Facilitating better outcomes: how positive species interactions can improve oyster reef restoration

Over 85% of the world's oyster reefs have been lost in the past two centuries, triggering a global effort to restore shellfish reef ecosystems and the ecosystem services they provide. While there has been considerable success in re-establishing oyster reefs, many challenges remain. These include: high incidence of failed restoration, high cost of restoration per unit area, and increasing stress from climate change. In order to leverage our past successes and progress the field, we must increase restoration efficiencies that not only reduce cost per unit area, but also increase the resilience of restored ecosystems. To help address this need, we qualitatively review the literature associated with the structure and function of oyster reef ecosystems to identify key positive species interactions (i.e., those species interactions where at least one partner benefits and no partners are harmed). We classified positive inter- and intraspecific interactions between oysters and organisms associated with oyster ecosystems into the following seven functional categories: (1) physical reef creation, (2) positive density dependence, (3) refugia from physical stress, (4) refugia from biological stress, (5) biodiversity enhancement, (6) settlement improvement, and (7) long-distance facilitation. We discuss each category of positive interaction and how restoration practitioners can use knowledge of such processes to enhance restoration success. We propose that systematic incorporation of positive species interactions into restoration practice will both enhance ecological services provided by restored reefs and increase restoration success

Transgenic increases in seed oil content are associated with the differential expression of novel Brassica-specific transcripts

<p>Abstract</p> <p>Background</p> <p>Seed oil accumulates primarily as triacylglycerol (TAG). While the biochemical pathway for TAG biosynthesis is known, its regulation remains unclear. Previous research identified microsomal diacylglycerol acyltransferase 1 (DGAT1, EC 2.3.1.20) as controlling a rate-limiting step in the TAG biosynthesis pathway. Of note, overexpression of <it>DGAT1 </it>results in substantial increases in oil content and seed size. To further analyze the global consequences of manipulating <it>DGAT1 </it>levels during seed development, a concerted transcriptome and metabolome analysis of transgenic <it>B. napus </it>prototypes was performed.</p> <p>Results</p> <p>Using a targeted <it>Brassica </it>cDNA microarray, about 200 genes were differentially expressed in two independent transgenic lines analyzed. Interestingly, 24–33% of the targets showing significant changes have no matching gene in <it>Arabidopsis </it>although these represent only 5% of the targets on the microarray. Further analysis of some of these novel transcripts indicated that several are inducible by ABA in microspore-derived embryos. Of the 200 <it>Arabidopsis </it>genes implicated in lipid biology present on the microarray, 36 were found to be differentially regulated in DGAT transgenic lines. Furthermore, kinetic reverse transcriptase Polymerase Chain Reaction (k-PCR) analysis revealed up-regulation of genes encoding enzymes of the Kennedy pathway involved in assembly of TAGs. Hormone profiling indicated that levels of auxins and cytokinins varied between transgenic lines and untransformed controls, while differences in the pool sizes of ABA and catabolites were only observed at later stages of development.</p> <p>Conclusion</p> <p>Our results indicate that the increased TAG accumulation observed in transgenic <it>DGAT1 </it>plants is associated with modest transcriptional and hormonal changes during seed development that are not limited to the TAG biosynthesis pathway. These might be associated with feedback or feed-forward effects due to altered levels of DGAT1 activity. The fact that a large fraction of significant amplicons have no matching genes in <it>Arabidopsis </it>compromised our ability to draw concrete inferences from the data at this stage, but has led to the identification of novel genes of potential interest.</p

A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds

Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality

Trophic consequences of non-native pumpkinseed Lepomis gibbosus for native pond fishes

Introduced non-native fishes can cause considerable adverse impacts on freshwater ecosystems. The pumpkinseed Lepomis gibbosus, a North American centrarchid, is one of the most widely distributed non-native fishes in Europe, having established self-sustaining populations in at least 28 countries, including the U.K. where it is predicted to become invasive under warmer climate conditions. To predict the consequences of increased invasiveness, a field experiment was completed over a summer period using a Control comprising of an assemblage of native fishes of known starting abundance and a Treatment using the same assemblage but with elevated L. gibbosus densities. The trophic consequences of L. gibbosus invasion were assessed with stable isotope analysis and associated metrics including the isotopic niche, measured as standard ellipse area. The isotopic niches of native gudgeon Gobio gobio and roach Rutilus rutilus overlapped substantially with that of non-native L. gibbosus, and were also substantially reduced in size compared to ponds where L. gibbosus were absent. This suggests these native fishes shifted to a more specialized diet in L. gibbosus presence. Both of these native fishes also demonstrated a concomitant and significant reduction in their trophic position in L. gibbosus presence, with a significant decrease also evident in the somatic growth rate and body condition of G. gobio. Thus, there were marked changes detected in the isotopic ecology and growth rates of the native fish in the presence of non-native L. gibbosus. The implications of these results for present and future invaded pond communities are discussed

Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm

<p>Abstract</p> <p>Background</p> <p>Nowadays, it is possible to collect expression levels of a set of genes from a set of biological samples during a series of time points. Such data have three dimensions: gene-sample-time (GST). Thus they are called 3D microarray gene expression data. To take advantage of the 3D data collected, and to fully understand the biological knowledge hidden in the GST data, novel subspace clustering algorithms have to be developed to effectively address the biological problem in the corresponding space.</p> <p>Results</p> <p>We developed a subspace clustering algorithm called Order Preserving Triclustering (OPTricluster), for 3D short time-series data mining. OPTricluster is able to identify 3D clusters with coherent evolution from a given 3D dataset using a combinatorial approach on the sample dimension, and the order preserving (OP) concept on the time dimension. The fusion of the two methodologies allows one to study similarities and differences between samples in terms of their temporal expression profile. OPTricluster has been successfully applied to four case studies: immune response in mice infected by malaria (<it>Plasmodium chabaudi</it>), systemic acquired resistance in <it>Arabidopsis thaliana</it>, similarities and differences between inner and outer cotyledon in <it>Brassica napus </it>during seed development, and to <it>Brassica napus </it>whole seed development. These studies showed that OPTricluster is robust to noise and is able to detect the similarities and differences between biological samples.</p> <p>Conclusions</p> <p>Our analysis showed that OPTricluster generally outperforms other well known clustering algorithms such as the TRICLUSTER, gTRICLUSTER and K-means; it is robust to noise and can effectively mine the biological knowledge hidden in the 3D short time-series gene expression data.</p

Endosperm development in Brachypodium distachyon

Grain development and its evolution in grasses remains poorly understood, despite cereals being our most important source of food. The grain, for which many grass species have been domesticated, is a single-seeded fruit with prominent and persistent endosperm. Brachypodium distachyon, a small wild grass, is being posited as a new model system for the temperate small grain cereals, but little is known about its endosperm development and how this compares with that of the domesticated cereals. A cellular and molecular map of domains within the developing Brachypodium endosperm is constructed. This provides the first detailed description of grain development in Brachypodium for the reference strain, Bd21, that will be useful for future genetic and comparative studies. Development of Brachypodium grains is compared with that of wheat. Notably, the aleurone is not regionally differentiated as in wheat, suggesting that the modified aleurone region may be a feature of only a subset of cereals. Also, the central endosperm and the nucellar epidermis contain unusually prominent cell walls that may act as a storage material. The composition of these cell walls is more closely related to those of barley and oats than to those of wheat. Therefore, although endosperm development is broadly similar to that of temperate small grain cereals, there are significant differences that may reflect its phylogenetic position between the Triticeae and rice

Induction of isoprenyl diphosphate synthases, plant hormones and defense signalling genes correlates with traumatic resin duct formation in Norway spruce (Picea abies)

Norway spruce (Picea abies) defends itself against herbivores and pathogens by formation of traumatic resin ducts filled with terpenoid-based oleoresin. An important group of enzymes in terpenoid biosynthesis are the short-chain isoprenyl diphosphate synthases which produce geranyl diphosphate (C10), farnesyl diphosphate (C15), and geranylgeranyl diphosphate (C20) as precursors of monoterpenes, sesquiterpenes, and diterpene resin acids, respectively. After treatment with methyl jasmonate (MJ) we investigated the expression of all isoprenyl diphosphate synthase genes characterized to date from Norway spruce and correlated this with formation of traumatic resin ducts and terpene accumulation. Formation of traumatic resin ducts correlated with higher amounts of monoterpenes, sesquiterpenes and diterpene resin acids and an upregulation of isoprenyl diphosphate synthase genes producing geranyl diphosphate or geranylgeranyl diphosphate. Among defense hormones, jasmonate and jasmonate-isoleucine conjugate accumulated to higher levels in trees with extensive traumatic resin duct formation, whereas salicylate did not. Jasmonate and ethylene are likely to both be involved in formation of traumatic resin ducts based on elevated transcripts of genes encoding lipoxygenase and 1-aminocyclopropane-1-carboxylic acid oxidase associated with resin duct formation. Other genes involved in defense signalling in other systems, mitogen-activated protein kinase3 and nonexpressor of pathogenesis-related gene1, were also associated with traumatic resin duct formation. These responses were detected not only at the site of MJ treatment, but also systemically up to 60 cm above the site of treatment on the trunk

Trophic consequences of an invasive, small-bodied non-native fish, sunbleak Leucaspius delineatus, for native pond fishes

Assessments of the trophic consequences of invasive fishes are important for quantifying their ecological impacts on native species more generally. A small-bodied cyprinid fish native to continental Europe and introduced in the 1970s to the U.K, the sunbleak Leuciscus delineatus, has been shown previously to establish closer social associations with native species of similar size than do native species amongst themselves. To assess the potential detrimental trophic consequences of native species associations with L. delineatus, a field-based experiment was undertaken in summer 2015 in six outdoor, artificial ponds containing three native cyprinid species (rudd Scardinius erthrophthalamus, gudgeon Gobio gobio, tench Tinca tinca). Three ponds were controls (no L. delineatus) and three were treatments (L. delineatus present). The results of stable isotope analysis (SIA) of fish tissue samples provided strong evidence that the isotopic niches of both native benthic fishes were reduced in the presence of L. delineatus, although there were no significant effects on the trophic position, body size or condition of two of the three native fish species. Introduced L. delineatus maintained a core isotopic niche that was distinct from the two native benthic fishes, with no overlap detected between native and non-native fishes when including 40 % and 95% of the data. These results indicate that the response of the native fishes to the introduction of L. delineatus was niche constriction via trophic specialisation, with this response sufficient to maintain their growth rates and condition. This result is similar to studies on a range of small-bodied invasive fishes, suggesting the trophic impacts of these invaders are relatively consistent across species and systems