern Hemisphere (SH) high latitudes over the past 3 millennia. Our continuous record is a composite of three high-resolution Antarctic ice core gas records and firn air measurements from seven Antarctic locations. The ice core gas [CO] records were measured by continuous flow analysis (CFA), using an optical feedback cavity-enhanced absorption spectrometer (OF-CEAS), achieving excellent external precision (2.8–8.8 ppb; 2σ) and consistently low blanks (ranging from 4.1±1.2 to 7.4±1.4 ppb), thus enabling paleo-atmospheric interpretations. Six new firn air [CO] Antarctic datasets collected between 1993 and 2016 CE at the DE08-2, DSSW19K, DSSW20K, South Pole, Aurora Basin North (ABN), and Lock-In sites (and one previously published firn CO dataset at Berkner) were used to reconstruct the atmospheric history of CO from ∼1897 CE, using inverse modeling that incorporates the influence of gas transport in firn. Excellent consistency was observed between the youngest ice core gas [CO] and the [CO] from the base of the firn and between the recent firn [CO] and atmospheric [CO] measurements at Mawson station (eastern Antarctica), yielding a consistent and contiguous record of CO across these different archives. Our Antarctic [CO] record is relatively stable from −835 to 1500 CE, with mixing ratios within a 30–45 ppb range (2σ). There is a ∼5 ppb decrease in [CO] to a minimum at around 1700 CE during the Little Ice Age. CO mixing ratios then increase over time to reach a maximum of ∼54 ppb by ∼1985 CE. Most of the industrial period [CO] growth occurred between about 1940 to 1985 CE, after which there was an overall [CO] decrease, as observed in Greenland firn air and later at atmospheric monitoring sites and attributed partly to reduced CO emissions from combustion sources. Our Antarctic ice core gas CO observations differ from previously published records in two key aspects. First, our mixing ratios are significantly lower than reported previously, suggesting that previous studies underestimated blank contributions. Second, our new CO record does not show a maximum in the late 1800s. The absence of a [CO] peak around the turn of the century argues against there being a peak in Southern Hemisphere biomass burning at this time, which is in agreement with (i) other paleofire proxies such as ethane or acetylene and (ii) conclusions reached by paleofire modeling. The combined ice core and firn air [CO] history, spanning −835 to 1992 CE, extended to the present by the Mawson atmospheric record, provides a useful benchmark for future atmospheric chemistry modeling studies

lpxC and yafS are the Most Suitable Internal Controls to Normalize Real Time RT-qPCR Expression in the Phytopathogenic Bacteria Dickeya dadantii

Background: Quantitative RT-PCR is the method of choice for studying, with both sensitivity and accuracy, the expression of genes. A reliable normalization of the data, using several reference genes, is critical for an accurate quantification of gene expression. Here, we propose a set of reference genes, of the phytopathogenic bacteria Dickeya dadantii and Pectobacterium atrosepticum, which are stable in a wide range of growth conditions. [br/] Results: We extracted, from a D. dadantii micro-array transcript profile dataset comprising thirty-two different growth conditions, an initial set of 49 expressed genes with very low variation in gene expression. Out of these, we retained 10 genes representing different functional categories, different levels of expression (low, medium, and high) and with no systematic variation in expression correlating with growth conditions. We measured the expression of these reference gene candidates using quantitative RT-PCR in 50 different experimental conditions, mimicking the environment encountered by the bacteria in their host and directly during the infection process in planta. The two most stable genes (ABF-0017965 (lpxC) and ABF-0020529 (yafS) were successfully used for normalization of RT-qPCR data. Finally, we demonstrated that the ortholog of lpxC and yafS in Pectobacterium atrosepticum also showed stable expression in diverse growth conditions. [br/] Conclusions: We have identified at least two genes, lpxC (ABF-0017965) and yafS (ABF-0020509), whose expressions are stable in a wide range of growth conditions and during infection. Thus, these genes are considered suitable for use as reference genes for the normalization of real-time RT-qPCR data of the two main pectinolytic phytopathogenic bacteria D. dadantii and P. atrosepticum and, probably, of other Enterobacteriaceae. Moreover, we defined general criteria to select good reference genes in bacteria

WNP: A Novel Algorithm for Gene Products Annotation from Weighted Functional Networks

Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational approaches based on Bayesian networks for data integration. The result of these computational approaches is an interaction network with weighted links representing connectivity likelihood between two functionally related GPs. The weighted network generated by these computational approaches can be used to predict annotations for functionally uncharacterized GPs. Here we introduce Weighted Network Predictor (WNP), a novel algorithm for function prediction of biologically uncharacterized GPs. Tests conducted on simulated data show that WNP outperforms other 5 state-of-the-art methods in terms of both specificity and sensitivity and that it is able to better exploit and propagate the functional and topological information of the network. We apply our method to Saccharomyces cerevisiae yeast and Arabidopsis thaliana networks and we predict Gene Ontology function for about 500 and 10000 uncharacterized GPs respectively

Functional Expression of Human Adenine Nucleotide Translocase 4 in Saccharomyces Cerevisiae

The adenine nucleotide translocase (ANT) mediates the exchange of ADP and ATP across the inner mitochondrial membrane. The human genome encodes multiple ANT isoforms that are expressed in a tissue-specific manner. Recently a novel germ cell-specific member of the ANT family, ANT4 (SLC25A31) was identified. Although it is known that targeted depletion of ANT4 in mice resulted in male infertility, the functional biochemical differences between ANT4 and other somatic ANT isoforms remain undetermined. To gain insight into ANT4, we expressed human ANT4 (hANT4) in yeast mitochondria. Unlike the somatic ANT proteins, expression of hANT4 failed to complement an AAC-deficient yeast strain for growth on media requiring mitochondrial respiration. Moreover, overexpression of hANT4 from a multi-copy plasmid interfered with optimal yeast growth. However, mutation of specific amino acids of hANT4 improved yeast mitochondrial expression and supported growth of the AAC-deficient yeast on non-fermentable carbon sources. The mutations affected amino acids predicted to interact with phospholipids, suggesting the importance of lipid interactions for function of this protein. Each mutant hANT4 and the somatic hANTs exhibited similar ADP/ATP exchange kinetics. These data define common and distinct biochemical characteristics of ANT4 in comparison to ANT1, 2 and 3 providing a basis for study of its unique adaptation to germ cells

A Novel Strategy to Construct Yeast Saccharomyces cerevisiae Strains for Very High Gravity Fermentation

Very high gravity (VHG) fermentation is aimed to considerably increase both the fermentation rate and the ethanol concentration, thereby reducing capital costs and the risk of bacterial contamination. This process results in critical issues, such as adverse stress factors (ie., osmotic pressure and ethanol inhibition) and high concentrations of metabolic byproducts which are difficult to overcome by a single breeding method. In the present paper, a novel strategy that combines metabolic engineering and genome shuffling to circumvent these limitations and improve the bioethanol production performance of Saccharomyces cerevisiae strains under VHG conditions was developed. First, in strain Z5, which performed better than other widely used industrial strains, the gene GPD2 encoding glycerol 3-phosphate dehydrogenase was deleted, resulting in a mutant (Z5ΔGPD2) with a lower glycerol yield and poor ethanol productivity. Second, strain Z5ΔGPD2 was subjected to three rounds of genome shuffling to improve its VHG fermentation performance, and the best performing strain SZ3-1 was obtained. Results showed that strain SZ3-1 not only produced less glycerol, but also increased the ethanol yield by up to 8% compared with the parent strain Z5. Further analysis suggested that the improved ethanol yield in strain SZ3-1 was mainly contributed by the enhanced ethanol tolerance of the strain. The differences in ethanol tolerance between strains Z5 and SZ3-1 were closely associated with the cell membrane fatty acid compositions and intracellular trehalose concentrations. Finally, genome rearrangements in the optimized strain were confirmed by karyotype analysis. Hence, a combination of genome shuffling and metabolic engineering is an efficient approach for the rapid improvement of yeast strains for desirable industrial phenotypes

Soil fungal networks maintain local dominance of ectomycorrhizal trees

The mechanisms regulating community composition and local dominance of trees in species-rich forests are poorly resolved, but the importance of interactions with soil microbes is increasingly acknowledged. Here, we show that tree seedlings that interact via root-associated fungal hyphae with soils beneath neighbouring adult trees grow faster and have greater survival than seedlings that are isolated from external fungal mycelia, but these effects are observed for species possessing ectomycorrhizas (ECM) and not arbuscular mycorrhizal (AM) fungi. Moreover, survival of naturally-regenerating AM seedlings over ten years is negatively related to the density of surrounding conspecific plants, while survival of ECM tree seedlings displays positive density dependence over this interval, and AM seedling roots contain greater abundance of pathogenic fungi than roots of ECM seedlings. Our findings show that neighbourhood interactions mediated by beneficial and pathogenic soil fungi regulate plant demography and community structure in hyperdiverse forests

Reference genes for gene expression studies in wheat flag leaves grown under different farming conditions

<p>Abstract</p> <p>Background</p> <p>Internal control genes with highly uniform expression throughout the experimental conditions are required for accurate gene expression analysis as no universal reference genes exists. In this study, the expression stability of 24 candidate genes from <it>Triticum aestivum </it>cv. Cubus flag leaves grown under organic and conventional farming systems was evaluated in two locations in order to select suitable genes that can be used for normalization of real-time quantitative reverse-transcription PCR (RT-qPCR) reactions. The genes were selected among the most common used reference genes as well as genes encoding proteins involved in several metabolic pathways.</p> <p>Findings</p> <p>Individual genes displayed different expression rates across all samples assayed. Applying geNorm, a set of three potential reference genes were suitable for normalization of RT-qPCR reactions in winter wheat flag leaves cv. Cubus: <it>TaFNRII </it>(ferredoxin-NADP(H) oxidoreductase; AJ457980.1), <it>ACT2 </it>(actin 2; TC234027), and <it>rrn26 </it>(a putative homologue to RNA 26S gene; AL827977.1). In addition of these three genes that were also top-ranked by NormFinder, two extra genes: <it>CYP18-2 </it>(Cyclophilin A, AY456122.1) and <it>TaWIN1 </it>(14-3-3 like protein, AB042193) were most consistently stably expressed.</p> <p>Furthermore, we showed that <it>TaFNRII, ACT2</it>, and <it>CYP18-2 </it>are suitable for gene expression normalization in other two winter wheat varieties (Tommi and Centenaire) grown under three treatments (organic, conventional and no nitrogen) and a different environment than the one tested with cv. Cubus.</p> <p>Conclusions</p> <p>This study provides a new set of reference genes which should improve the accuracy of gene expression analyses when using wheat flag leaves as those related to the improvement of nitrogen use efficiency for cereal production.</p