Cross-taxon congruence and environmental conditions

Background  

Diversity patterns of different taxa typically covary in space, a phenomenon called cross-taxon congruence. This pattern has been explained by the effect of one taxon diversity on taxon diversity, shared biogeographic histories of different taxa, and/or common responses to environmental conditions. A meta-analysis of the association between environment and diversity patterns found that in 83 out of 85 studies, more than 60% of the spatial variability in species richness was related to variables representing energy, water or their interaction. The role of the environment determining taxa diversity patterns leads us to hypothesize that this would explain the observed cross-taxon congruence. However, recent analyses reported the persistence of cross-taxon congruence when environmental effect was statistically removed. Here we evaluate this hypothesis, analyzing the cross-taxon congruence between birds and mammals in the Brazilian Cerrado, and assess the environmental role on the spatial covariation in diversity patterns.     

Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products

Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.     

Behavioural and chemical evidence for multiple colonisation of the Argentine ant, Linepithema humile, in the Western Cape, South Africa

Background

The Argentine ant, Linepithema humile, is a widespread invasive ant species that has successfully established in nearly all continents across the globe. Argentine ants are characterised by a social structure known as unicoloniality, where territorial boundaries between nests are absent and intraspecific aggression is rare. This is particularly pronounced in introduced populations and results in the formation of large and spatially expansive supercolonies. Although it is amongst the most well studied of invasive ants, very little work has been done on this ant in South Africa. In this first study, we investigate the population structure of Argentine ants in South Africa. We use behavioural (aggression tests) and chemical (CHC) approaches to investigate the population structure of Argentine ants within the Western Cape, identify the number of supercolonies and infer number of introductions.

Results

Both the aggression assays and chemical data revealed that the Western Cape Argentine ant population can be divided into two behaviourally and chemically distinct supercolonies. Intraspecific aggression was evident between the two supercolonies of Argentine ants with ants able to discriminate among conspecific non-nestmates. This discrimination is linked to the divergence in cuticular hydrocarbon profiles of ants originating from the two supercolonies.

Conclusions

The presence of these two distinct supercolonies is suggestive of at least two independent introductions of this ant within the Western Cape. Moreover, the pattern of colonisation observed in this study, with the two colonies interspersed, is in agreement with global patterns of Argentine ant invasions. Our findings are of interest because recent studies show that Argentine ants from South Africa are different from those identified in other introduced ranges and therefore provide an opportunity to further understand factors that determine the distributional and spread patterns of Argentine ant supercolonies.     

Biotechnological Enhancement of Probiotics through Co-Cultivation with Algae: Future or a Trend?

The diversity of algal species is a rich source of many different bioactive metabolites. The compounds extracted from algal biomass have various beneficial effects on health. Recently, co-culture systems between microalgae and bacteria have emerged as an interesting solution that can reduce the high contamination risk associated with axenic cultures and, consequently, increase biomass yield and synthesis of active compounds. Probiotic microorganisms also have numerous positive effects on various aspects of health and represent potent co-culture partners. Most studies consider algae as prebiotics that serve as enhancers of probiotics performance. However, the extreme diversity of algal organisms and their ability to produce a plethora of metabolites are leading to new experimental designs in which these organisms are cultivated together to derive maximum benefit from their synergistic interactions. The future success of these studies depends on the precise experimental design of these complex systems. In the last decade, the development of high-throughput approaches has enabled a deeper understanding of global changes in response to interspecies interactions. Several studies have shown that the addition of algae, along with probiotics, can influence the microbiota, and improve gut health and overall yield in fish, shrimp, and mussels aquaculture. In the future, such findings can be further explored and implemented for use as dietary supplements for humans.     

Quorum Quenching Agents: Resources for Antivirulence Therapy

The continuing emergence of antibiotic-resistant pathogens is a concern to human health and highlights the urgent need for the development of alternative therapeutic strategies. Quorum sensing (QS) regulates virulence in many bacterial pathogens, and thus, is a promising target for antivirulence therapy which may inhibit virulence instead of cell growth and division. This means that there is little selective pressure for the evolution of resistance. Many natural quorum quenching (QQ) agents have been identified. Moreover, it has been shown that many microorganisms are capable of producing small molecular QS inhibitors and/or macromolecular QQ enzymes, which could be regarded as a strategy for bacteria to gain benefits in competitive environments. More than 30 species of marine QQ bacteria have been identified thus far, but only a few of them have been intensively studied. Recent studies indicate that an enormous number of QQ microorganisms are undiscovered in the highly diverse marine environments, and these marine microorganism-derived QQ agents may be valuable resources for antivirulence therapy.     

Mixing of propagules from discrete sources at long distance: comparing a dispersal tail to an exponential

Background  

Rare long distance dispersal events impact the demography and the genetic structure of populations. When dispersal is modelled via a dispersal kernel, one possible characterisation of long-distance dispersal is given by the shape of the tail of the kernel, i.e. its type of decay. This characteristic is known to directly act on the speed and pattern of colonization, and on the spatial structure of genetic diversity during colonization. In particular, colonization waves behave differently depending on whether the kernel decreases faster or slower than an exponential (i.e. is thin-tailed vs. fat-tailed). To interpret and extend published results on the impact of long-distance dispersal on the genetic structure of populations, we examine a classification of dispersal kernels based on the shape of their tails and formally demonstrate qualitative differences among them that can influence the predicted diversity of a propagule pool sampled far from two distinct sources.     

Complementing endozoochorous seed dispersal patterns by donkeys and goats in a semi-natural island ecosystem

Background

Endozoochory is, in grazing systems, a substantial vector for seed dispersal. It can play an important role in vegetation dynamics, especially in colonization processes through seed input on the vegetation and on the soil seed bank. We investigated the endozoochorous seed input of donkeys and goats on a semi-natural island ecosystem in the Mediterranean. Through germination experiments, we assessed the viable seed content of the dung of these grazing animals to estimate their suitability and efficiency for seed dispersal of the vegetation types of the island.

Results

We show different dispersal patterns of donkeys and goats. Goats disperse a high number of diaspores from shrubs while donkeys disperse more diaspores of grasses. In addition, goats disperse plants of greater growth height and donkeys plants of shorter height. These dispersal patterns are in accordance with the vegetation types of which donkeys and goats disperse indicator species. Both, donkeys and goats, feed on and disperse species of the vegetation types, open grassland and temporarily wet grassland. In addition, goats feed on and disperse diagnostic species of the semi-open maquis and preforest formations.

Conclusions

Overall, our results show that donkeys and goats are complementing each other in their endozoochorous seed dispersal potential. This emphasizes the importance of both grazing animals for the vegetation dynamics of the semi-natural island ecosystem. Therefore, the adaption of the goat management to a traditional land management based on directed transhumance might maintain and enrich vegetation types.

     

玉米穗型和粒型性状的GWAS及其关联位点驯化和改良分析

以32份大刍草、68份玉米地方品种和来源广泛的294份玉米自交系为材料,在对294份玉米自交系进行简化基因组测序的基础上,采用GWAS方法对11个玉米穗型和粒型性状进行关联分析。结果表明,11个性状共检测到44个关联的SNP位点,其中,28个位点与6个穗型性状相关联,16个位点与3个粒型性状相关联。进一步整合32份大刍草和68份地方品种相应位点的序列数据,44个关联位点中共发现29个SNP在3类群体间共有。通过Fisher的精确检验发现,7个SNP的等位基因频率在大刍草到地方品种中发生了显著变化,14个SNP的等位基因频率在地方品种到自交系中发生了显著变化,3个SNP的等位基因频率则在大刍草到地方品种以及地方品种到自交系中均发生了显著变化,表明这些位点可能经历了驯化或/和人工改良。     

Beneficial Microorganisms and Metabolites Derived from Agriculture Wastes in Improving Plant Health and Protection

Summary

There is growing interest in the presence of certain naturally-occurring, beneficial microorganisms in agricultural wastes (e.g., processing wastes, composts and anaerobic slurries) that have considerable potential to enhance the growth, health and protection of crops. The numbers of these organisms can be increased through incubation procedures and they can be applied as mixed or pure culture inoculants to soils and plants in waste materials or as sprays and suspensions. The various mechanisms of disease control and plant protection imparted by these beneficial microorganisms may be related to (a) microbe-microbe interactions, (b) plant-microbe interactions, (c) metabolites produced and /or, (d) induced systemic-acquired resistance. Research is needed to elucidate their exact mechanisms or modes-of-action to determine the optimum time, rate and frequency of application for improving plant health and protection.     

What makes us human? A biased view from the perspective of comparative embryology and mouse genetics

For a neurobiologist, the core of human nature is the human cerebral cortex, especially the prefrontal areas, and the question "what makes us human?" translates into studies of the development and evolution of the human cerebral cortex, a clear oversimplification. In this comment, after pointing out this oversimplification, I would like to show that it is impossible to understand our cerebral cortex if we focus too narrowly on it. Like other organs, our cortex evolved from that in stem amniotes, and it still bears marks of that ancestry. More comparative studies of brain development are clearly needed if we want to understand our brain in its historical context. Similarly, comparative genomics is a superb tool to help us understand evolution, but again, studies should not be limited to mammals or to comparisons between human and chimpanzee, and more resources should be invested in investigation of many vertebrate phyla. Finally, the most widely used rodent models for studies of cortical development are of obvious interest but they cannot be considered models of a "stem cortex" from which the human type evolved. It remains of paramount importance to study cortical development directly in other species, particularly in primate models, and, whenever ethically justifiable, in human.     

A Genetic Focus on the Peopling History of East Asia: Critical Views

Population genetic studies may provide crucial information for our knowledge on human peopling history and have been extensively applied to reconstruct East Asian prehistory in the last 10 years. However, different genetic investigations are not always consistent with each other and some results are conflicting or misinterpreted. This represents a main obstacle for scholars of other disciplines like archaeologists and linguists who try to relate the genetic information on past human migrations to their own results on the spread of domesticated crops or animals or on the dispersal of the main language families. In this paper, we review the current genetic evidence related to the peopling history of East Asia with a critical view on some interpretations. In this way, we hope to provide a useful reference for further interdisciplinary studies on our past.     

Behavioral Effects and Retention of Protein Immunomarkers on Plum Curculio Conotrachelus nenuphar (Coleoptera: Curculionidae)

Protein immunomarking can be used to track the dispersal of insects in the field or identify plant–insect interactions. By marking insects with known proteins and recapturing them, their movement or host use can be quantified with Enzyme Linked Immunosorbent Assay (ELISA). Before using this technique, retention and behavioral effects of these markers should be evaluated to ensure that the insect’s natural behaviors are conserved. Here, we tested the effects of protein markers on the plum curculio, Conotrachelus nenuphar (Coleoptera: Curculionidae) using two different application methods. This weevil is native to North American and a pest of tree fruit and blueberry in the United States and causes damage resulting in near complete crop loss if left untreated. We tested the effects of marking adult C. nenuphar with two inexpensive food-based immunoprotein markers, bovine casein (cow’s milk) and chicken albumin (egg whites) on climbing distance (total cm), lateral movement (total cm), and lateral movement speed (cm/s), as well as retention time of protein immunomarkers. Neither protein immunomarker affected C. nenuphar movement or climbing, although females climbed significantly greater distances than males. ELISA assays detected 37.5–56.2% of milk protein and 56.2–59.3% of egg on the insect 7 d after application depending on application method. Our findings indicate that food-based protein immunomarkers can be used in future studies to test C. nenuphar movement within host plants without impacting behavior. The use of protein immunomarking will allow studies that will lead to behaviorally based management tactics.     

Co-Cultivation—A Powerful Emerging Tool for Enhancing the Chemical Diversity of Microorganisms

Marine-derived bacteria and fungi are promising sources of novel bioactive compounds that are important for drug discovery programs. However, as encountered in terrestrial microorganisms there is a high rate of redundancy that results in the frequent re-discovery of known compounds. Apparently only a part of the biosynthetic genes that are harbored by fungi and bacteria are transcribed under routine laboratory conditions which involve cultivation of axenic microbial strains. Many biosynthetic genes remain silent and are not expressed in vitro thereby seriously limiting the chemical diversity of microbial compounds that can be obtained through fermentation. In contrast to this, co-cultivation (also called mixed fermentation) of two or more different microorganisms tries to mimic the ecological situation where microorganisms always co-exist within complex microbial communities. The competition or antagonism experienced during co-cultivation is shown to lead to a significantly enhanced production of constitutively present compounds and/or to an accumulation of cryptic compounds that are not detected in axenic cultures of the producing strain. This review highlights the power of co-cultivation for increasing the chemical diversity of bacteria and fungi drawing on published studies from the marine and from the terrestrial habitat alike.     

Marine Microbial Fibrinolytic Enzymes: An Overview of Source,Production, Biochemical Properties and Thrombolytic Activity

Cardiovascular diseases (CVDs) have emerged as a major threat to global health resulting in a decrease in life expectancy with respect to humans. Thrombosis is one of the foremost causes of CVDs, and it is characterized by the unwanted formation of fibrin clots. Recently, microbial fibrinolytic enzymes due to their specific features have gained much more attention than conventional thrombolytic agents for the treatment of thrombosis. Marine microorganisms including bacteria and microalgae have the significant ability to produce fibrinolytic enzymes with improved pharmacological properties and lesser side effects and, hence, are considered as prospective candidates for large scale production of these enzymes. There are no studies that have evaluated the fibrinolytic potential of marine fungal-derived enzymes. The current review presents an outline regarding isolation sources, production, features, and thrombolytic potential of fibrinolytic biocatalysts from marine microorganisms identified so far.     

Towards Generating Caffeine-free Tea by Metabolic Engineering

Tea is a rich source of antioxidants which are contributing substantially to the promotion of health and the prevention of various chronic diseases. Despite the fact that tea has various important compounds, it also contains a purine alkaloid, caffeine. High intake of tea leads to an increase in level of caffeine in addition to its important antioxidant constituents. Increased level of caffeine causes several health related problems. Therefore, tea can become a most useful source of beneficial compounds, if only its caffeine level is either decreased or eliminated all together from the plant itself. This could be achieved through either of the techniques; overexpressing caffeine degradative pathway genes or silencing caffeine biosynthesis pathway gene. The identification and cloning of caffeine biosynthesis in tea and degradative genes in microorganisms opens up the possibility of using genetic engineering to produce naturally decaffeinated tea. Here we review these different strategies which can be employed to make caffeine-free tea, a human health beneficial drink.     

Issues of scale in water productivity in the Zhanghe irrigation system: implications for irrigation in the basin context

In the context of increased competition for water, growing more rice with less water will be one of the major challenges of the 21st century. This paper examines water savings and issues of scale in water productivity. The main objective is to understand if and how field-scale interventions scale up to subbasin-scale water savings in the Zhanghe Irrigation District (ZID) in Hubei Province, central China. Our results confirmed that on-farm water-saving practices result in higher water productivity per unit of irrigation water at the field scale due to lower irrigation water input. However, the question is, if these field-scale practices have led to real water savings; savings which can be transferred to other agricultural and non-agricultural uses without lowering existing production levels. To investigate this question, we examined water use and productivity at four different scales: field scale, meso scale, main canal command scale, and subbasin scale using the water accounting methodology. The study clearly demonstrates the high dependence on the scale of water use and productivity parameters. Depleted fraction and water productivity per unit of gross inflow and irrigation water varied dramatically across scale. Thus, it is not possible to conclude from field-scale observations that basin level water savings will or will not take place. The major reasons for these scale effects are the lateral flow of water across boundaries, differing land use patterns across scales, and changing water management patterns across scales. In the ZID, going from field and meso scale to even larger scales, water productivity per unit of irrigation increases to even higher levels than at the field scale. Here it becomes clear that the ZID, with its possibilities of reuse of drainage return flows and capturing rainfall and runoff in all the reservoirs within the system, is very effective in capturing and using water productively. Factors that influence water productivity and depleted fraction are on-farm water savings as well as the reuse of drainage water, effective capturing and utilization of rain, and canal water management. The scope for additional real water savings in the Zhanghe Irrigation District is limited. Only 13% of the combined rainfall and Zhanghe reservoir irrigation water releases flow out of the basin. A further reduction in drainage surface outflow from the ZID may have negative downstream effects on other water uses, including environmental uses. The main lessons learned are that (1) employing a combination of factors—on-farm practices, reuse, and canal operations—can be an effective means of conserving water resources within irrigation systems, (2) the scope for savings must be considered by an analysis at larger scales (i.e. irrigation system or basin scale), and may be less than thought because of the interactions of these factors. The results clearly indicate that scale effects are important for understanding and planning for water savings and water productivity.     

Natural Products in Polyclad Flatworms

Marine invertebrates are promising sources of novel bioactive secondary metabolites, and organisms like sponges, ascidians and nudibranchs are characterised by possessing potent defensive chemicals. Animals that possess chemical defences often advertise this fact with aposematic colouration that potential predators learn to avoid. One seemingly defenceless group that can present bright colouration patterns are flatworms of the order Polycladida. Although members of this group have typically been overlooked due to their solitary and benthic nature, recent studies have isolated the neurotoxin tetrodotoxin from these mesopredators. This review considers the potential of polyclads as potential sources of natural products and reviews what is known of the activity of the molecules found in these animals. Considering the ecology and diversity of polyclads, only a small number of species from both suborders of Polycladida, Acotylea and Cotylea have been investigated for natural products. As such, confirming assumptions as to which species are in any sense toxic or if the compounds they use are biosynthesised, accumulated from food or the product of symbiotic bacteria is difficult. However, further research into the group is suggested as these animals often display aposematic colouration and are known to prey on invertebrates rich in bioactive secondary metabolites.     

The importance of habitat resistance for movement decisions in the common lizard, Lacerta vivipara

ABSTRACT: BACKGROUND: Movement behaviour can be influenced by a multitude of biotic and abiotic factors. Here, we investigate the speed of movement in relation to environmental and individual phenotypic properties in subadult common lizards (Lacerta vivipara). We aim to disentangle the importance of substrate, cover, humidity, basking opportunity and individual phenotype on moving tendencies in 12 treatment combinations, at which each lizard was tested. RESULTS: We find that movement behaviour depends on the starting conditions, the physical properties of the dispersal corridor, and on the individuals' phenotype. Specifically, the presence of cover and substrate providing suitable traction in the corridor had positive effects on individual movement decisions. Additionally, we find high phenotypic variation in the propensity to move dependent on the presence of cover. Individual back patterns also strongly affected movement decisions in interaction with the physical properties of the dispersal corridor. CONCLUSIONS: Our results highlight the importance of understanding the habitat resistance for movement patterns, with humid habitats with covering vegetation providing the best conditions to initiate movement in the common lizard. In addition, population effects, differences in back pattern phenotype and individual plasticity were identified as key parameters influencing movement behaviour.     

Screening of microorganisms producing cold-active oxidoreductases to be applied in enantioselective alcohol oxidation. An Antarctic survey

Several microorganisms were isolated from soil/sediment samples of Antarctic Peninsula. The enrichment technique using (RS)-1-(phenyl)ethanol as a carbon source allowed us to isolate 232 psychrophile/psychrotroph microorganisms. We also evaluated the enzyme activity (oxidoreductases) for enantioselective oxidation reactions, by using derivatives of (RS)-1-(phenyl)ethanol as substrates. Among the studied microorganisms, 15 psychrophile/psychrotroph strains contain oxidoreductases that catalyze the (S)-enantiomer oxidation from racemic alcohols to their corresponding ketones. Among the identified microorganisms, Flavobacterium sp. and Arthrobacter sp. showed excellent enzymatic activity. These new bacteria strains were selected for optimization study, in which the (RS)-1-(4-methyl-phenyl)ethanol oxidation was evaluated in several reaction conditions. From these studies, it was observed that Flavobacterium sp. has an excellent enzymatic activity at 10 °C and Arthrobacter sp. at 15 and 25 °C. We have also determined the growth curves of these bacteria, and both strains showed optimum growth at 25 °C, indicating that these bacteria are psychrotroph.