The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

We discuss the physical and enzymatic bases of carbone isotope discrimination during photosynthesis, noting how knowledge of discrimination can be used to provide additional insight into photosynthetic metabolism and the environmental influences on that process

Carbon Isotope Discrimination and Photosynthesis

Contents

 Summary 1

I. What is FACE? 2
II. Materials and methods 2
III. Photosynthetic carbon uptake 3
IV. Acclimation of photosynthesis 6
V. Growth, above-ground production and yield 8
VI. So, what have we learned? 10

 Acknowledgements 11


 References 11


Appendix 1. References included in the database for meta-analyses  14


 Appendix 2. Results of the meta-analysis of FACE effects 18



Summary
Free-air CO2 enrichment (FACE) experiments allow study of the effects of elevated [CO2] on plants and ecosystems grown under natural conditions without enclosure. Data from 120 primary, peer-reviewed articles describing physiology and production in the 12 large-scale FACE experiments (475–600 ppm) were collected and summarized using meta-analytic techniques. The results confirm some results from previous chamber experiments: light-saturated carbon uptake, diurnal C assimilation, growth and above-ground production increased, while specific leaf area and stomatal conductance decreased in elevated [CO2]. There were differences in FACE. Trees were more responsive than herbaceous species to elevated [CO2]. Grain crop yields increased far less than anticipated from prior enclosure studies. The broad direction of change in photosynthesis and production in elevated [CO2] may be similar in FACE and enclosure studies, but there are major quantitative differences: trees were more responsive than other functional types; C4 species showed little response; and the reduction in plant nitrogen was small and largely accounted for by decreased Rubisco. The results from this review may provide the most plausible estimates of how plants in their native environments and field-grown crops will respond to rising atmospheric [CO2]; but even with FACE there are limitations, which are also discussed.

What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2.

Much has been written about theory and practice in the law, and the tension between practitioners and theorists. Judges do not cite theoretical articles often; they rarely "apply" theories to particular cases. These arguments are not revisited. Instead the Essay explores the working and interaction of theory and practice, practitioners and theorists. The Essay starts with a story about solving a legal issue using our intellectual tools - theory, practice, and their progenies: experience and "gut." Next the Essay elaborates on the nature of theory, practice, experience and "gut." The third part of the Essay discusses theories that are helpful to practitioners and those that are less helpful. The Essay concludes that practitioners theorize, and theorists practice. They use these intellectual tools differently because the goals and orientations of theorists and practitioners, and the constraints under which they act, differ. Theory, practice, experience and "gut" help us think, remember, decide and create. They complement each other like the two sides of the same coin: distinct but inseparable.

Of Theory and Practice

Water deficits cause a reduction in the rate of photosynthesis. Exposure to mild water deficits, when relative water content (RWC) remains above 70%, primarily causes limitation to carbon dioxide uptake because of stomatal closure. With greater water deficits, direct inhibition of photosynthesis occurs. In both cases limitation of carbon dioxide fixation results in exposure of chloroplasts to excess excitation energy. Much of this can be dissipated by various photoprotective mechanisms. These include dissipation as heat via carotenoids, photorespiration, CAM idling and, in some species, leaf movements and other morphological features which minimize light absorption. The active oxygen species superoxide and singlet oxygen are produced in chloroplasts by photoreduction of Oxygen and energy transfer from triplet excited chlorophyll to oxygen, respectively. Hydrogen peroxide and hydroxyl radicals can form as a result of the reactions of superoxide. All these species are reactive and potentially damaging, causing lipid peroxidation and inactivation of enzymes. They are normally scavenged by a range of antioxidants and enzymes which are present in the chloroplast and other subcellular compartments. When carbon dioxide fixation is limited by water deficit, the rate of active oxygen formation increases in chloroplasts as excess excitation energy, not dissipated fay the photoprotective mechanisms, is used to form superoxide and singlet oxygen. However, photorespiratory hydrogen peroxide production in peroxisomes decreases. Increased superoxide can be detected by EPR (electron paramagnetic resonance) in chloroplasts from droughted plants. Stiperoxide formation leads to changes suggestive of oxidative damage including lipid peroxidation and a decrease in ascorbate. These changes are not, however, apparent until severe water deficits develop, and they could also be interpreted as secondary effects of water deficit-induced senescence or wounding. Non-lethal water deficits often result in increased activity of superoxide dismutase, glutathione reductase and monodehydroascorbate reductase. Increased capacity of these protective enzymes may be part of a general antioxidative response in plants involving regulation of protein synthesis or gene expression. Since the capacity of these enzymes is also increased by other treatments which cause oxidative damage, and which alter the balance between excitation energy input and carbon dioxide fixation such as low temperature and high irradiance, it is suggested that water deficit has the same effect. Light levels that are not normally excessive do become excessive and photoprotective/antioxidative systems are activated. Some of the photoprotective mechanisms themselves could result in active oxygen formation. Photoinhibitory damage also includes a component of oxidative damage. During normally-encountered degrees of water deficit the capacity of the antioxidant systems and their ability to respond to increased active oxygen generation may be sufficient to prevent overt expression of damage. Desiccation-tolerant tissues such as bryophytes, lichens, spores, seeds, some algae and a few vascular plant leaves can survive desiccation to below 30-40% RWC, A component of desiccation damage in seeds and bacteria is oxygen-dependent. Desiccation causes oxidation of glutathione, a major antioxidant, and appearance of a free radical signal detected by EPR in a number of tissues suggesting that oxidative damage has occurred. In photosynthetic cells damage may arise from photooxidation. Disruption of membrane-bound electron tranport systems in partially hydrated tissue could lead to reduction of oxygen to superoxide. Oxidation of lipids and sulphydryl groups may also occur in dry tissue. Tolerant cells recover upon rehydration and arc able to reduce their glutathione pool. Non-tolerant species go on to show further oxidative damage including lipid peroxidation. It is difficult to attribute this subsequent damage to the cause or effect of death. Embryos in seeds lose desiccation tolerance soon after imbibition. This is associated with membrane damage that has been attributed to superoxide-mediated deesterification of phospholipids and loss of lipophilic antioxidants. These effects are discussed in relation to other mechanisms involved in desiccation tolerance. Contents Summary 27 I. Introduction 28 II. Generation of active oxygen and defence mechanisms in plant cells 29 III. The effect of water deficit on photosynthesis 31 IV. Mechanisms for active oxygen generation during water deficit 36 V. Evidence for oxidative damage during water deficit 39 VI. Desiccation 47 VII. Conclusions 52 Acknowledgements 53 References 53.

The role of active oxygen in the response of plants to water deficit and desiccation.

A recently developed integrative framework proposes that the vulnerability of a species to environmental change depends on the species' exposure and sensitivity to environmental change, its resilience to perturbations and its potential to adapt to change. These vulnerability criteria require behavioural, physiological and genetic data. With this information in hand, biologists can predict organisms most at risk from environmental change. Biologists and managers can then target organisms and habitats most at risk. Unfortunately, the required data (e.g. optimal physiological temperatures) are rarely available. Here, we evaluate the reliability of potential proxies (e.g. critical temperatures) that are often available for some groups. Several proxies for ectotherms are promising, but analogous ones for endotherms are lacking. We also develop a simple graphical model of how behavioural thermoregulation, acclimation and adaptation may interact to influence vulnerability over time. After considering this model together with the proxies available for physiological sensitivity to climate change, we conclude that ectotherms sharing vulnerability traits seem concentrated in lowland tropical forests. Their vulnerability may be exacerbated by negative biotic interactions. Whether tropical forest (or other) species can adapt to warming environments is unclear, as genetic and selective data are scant. Nevertheless, the prospects for tropical forest ectotherms appear grim.

https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2012.0005

Predicting organismal vulnerability to climate warming: roles of behaviour, physiology and adaptation

Summary Stable carbon isotope ratios (d 13 C) of terrestrial plants are employed across a diverse range of applicationsinenvironmentalandplantsciences;however,thekindofinformationthatisdesired fromthed 13 Csignaloftendiffers.Attheextremes,itrangesbetweenpurely environmentaland purely biological. Here, we review environmental drivers of variation in carbon isotope discrimination (D) in terrestrial plants, and the biological processes that can either damp or amplifytheresponse.ForC3plants,whereDisprimarilycontrolledbytheratioofintercellularto ambient CO2 concentrations (ci/ca), coordination between stomatal conductance and photo- synthesisandleafareaadjustmenttendstoconstrainthepotentialenvironmentallydrivenrange of D. For C4 plants, variation in bundle-sheath leakiness to CO2 can either damp or amplify the effects of ci/ca on D. For plants with crassulacean acid metabolism (CAM), D varies over a relatively largerange asafunctionoftheproportion ofdaytimetonight-time CO2fixation. This range can be substantially broadened by environmental effects onD when carbon uptake takes place primarily during the day. The effective use of D across its full range of applications will require a holistic view of the interplay between environmental control and physiological modulation of the environmental signal.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12423

Environmental and physiological determinants of carbon isotope discrimination in terrestrial plants

The late 1980s saw an explosion in the amount and diversity of herbicide resistance, posing a threat to crop production in many countries. The rapid escalation in herbicide resistance worldwide has meant that the understanding of resistance at the population, biochemical and molecular level has also been developed. Leading researchers from North America, Australia and Western Europe present reviews which consider the population dynamics and genetics, biochemistry and argo-ecology of resistance. This text should be a useful reference for those interested in evolution and the ability of species to overcome severe environmental stress.

Herbicide Resistance in Plants: Biology and Biochemistry

CONTENTS INTRODUCTION 204 RESISTANCE TO AMINO ACID SYNTHESIS INHIBITORS .. . . .... ... ...... 204 Acetolactate Synthase (ALS) Inhibitors .... . . ... 204 5E(?Jl;h;;;��:j.��'!:: ����.�.����������.��.�.��.���.�������.��.�!.�.����� 207 Glu tamine Synthetase (GS) Inhibitors ... . ...... ........ 208 RESISTANCE TO PHOTOSYSTEM II (PSII) INHIBITORS... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208 RESISTANCE TO LIPID SYNTHESIS INHIBITORS .. . ... ... ... ... ........ ....... 211 Acetyl Coenzyme A Carboxylase (ACCase) Inhibitors . 211 RESISTANCE TO AUXIN-TYPE HERBICIDES 213 Phenoxyacetic Acids ......... .. ... ... ..... , 213 RESISTANCE TO MITOTIC INHIBITORS ... ... ... ... . 215 Dinitroanilines . . . . .. .... . . . . . . .. ... .. . .. ......... .. .. ...... 215 RESISTANCE TO PHOTOSYSTEM I (PSI) INHIBITORS 217 Bipyridiliums 217 CROSSAND MULTIPLE-HERBICIDE RESISTANCE 219 AGRONOMIC IMPLICATIONS OF HERBICIDE RESISTANCE ........ ...... 221

Mechanisms and Agronomic Aspects of Herbicide Resistance

Aspects of xylem anatomy and vulnerability to water stress-induced embolism were examined in stems of two drought-deciduous species, Brachychiton australis (Schott and Endl.) A. Terracc. and Cochlospermum gillivraei Benth., and two evergreen species, Alphitonia excelsa (Fenzal) Benth. and Austromyrtus bidwillii (Benth.) Burret., growing in a seasonally dry rainforest. The deciduous species were more vulnerable to water stress-induced xylem embolism. B. australis and C. gillivraei reached a 50% loss of hydraulic conductivity at −3.17 MPa and −1.44 MPa, respectively; a 50% loss of hydraulic conductivity occurred at −5.56 MPa in A. excelsa and −5.12 MPa in A. bidwillii . To determine whether pit membrane porosity was responsible for greater vulnerability to embolism (air seeding hypothesis), pit membrane structure was examined. Expected pore sizes were calculated from vulnerability curves; however, the predicted inter-specific variation in pore sizes was not detected using scanning electron microscopy (pores were not visible to a resolution of 20 nm). Suspensions of colloidal gold particles were then perfused through branch sections. These experiments indicated that pit membrane pores were between 5 and 20 nm in diameter in all four species. The results may be explained by three possibilities: (a) the pores of the expected size range were not present, (b) larger pores, within the size range to cause air seeding, were present but were rare enough to avoid detection, or (c) pore sizes in the expected range only develop while the membrane is under mechanical stress (during air seeding) due to stretching/flexing.

Joseph A. M. Holtum

Papers

Predicting organismal vulnerability to climate warming: roles of behaviour, physiology and adaptation

Environmental and physiological determinants of carbon isotope discrimination in terrestrial plants

Herbicide Resistance in Plants: Biology and Biochemistry

Mechanisms and Agronomic Aspects of Herbicide Resistance

Pit membrane porosity and water stress-induced cavitation in four co-existing dry rainforest tree species.