Art-omics: multi-omics meet archaeology and art conservation

Multi-omics can informally be described as the combined use of high-throughput techniques allowing the characterization of complete microbial communities by the sequencing/identification of total pools of biomolecules including DNA, proteins or metabolites. These techniques have allowed an unprecedented level of knowledge on complex microbial ecosystems, which is having key implications in land and marine ecology, industrial biotechnology or biomedicine. Multi-omics have recently been applied to artistic or archaeological objects, with the goal of either contributing to shedding light on the original context of the pieces and/or to inform conservation approaches. In this minireview, we discuss the application of -omic techniques to the study of prehistoric artworks and ancient man-made objects in three main technical blocks: metagenomics, proteomics and metabolomics. In particular, we will focus on how proteomics and metabolomics can provide paradigm-breaking results by unambiguously identifying peptides associated with a given, palaeo-cultural context; and we will discuss how metagenomics can be central for the identification of the microbial keyplayers on artworks surfaces, whose conservation can then be approached by a range of techniques, including using selected microorganisms as ‘probiotics’ because of their direct or indirect effect in the stabilization and preservation of valuable art objects.     

Viable and not viable spore concentrations in National Gallery of Umbria (Italy)

The conservation actions towards artworks holding a common patrimony for the community are of primary importance, but also those related to their "container" as museums, libraries or archives are to consider. Fungal spores and bacteria carried by air flows to the artwork surface can colonize it causing biodeterioration through physical and/or chemical alterations of the materials with the irreversible loss of their value. The quality control of the indoor air surrounding the historic building is essential, as well as for the protection and conservation of the artwork, also for the protection of the health of operators and visitors. The aim of this study was to monitor airborne fungal particles, through volumetric spore traps, for improving the knowledge about the conservation and protection of artworks in the museum environment analysing the principal relationships between indoor environmental conditions and potentially biodeteriogen fungal spore growth. The evidence of no significant relationships between spore concentrations and environmental conditions recorded inside the different expositive rooms testified the regular and correct maintenance of the air conditioning system inside the considered building (National Gallery of Umbria, central Italy). Moreover, in a specific museum room a significant spore concentration decreasing trend was recorded mainly due to a structural modification in the same building.

     

微生物系统发育多样性及其保护生物学意义

近年来,分子系统发育分析方法,特别是rBNA基因同源性分析方法,在微生物多样性的研究中发挥着越来越重要的作用．它克服了传统的微生物分离培养方法的限制,极大地促进了人们对微生物多样性的理解．在遗传信息同源性分析基础上得出的微生物系统发育多样性为多样性的保护提供了新的视点．它不但可以作为微生物多样性评价的手段,而且为多样性保护中优先秩序的确定提供了依据．同时也为生物多样性保护确定了目标,即最大程度地保护系统发育关系中所包含的信息．本文对微生物系统发育多样性的特点及其保护生物学意义进行了简要评述．     

Inhibition of Methanogenesis by Methyl Fluoride: Studies of Pure and Defined Mixed Cultures of Anaerobic Bacteria and Archaea

Methyl fluoride (fluoromethane [CH(inf3)F]) has been used as a selective inhibitor of CH(inf4) oxidation by aerobic methanotrophic bacteria in studies of CH(inf4) emission from natural systems. In such studies, CH(inf3)F also diffuses into the anaerobic zones where CH(inf4) is produced. The effects of CH(inf3)F on pure and defined mixed cultures of anaerobic microorganisms were investigated. About 1 kPa of CH(inf3)F, similar to the amounts used in inhibition experiments, inhibited growth of and CH(inf4) production by pure cultures of aceticlastic methanogens (Methanosaeta spp. and Methanosarcina spp.) and by a methanogenic mixed culture of anaerobic microorganisms in which acetate was produced as an intermediate. With greater quantities of CH(inf3)F, hydrogenotrophic methanogens were also inhibited. At a partial pressure of CH(inf3)F of 1 kPa, homoacetogenic, sulfate-reducing, and fermentative bacteria and a methanogenic mixed culture of anaerobic microorganisms based on hydrogen syntrophy were not inhibited. The inhibition by CH(inf3)F of the growth and CH(inf4) production of Methanosarcina mazei growing on acetate was reversible. CH(inf3)F inhibited only acetate utilization by Methanosarcina barkeri, which is able to use acetate and hydrogen simultaneously, when both acetate and hydrogen were present. These findings suggest that the use of CH(inf3)F as a selective inhibitor of aerobic CH(inf4) oxidation in undefined systems must be interpreted with great care. However, by a careful choice of concentrations, CH(inf3)F may be useful for the rapid determination of the role of acetate as a CH(inf4) precursor.     

合成生物学技术在环境保护中的应用

合成生物学是一个基于生物学和工程学原理的科学领域,其目的是重新设计和重组微生物,以优化或创建具有增强功能的新生物系统。该领域利用分子工具、系统生物学和遗传框架的重编程,从而构建合成途径以获得具有替代功能的微生物。传统上,合成生物学方法通常旨在开发具有成本效益的微生物细胞工厂进而从可再生资源中生产化学物质。然而,近年来合成生物学技术开始在环境保护中发挥着更直接的作用。本综述介绍了基因工程中的合成生物学工具,讨论了基于基因工程的微生物修复策略,强调了合成生物学技术可以通过响应特定污染物进行生物修复来保护环境。其中,规律间隔成簇短回文重复序列(Clustered Regularly Interspersed Short Palindromic Repeats, CRISPR)技术在基因工程细菌和古细菌的生物修复中得到了广泛应用,生物修复领域也出现了很多新的先进技术,包括生物膜工程、人工微生物群落的构建、基因驱动、酶和蛋白质工程等。有了这些新的技术和工具,生物修复将成为当今最好和最有效的污染物去除方式之一。     

Designing Graduate Training Programs in Conservation Medicine—Producing the Right Professionals with the Right Tools

New challenges to human, animal, and ecosystem health demand novel solutions: New diseases are emerging from new configurations of humans, their domestic animals and wildlife; new pressures on once robust and resilient ecosystems are compromising their integrity; synthetic compounds and engineered organisms, new to the natural world, are spreading unpredictably around the globe. Globalization provides opportunities for infectious organisms to gain access to new hosts, changing in distribution and virulence. What type of training should be developed to provide professionals with the right tools to meet these challenges? In this article, we offer recommendations for developing academic programs in conservation medicine. We discuss the need for, and the advantages to, using a conservation medicine approach to address real world situations and present illustrations of how this is applied today. We suggest a core set of skills that are needed in a conservation medicine practitioner, and recommend key considerations for designing new conservation medicine training programs. We review existing programs that offer conservation medicine content, and provide examples of where opportunities exist for those interested in pursuing a conservation medicine career.     

The use of a GIS-based multi-criteria evaluation technique for the development of a zoning plan for a seasonally variable Ramsar wetland site in Syria: Sabkhat Al-Jabboul

Zoning is an important tool used in the management of protected areas and wetlands. It has been developed to apply conservation objectives at different levels of management where conflicting uses can be taking place. GIS is increasingly used to solve land allocation problem with techniques based on zoning, varying from simple overlays to complex multi-criteria evaluation techniques (MCE). This study presents a new approach to the development of zoning plans for Ramsar sites that exhibit major seasonal variations in conservation value and human use and threats. It employs a well-defined GIS-based MCE technique which involves both expert judgment and a set of criteria based on ecological and potential threats. A GIS model using the additive approach in MCE was developed to evaluate Sabkhat Al-Jabboul the only Ramsar site in Syria. The model was applied separately for the spring and winter to accommodate seasonal changes in the intensity and spatial distribution of conservation areas and threats across the site. Separate zoning plans were developed for each of the two main seasons. The zoning plan of the spring season, which is the birds breeding season, included three management zones; the special conservation zone, the conservation buffer zone, and the wise use zone. The winter zoning plan, where the bird feeding activity was the major activity includes two zones: a special conservation zone and a wise use zone. Thus, in cases like Sabkhat Al-Jabboul, where the wetlands are subject to significant seasonal variations, in their ecology and human utilization, it is recommended that flexible seasonal zoning plans are developed to assist in the organization of permitted activities, and to reduce the potential human impacts throughout the year.     

Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time

Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra‐low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.     

Protected areas and prime hoverfly areas: Safe haven for hoverflies or not?

The efficiency of protected areas (PAs) has often been questioned due to global decline of biodiversity. Invertebrates, especially insects, have been historically underrepresented in conservation studies. Our study focuses on hoverflies, an important group of insect pollinators and proven to be good bioindicators. Research was focused in Serbia, one of Europe's hotspots of hoverfly diversity, with a long tradition of hoverfly research, which provided sufficient information for achieving our aims: identifying areas of high hoverfly diversity, evaluating the efficiency of PAs and prime hoverfly areas (PHAs) in the conservation of hoverflies, determining how well they cover the distribution of hoverfly species, especially those of conservation concern, and testing the importance of the size of the area for conservation of hoverfly diversity. We applied weighting of the species to help stress the importance of species of conservation concern. The results indicated that PHAs cover the areas with high hoverfly diversity better than PA networks, especially when it comes to species of conservation concern. Generalized linear model results showed that the area size was a significant predictor of number of species in both PA and PHA. This indicates that area size is key when designating new areas important for conservation, but there are also other factors that need to be taken into account, such as habitat quality or suitability. Studies like this are useful in aiding designation of new areas important for conservation of certain species and in identifying sampling gaps, which could potentially aim future research in that direction.     

Maximizing species conservation in continental Ecuador: a case of systematic conservation planning for biodiverse regions

Ecuador has the largest number of species by area worldwide, but also a low representation of species within its protected areas. Here, we applied systematic conservation planning to identify potential areas for conservation in continental Ecuador, with the aim of increasing the representation of terrestrial species diversity in the protected area network. We selected 809 terrestrial species (amphibians, birds, mammals, and plants), for which distributions were estimated via species distribution models (SDMs), using Maxent. For each species we established conservation goals based on conservation priorities, and estimated new potential protected areas using Marxan conservation planning software. For each selected area, we determined their conservation priority and feasibility of establishment, two important aspects in the decision-making processes. We found that according to our conservation goals, the current protected area network contains large conservation gaps. Potential areas for conservation almost double the surface area of currently protected areas. Most of the newly proposed areas are located in the Coast, a region with large conservation gaps and irreversible changes in land use. The most feasible areas for conservation were found in the Amazon and Andes regions, which encompass more undisturbed habitats, and already harbor most of the current reserves. Our study allows defining a viable strategy for preserving Ecuador''s biodiversity, by combining SDMs, GIS-based decision-support software, and priority and feasibility assessments of the selected areas. This approach is useful for complementing protected area networks in countries with great biodiversity, insufficient biological information, and limited resources for conservation.     

Conservation Action Based on Threatened Species Capture Taxonomic and Phylogenetic Richness in Breeding and Wintering Populations of Central Asian Birds

Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.     

Cytological Investigations of Lithobiontic Microorganisms in Granitic Rocks

This paper shows the ultrastructure of lithobiontic organisms in a granitic rock from the exterior to the interior, where fissures are found 1–2 mm from the surface. There is clear differentiation at cell level between mycobiont and photobiont cells located on the rock surface which forms part of the lichen thallus and prokaryotic and eukaryotic cells (algae and fungi) found in the fissures. As well as the observations at the ultrastructural level of the microorganisms which live in fissures and cavities, immunolabelling techniques with colloidal gold have been applied to obtain an immunolocalization of Rubisco enzyme in some of the cells. The technique applied here permits Rubisco enzyme to be identified in algae-like cells belonging to fissures where it is difficult to identify the pyrenoid. The mineral environment of the cells situated inside the fissures is investigated by Energy Dispersive Spectrometry (EDS). The biotite particles present in the fissure walls, as well as some lithobiont microorganisms, show a depletion of potassium from interlayer positions.     

Cloning and sequence analysis of channel catfish heavy chain cDNA indicate phylogenetic diversity within the IgM immunoglobulin family

Catfish cDNA libraries were constructed using the poly(A+) RNA obtained from in vitro stimulated catfish leukocytes. Antigenic analysis with different antisera to catfish Ig resulted in the definition of cDNA clones encoding the catfish H chain. Sequence analysis confirmed that the catfish H chain was definitively identified, based on its similarities with chicken and mouse mu chains. Two clones were each shown to encode part of the CH2 domain, the complete CH3 and CH4 domains, the C-terminus, and a 184-bp 3' untranslated region before the poly(A+) tail. The conservation of domain size and structure is clearly evident. The two cysteines forming the intradomain disulfide bridge, as well as the tryptophans located within each domain, are absolutely conserved. There are four carbohydrate acceptor sites in the catfish H chain, only one of which is phylogenetically conserved. Of the six sequenced H chain clones, one was found to differ in a single base in the CH3, which results in the loss of a carbohydrate acceptor site. Whether this difference indicates isotypic variation between closely related genes or somatic mutation is unresolved. Amino acid sequence comparisons indicate that there is a approximately 24% similarity when the catfish H chain is aligned with mouse mu chains. This is considerably less than the approximately 40% amino acid conservation found between the chicken and mouse mu chain. The amino acid sequence of the catfish H chain is most conserved in the C-terminus (approximately 30%) and the CH4 (approximately 26%); there is less conservation in the CH3 (approximately 20%) when comparisons are made with mouse mu chain. The CH3 domain of the catfish H chain also has different hydropathy properties, when compared with the CH3 domain of the higher vertebrate mu chains. Finally, the sequence of the catfish H chain indicates an unusual arrangement of the cysteines that likely participate in intersubunit and inter-H chain disulfide linkages. The disulfide linkage of these cysteines during Ig polymerization may account for the unusual covalent architecture associated with the catfish tetramer.     

Using a goal programming approach to design and evaluate protected areas for the conservation of multiple dimensions of biodiversity

The decline and loss of biodiversity provoked by human activities have caused ecologists and conservationists to center their attention on the design of conservation priority areas (PAs), focusing mainly on species conservation in terms of richness, rarity and/or vulnerability. However, biodiversity has multiple dimensions, evolutionary processes have recently been labeled the ‘missing component’ of conservation strategies, and increasingly more authors are suggesting that the ecological, evolutionary and historical aspects of biodiversity are key components of conservation planning. In this study we develop a prioritization system to design conservation PAs using the wild terrestrial mammals of the Iberian Peninsula as an example. We aim to contribute to the design of more suitable PAs by integrating ecological components of biodiversity (species richness, vulnerability and rarity), evolutionary aspects (accumulated genetic diversification) and historical information relevant to the study area. After selecting a set of biodiversity indicators, we applied a multi-objective technique (extended goal programming) to construct a combined index, where values in the top 90th percentile were then used to select the PAs. According to our most efficient and satisfactory results, some areas highlighted for their conservation are currently categorized as PAs, however, we found that it would be necessary to reconsider their extent, especially in northern Spain, where the historical aspects of biodiversity (the missing component) are more widely present. The need to determine PAs is unquestionable. However, it should also be a priority to move towards a model of sustainable and fair development.     

Implications of bacterial,viral and mycotic microorganisms in vultures for wildlife conservation,ecosystem services and public health

The effects that microorganisms (bacteria, viruses and fungi) have on their hosts remain unexplored for most vulture species. This is especially relevant for vultures, as their diet consists of carcasses in various stages of decomposition, which are breeding grounds for potentially pathogenic microorganisms. Here we review current knowledge of bacterial, viral and mycotic microorganisms present in wild vultures. We consider their potential to cause disease in vultures and whether this poses any population-level threats. Furthermore, we address the question of whether vultures may act as disease spreaders or mitigators. We found 76 articles concerning bacterial, viral and mycotic microorganisms present in 13 vulture species, 57 evaluating bacteria, 13 evaluating viruses and six evaluating mycotic microorganisms. These studies come from all continents where vultures are present, but mainly from Europe and North America, and the most studied species was the Griffon Vulture Gyps fulvus. We found that vultures are colonized by zoonotic pathogens, and even host-specific human pathogens. Some recorded bacteria showed multi-antibiotic resistance, especially those that can be associated with anthropogenic food subsides such as supplementary feeding stations. We found evidence that vulture health can be affected by some microorganisms, producing a wide array of clinical alterations that have the potential to influence mortality risk and fitness. We did not find clear scientific evidence that vultures play an epidemiological role spreading microorganisms to humans and other species. However, there is evidence that vultures could prevent the spread of infectious diseases through their removal of decomposing organic material. The evaluation of vulture exposure to microorganisms is of fundamental importance to design better conservation policies for this threatened group, which may serve a key role as ecosystem cleaners.     

Conservation status of tropical dry forest remnants in Nicaragua: Do ecological indicators and social perception tally?

Intensive deforestation is reducing dry tropical forest areas worldwide and increasing its fragmentation. Forest remnants can be the basis for the future recovery of this forest type if appropriate management practices are applied. This requires a better knowledge of their conservation status and the assessment of their perceived value by land users. In this study we compare the structure, species richness and diversity of different types of tropical dry forest remnants in Nicaragua and we assess their conservation status based on a new index: Social simplified Importance Value Index (SsIVI). This index summarizes both ecological indicators and the perception by local stakeholders of the conservation status of the tree species present. Results show that gallery and hillslope forest remnants have higher species richness and diversity than isolated vestigial patches. In all remnants, species richness and diversity is higher in the tree layer than in the regeneration layer. No differences are observed in valorisation among different types of remnants either for the tree layer or for the regeneration layer. In the hillslope forests, where several degrees of disturbance are present, the valorisation decreases with increasing degradation. Results of species composition and forest structure indicate a strong degradation of dry tropical forest remnants in Nicaragua. However, the similar social valorisation of the three types of remnants suggests that they face similar threats but also similar opportunities to be preserved. A decrease in valorisation with increasing degradation warns about the potential loss of the most degraded areas, unless forest restoration is applied.     

Changing attitudes to nature conservation: the entomological perspective

Unlike some other kinds of wildlife, insects have little attraction for the public. Insects tend to be a specialist interest, partly because the numbers of species are so large. This concentrates attention on insect identification and the impossibility of accomplishing this in the field except in a few cases. Some conflict between economic entomologists and conservationists has been apparent. Conservation organizations, including those specifically interested in insects, have influenced attitudes, as has the development of ecology, applied biogeography, and other scientific disciplines. Legislation for insect conservation is not satisfactory; not enough emphasis is laid on habitat conservation and the concepts of protected and endangered species are confused. Better cooperation and understanding between legislators and field entomologists are desirable. Species conservation in Britain emphasises butterflies. Many of the species thought to be threatened with extinction in 1925 are also of priority concern today. Better habitat management and re-establishments, both national and local, are important conservation activities. In the Third World, conservation is closely linked with utilization of the resource. This rational and sustainable use is in accordance with the World Conservation Strategy and benefits the rural poor in areas where attitudes to conservation in the developed world are inappropriate.     

Recent advances in biodegradation in China: New microorganisms and pathways,biodegradation engineering,and bioenergy from pollutant biodegradation

We are facing serious environmental challenges, and environmental biotechnology is an enabling technology to reduce or eliminate pollution. In recent years, environmental pollution in China has been receiving great attention, and this paper provides an up-to-date review on progress in biodegradation research in China. This progress includes the isolation of extremophilic microorganisms for pollutant degradation in extreme conditions and the study of genes and enzymes related to biodegradation pathways. Biodegradation engineering has potential as an interesting and powerful platform, where genetic engineering, process engineering, and signal transduction engineering are applied together. In addition, pollutant treatment combined with the production of renewable sources of bioenergy by microorganisms is attractive.