The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry

peer-reviewedThe genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two ‘types’, G-type and P-type that differ in trichome density, and their glucosinolate and saponin profiles. A key difference is the stereochemistry of hydroxylation of their common phenethylglucosinolate backbone, leading to epimeric glucobarbarins. Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. B. vulgaris is resistant to the diamondback moth, and may be exploited for “dead-end” trap cropping where glucosinolates stimulate oviposition and saponins deter larvae to the extent that they die. The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding

Microbial communities and bioactive compounds in marine sponges of the family Irciniidae-a review

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.Portuguese Foundation [PTDC/MAR/101431/2008, PTDC/BIA-MIC/3865/2012]; European Regional Development Fund (ERDF) through the Operational Competitiveness Programme (COMPETE); national funds through FCT (Foundation for Science and Technology) [PEst-C/MAR/LA0015/2011]; FCT [SFRH/BD/60873/2009]info:eu-repo/semantics/publishedVersio

Last Bite: No Fish Oil No Footnotes

The exponential growth of off-shore mariculture that has occurred worldwide over the last 10 years has raised concern about the impact of the waste produced by this industry on the ecological integrity of the sea bottom. Investigations into this potential source of impact on the biochemistry of the sea floor have provided contrasting results, and no compelling explanations for these discrepancies have been provided to date. To quantify the impact of fish-farm activities on the biochemistry of sediments, we have investigated the quantity and biochemical composition of sediment organic matter in four different regions in the temperate-warm Mediterranean Sea: Akrotiri Bay (Cyprus), Sounion Bay (Greece), Pachino Bay (Italy), and the Gulf of Alicante (Spain). In these four study regions, the concentrations of phytopigments, proteins, carbohydrates, and lipids in the sediments were measured, comparing locations receiving wastes from fish farms to control locations in two different habitats: seagrass beds and soft nonvegetated substrates. Downward fluxes were also measured in all of the regions, up to 200 m from the fish farms, to assess the potential spatial extent of the impact. In all four regions, with the exception of seagrass sediments in Spain, the biochemistry of the sediments showed significant differences between the control and fish-farm locations. However, the variables explaining the differences observed varied among the regions and between habitats, suggesting idiosyncratic effects of fish-farm waste on the biochemistry of sediments. These are possibly related to differences in the local physicochemical variables that could explain a significant proportion of the differences seen between the control and fish-farm locations. Biodeposition derived from the fish farms decreased with increasing distance from the fish-farm cages, but with different patterns in the four regions. Our results indicate that quantitative and qualitative changes in the organic loads of the sediments that arise from intensive aquaculture are dependent upon the ecological context and are not predictable only on the basis of fish-farm attributes and hydrodynamic regimes. Therefore, the siting of fish farms should only be allowed after a case-by-case assessment of the ecological context of the region, especially in terms of the organic matter load and its biochemical composition

Towards an ecological index for tropical soil quality based on soil macrofauna

The objective of this work was to construct a simple index based on the presence/absence of different groups of soil macrofauna to determine the ecological quality of soils. The index was tested with data from 20 sites in South and Central Tabasco, Mexico, and a positive relation between the model and the field observations was detected. The index showed that diverse agroforestry systems had the highest soil quality index (1.00), and monocrops without trees, such as pineapple, showed the lowest soil quality index (0.08). Further research is required to improve this model for natural systems that have very low earthworm biomass

Fitness costs associated with evolved herbicide resistance alleles in plants

Predictions based on evolutionary theory suggest that the adaptive value of evolved herbicide resistance alleles may be compromised by the existence of fitness costs. There have been many studies quantifying the fitness costs associated with novel herbicide resistance alleles, reflecting the importance of fitness costs in determining the evolutionary dynamics of resistance. However, many of these studies have incorrectly defined resistance or used inappropriate plant material and methods to measure fitness. This review has two major objectives. First, to propose a methodological framework that establishes experimental criteria to unequivocally evaluate fitness costs. Second, to present a comprehensive analysis of the literature on fitness costs associated with herbicide resistance alleles. This analysis reveals unquestionable evidence that some herbicide resistance alleles are associated with pleiotropic effects that result in plant fitness costs. Observed costs are evident from herbicide resistance-endowing amino acid substitutions in proteins involved in amino acid, fatty acid, auxin and cellulose biosynthesis, as well as enzymes involved in herbicide metabolism. However, these resistance fitness costs are not universal and their expression depends on particular plant alleles and mutations. The findings of this review are discussed within the context of the plant defence trade-off theory and herbicide resistance evolution

High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests.

During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel, fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-yr high-severity fire chronosequence in the Sierra Nevada where forests were historically adapted to frequent, low-severity fire, but were fire suppressed for at least 70 yr. High-severity fire in the Sierra Nevada resulted in a long-term (44 +yr) decrease (>50%, P < 0.05) in soil extracellular enzyme activities, basal microbial respiration (56-72%, P < 0.05), and organic carbon (>50%, P < 0.05) in the upper 5 cm compared to sites that had not been burned for at least 115 yr. However, nitrogen (N) processes were only affected in the most recent fire site (4 yr post-fire). Net nitrification increased by over 600% in the most recent fire site (P < 0.001), but returned to similar levels as the unburned control in the 13-yr site. Contrary to previous studies, we did not find a consistent effect of plant cover type on soil biogeochemical processes in mid-successional (10-50 yr) forest soils. Rather, the 44-yr reduction in soil organic carbon (C) quantity correlated positively with dampened C cycling processes. Our results show the drastic and long-term implication of ecologically novel, high-severity fire on soil biogeochemistry and underscore the need for long-term fire ecological experiments

The Automated Root Exudate System (ARES): a method to apply solutes at regular intervals to soils in the field.

Root exudation is a key component of nutrient and carbon dynamics in terrestrial ecosystems. Exudation rates vary widely by plant species and environmental conditions, but our understanding of how root exudates affect soil functioning is incomplete, in part because there are few viable methods to manipulate root exudates in situ. To address this, we devised the Automated Root Exudate System (ARES), which simulates increased root exudation by applying small amounts of labile solutes at regular intervals in the field. The ARES is a gravity-fed drip irrigation system comprising a reservoir bottle connected via a timer to a micro-hose irrigation grid covering c. 1 m2; 24 drip-tips are inserted into the soil to 4-cm depth to apply solutions into the rooting zone. We installed two ARES subplots within existing litter removal and control plots in a temperate deciduous woodland. We applied either an artificial root exudate solution (RE) or a procedural control solution (CP) to each subplot for 1 min day-1 during two growing seasons. To investigate the influence of root exudation on soil carbon dynamics, we measured soil respiration monthly and soil microbial biomass at the end of each growing season. The ARES applied the solutions at a rate of c. 2 L m-2 week-1 without significantly increasing soil water content. The application of RE solution had a clear effect on soil carbon dynamics, but the response varied by litter treatment. Across two growing seasons, soil respiration was 25% higher in RE compared to CP subplots in the litter removal treatment, but not in the control plots. By contrast, we observed a significant increase in microbial biomass carbon (33%) and nitrogen (26%) in RE subplots in the control litter treatment. The ARES is an effective, low-cost method to apply experimental solutions directly into the rooting zone in the field. The installation of the systems entails minimal disturbance to the soil and little maintenance is required. Although we used ARES to apply root exudate solution, the method can be used to apply many other treatments involving solute inputs at regular intervals in a wide range of ecosystems

Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila stipulacea along a Depth Gradient in the Northern Red Sea

Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1-50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species’ capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4-28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4-28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness