PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.

The Mass of Kepler-93b and The Composition of Terrestrial Planets

Kepler-93b is a 1.478 ± 0.019 R ⊕ planet with a4.7 day period around a bright (V = 10.2), astroseismicallycharacterized host star with a mass of 0.911 ± 0.033 M⊙ and a radius of 0.919 ± 0.011 R⊙. Based on 86 radial velocity observations obtainedwith the HARPS-N spectrograph on the Telescopio Nazionale Galileo and 32archival Keck/HIRES observations, we present a precise mass estimate of4.02 ± 0.68 M ⊕. The corresponding high densityof 6.88 ± 1.18 g cm-3 is consistent with a rockycomposition of primarily iron and magnesium silicate. We compareKepler-93b to other dense planets with well-constrained parameters andfind that between 1 and 6 M ⊕, all dense planetsincluding the Earth and Venus are well-described by the same fixed ratioof iron to magnesium silicate. There are as of yet no examples of suchplanets with masses >6 M ⊕. All known planets inthis mass regime have lower densities requiring significant fractions ofvolatiles or H/He gas. We also constrain the mass and period of theouter companion in the Kepler-93 system from the long-term radialvelocity trend and archival adaptive optics images. As the sample ofdense planets with well-constrained masses and radii continues to grow,we will be able to test whether the fixed compositional model found forthe seven dense planets considered in this paper extends to the fullpopulation of 1-6 M ⊕ planets.Based on observations made with the Italian Telescopio Nazionale Galileo(TNG) operated on the island of La Palma by the Fundación GalileoGalilei of the INAF (Istituto Nazionale di Astrofisica) at the SpanishObservatorio del Roque de los Muchachos of the Instituto de Astrofisicade Canarias.

The neurotoxin β-N-methylamino-L-alanine (BMAA) : Sources, bioaccumulation and extraction procedures

β-methylamino-L-alanine (BMAA) is a neurotoxin linked to neurodegeneration, which is manifested in the devastating human diseases amyotrophic lateral sclerosis, Alzheimer’s and Parkinson’s disease. This neurotoxin is known to be produced by almost all tested species within the cyanobacterial phylum including free living as well as the symbiotic strains. The global distribution of the BMAA producers ranges from a terrestrial ecosystem on the Island of Guam in the Pacific Ocean to an aquatic ecosystem in Northern Europe, the Baltic Sea, where annually massive surface blooms occur. BMAA had been shown to accumulate in the Baltic Sea food web, with highest levels in the bottom dwelling fish-species as well as in mollusks. One of the aims of this thesis was to test the bottom-dwelling bioaccumulation hypothesis by using a larger number of samples allowing a statistical evaluation. Hence, a large set of fish individuals from the lake Finjasjön, were caught and the BMAA concentrations in different tissues were related to the season of catching, fish gender, total weight and species. The results reveal that fish total weight and fish species were positively correlated with BMAA concentration in the fish brain. Therefore, significantly higher concentrations of BMAA in the brain were detected in plankti-benthivorous fish species and heavier (potentially older) individuals. Another goal was to investigate the potential production of BMAA by other phytoplankton organisms. Therefore, diatom cultures were investigated and confirmed to produce BMAA, even in higher concentrations than cyanobacteria. All diatom cultures studied during this thesis work were show to contain BMAA, as well as one dinoflagellate species. This might imply that the environmental spread of BMAA in aquatic ecosystems is even higher than previously thought. Earlier reports on the concentration of BMAA in different organisms have shown highly variable results and the methods used for quantification have been intensively discussed in the scientific community. In the most recent studies, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the instrument of choice, due to its high sensitivity and selectivity. Even so, different studies show quite variable concentrations of BMAA. In this thesis, three of the most common BMAA extraction protocols were evaluated in order to find out if the extraction could be one of the sources of variability. It was found that the method involving precipitation of proteins using trichloroacetic acid gave the best performance, complying with all in-house validation criteria. However, extractions of diatom and cyanobacteria cultures with this validated method and quantified using LC-MS/MS still resulted in variable BMAA concentrations, which suggest that also biological reasons contribute to the discrepancies. The current knowledge on the environmental factors that can induce or reduce BMAA production is still limited. In cyanobacteria, production of BMAA was earlier shown to be negative correlated with nitrogen availability – both in laboratory cultures as well as in natural populations. Based on this observation, it was suggested that in unicellular non-diazotrophic cyanobacteria, BMAA might take part in nitrogen metabolism. In order to find out if BMAA has a similar role in diatoms, BMAA was added to two diatom species in culture, in concentrations corresponding to those earlier found in the diatoms. The results suggest that BMAA might induce a nitrogen starvation signal in diatoms, as was earlier observed in cyanobacteria. However, diatoms recover shortly by the extracellular presence of excreted ammonia. Thus, also in diatoms, BMAA might be involved in the nitrogen balance in the cell.

Biomarker Geochemistry of Core Sediments in the Mangrove Ecosystems along Northern Kerala Coast

Mangroves are diverse group of trees, palms, shrubs, and ferns that share a common ability to live in waterlogged saline soils exposed to regular flooding, and are highly specialised plants which have developed unusual adaptations to the unique environmental conditions. They are sites of accumulation and preservation of both allochthonous and autochthonous organic matter owing to their strategic loction at the interface between land and sea and prevailing reducing environment. They are among the most productive ecosystems and are efficient carbon sinks with most of the carbon stored in sediments.Mangrove ecosystems play a significant role in global carbon cycle and hence the knowledge on the processes controlling the delivery of organic matter to coastal sediments, and how these signatures are preserved in the sediment is a prerequisite for the understanding of biogeochemical cycles. The evaluation of nature and sources of organic matter can be accomplished by the determination of biochemical constituents like carbohydrates, proteins and lipids. When characterised at molecular level, lipids provide valuable information about the sources of organic matter, even though they account only small fraction of organic matter. They are useful for the paleo-environmental reconstruction because of their low reactivity, high preservation potential and high source specificity relative to other organic class of compounds. The application of recent analytical techniques has produced a wealth of useful information but has also indicated the gaps in our knowledge on cycling of organic matter in the coastal ecosystems. The quantity and quality of organic matter preserved in sediments vary depending up on the nature of material delivered to the sediment and on the depositional environment. The input from both autochthonous and allochthonous sources sharpens the complexity of biogeochemistry of mangrove ecosystem and hence bulk sedimentary parameters are not completely successful in evaluating the sources of organic matter in mangrove sediments. An effective tool for the source characterisation of organic matter in coastal ecosystems is biomarker approach. Biomarkers are chemical "signatures" present in environmental samples whose structural information can be linked to its biological precursor. The usefulness of molecular biomarkers depends on high taxonomic specificity, potential for preservation, recalcitrant against geochemical changes, easily analysable in environmental samples and should have a limited number of well-defined sources.

MERIS Terrestrial Chlorophyll Index

Resources created at the University of Southampton for the module Remote Sensing for Earth Observation

Exploring Habitability Markers, Biosignatures, and Their False Positives Using Spectral Models of Terrestrial Exoplanets

Thesis (Ph.D.)--University of Washington, 2016-08

The Role of the Ocean Economy in the National Income Accounts of Indonesia

This paper presents the role of the Ocean Economy in the National Income Accounts of Indonesia including the concept and methodology used to estimate the contribution of this ecosystem to Indonesian value added. Currently, the national income account of Indonesia only recognizes the fishery sector. Fishery activities have been considered as one of the sub-sectors of agricultural sector together with sub-sectors of farm food crops, plantation or non-food crops, forestry, and livestock. There are some drawbacks in the concept of national income accounts, since it follows the UN system of national accounts (SNA) that recognize only economic sectors or activities which produce the value added, while it does not recognize the ecosystems such as lakes and river ecosystems, forests as well as terrestrial and ocean ecosystems as production sectors. The present concept of the SNA produces an undervaluation of forest and ocean sectors, which in turn may direct the policy makers to have a tendency to deplete the forestry and fishery resources in order to increase the contribution of those two sectors to the national income accounts. Otherwise, the two sectors will be allocated small national budget for their operations. Therefore the paper concludes that a new concept of national income accounts based on ecosystem products and services to be developed, as a satellite account to the national income account is needed. Furthermore the new concept of national income account for the ocean economy should adopt the UN System of Environmental and Economic Accounts, which takes into account the extractive and non-extractive products as environmental and biological services in to the ocean income account. The new concept of ocean accounting based on both extractive and non-extractive products instead of only based on the extractive one which have market values may guarantee the sustainability of the ocean in particular and will be good for the whole economy of the country in generally. Hence the national income accounts of the ocean economy will show how the blue economy or the ocean economy really function as one of the important sectors for the whole economy of the country.

Peat Bog Ecosystems: Peatland Restoration

Peatland restoration involves giving aid to a complex ecosystem which has been damaged in some way. A reasonable analogy is a patient brought to a hospital for urgent treatment. When arriving at Accident & Emergency , the first priority of the medical team is to stabilise the patient’s condition. Only after the patient’s condition has been assessed and then stabilised can the team begin to think about the longer - term process of healing and recovery. A similar logic is applied to peatland s . First , stabilisation is required to prevent further degradation, following which restoration can focus on the recovery of the ecosystem.

Peat Bog Ecosystems: Tracks across peatlands

Tracks have been made across peatlands for as long as human society has existed. Un - made tracks (i.e. those created simply by regular use, with no construction involved) were probably first created by grazing animals and then presumably also used by early human communities. F ind ing these increasingly impassable with regular use , human societies began to construct ' corduroy roads ' during Neolithic, Bronze and Iron Age times. These first constructed tracks were made from cut timbers ( below ) . Across Europe, ma ny examples of these corduroy roads have been found preserved in lowland bogs, perhaps most famously in the Somerset Levels and more recently at Hatfield Moors on the Humberhead Levels.

Peat Bog Ecosystems: Atmospheric pollution

Peatlands can be damaged by deposition of pollutants from the atmosphere – often termed ‘ acid rain ’ . This results from the release of sulphur and nitrogen pollutants into the atmosphere . Originally associated with the Industrial Revolution, ‘acid rain’ was first described by Robert Angus Smith, a Manchester chemist of the 1800s , whose obser vations were made in close proximity to the peatlands of the South Pennines. Sulphur dioxide (SO 2 ) pollution, which is mainly emitted from coal burning power stations, peaked in the 1970s and has since decreased by over 90% due to emission controls and ch anges in energy supply. N itrogen ous air pollutants have decreased less . N itrogen oxide (NO x ) emissions , which are mainly from vehicle s , have decreased by two thirds since their peak in 1990 , but the decrease in ammonia ( NH 3 ) emissions , which are mainly from intensive livestock farming, is much less certain and may be only about 20%.

Environmental impacts of freshwater use and suspended solids in life cycle assessment

Perturbation of natural ecosystems, namely by increasing freshwater use and its degradative use, as well as topsoil erosion by water of land-use production systems, have been emerging as topics of high environmental concern. Freshwater use has become a focus of attention in the last few years for all stakeholders involved in the production of goods, mainly agro-industrial and forest-based products, which are freshwater-intensive consumers, requiring large inputs of green and blue water. This thesis presents a global review on the available Water Footprint Assessment and Life Cycle Assessment (LCA)-based methods for measuring and assessing the environmental relevance of freshwater resources use, based on a life cycle perspective. Using some of the available midpoint LCA-based methods, the freshwater use-related impacts of a Portuguese wine (white ‘vinho verde’) were assessed. However, the relevance of environmental green water has been neglected because of the absence of a comprehensive impact assessment method associated with green water flows. To overcome this constraint, this thesis helps to improve and enhance the LCA-based methods by providing a midpoint and spatially explicit Life Cycle Impact Assessment (LCIA) method for assessing impacts on terrestrial green water flow and addressing reductions in surface blue water production caused by reductions in surface runoff due to land-use production systems. The applicability of the proposed method is illustrated by a case study on Eucalyptus globulus conducted in Portugal, as the growth of short rotation forestry is largely dependent on local precipitation. Topsoil erosion by water has been characterised as one of the most upsetting problems for rivers. Because of this, this thesis also focuses on the ecosystem impacts caused by suspended solids (SS) from topsoil erosion that reach freshwater systems. A framework to conduct a spatially distributed SS delivery to freshwater streams and a fate and effect LCIA method to derive site-specific characterisation factors (CFs) for endpoint damage on aquatic ecosystem diversity, namely on algae, macrophyte, and macroinvertebrates organisms, were developed. The applicability of this framework, combined with the derived site-specific CFs, is shown by conducting a case study on E. globulus stands located in Portugal as an example of a land use based system. A spatially explicit LCA assessment was shown to be necessary, since the impacts associated with both green water flows and SS vary greatly as a function of spatial location.

Co-digestion of terrestrial plant biomass with marine macro-algae for biogas production

This paper investigates factors affecting anaerobic degradation of marine macro-algae (or seaweed), when used as a co-substrate with terrestrial plant biomass for the production of biogas. Using Laminaria digitata, a brown marine seaweed species and green peas, results showed that when only 2% of feedstock of a reactor treating the green peas at an organic loading rate (OLR) of 2.67 kg VS.m3.day-1 was replaced with the seaweed, methane production was disrupted, whilst acidogenesis, seemed to be less adversely affected, resulting in excessive volatile acids accumulation. Reactor stability was difficult to achieve thereafter. The experiment was repeated with a lower initial OLR of green peas of 0.70 kg VS.m3.day-1 before the addition of the seaweed. Although similar symptoms as in first trial were observed, process stability was restored through the control of OLR and alkalinity. These measures led to an increase in overall OLR of 1.25 kg VS.m3.day-1 comprising of 35% seaweed. This study has shown that certain seaweed constituents are more inhibitory to the methanogens even at trace concentrations than to the other anaerobic digestion microbial groups. Appropriate adaptation strategy, involving initial low proportion of the seaweed relative to the total OLR, and overall low OLR, is necessary to ensure effective adaptation of the microorganisms to the inhibitory constituents of seaweed. Where there is seasonal availability of seaweed, the results of this study suggest that a fresh adaptation or start-up strategy must be implemented during each cycle of seaweed availability in order to ensure sustainable process stability.