Open AccessReview
Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities
Diversity 2017, 9(4), 55; doi:10.3390/d9040055 -
Abstract
Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x) and tetraploid durum wheat (
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Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x) and tetraploid durum wheat (T. durum, 4x), widening the genetic base is a priority and primary target to cope with the many challenges that the crop has to face. These include recent climate changes, as well as actual and projected demographic growth, contrasting with reduction of arable land and water reserves. All of these environmental and societal modifications pose major constraints to the required production increase in the wheat crop. A sustainable approach to address this task implies resorting to non-conventional breeding strategies, such as “chromosome engineering”. This is based on cytogenetic methodologies, which ultimately allow for the incorporation into wheat chromosomes of targeted, and ideally small, chromosomal segments from the genome of wild relatives, containing the gene(s) of interest. Chromosome engineering has been successfully applied to introduce into wheat genes/QTL for resistance to biotic and abiotic stresses, quality attributes, and even yield-related traits. In recent years, a substantial upsurge in effective alien gene exploitation for wheat improvement has come from modern technologies, including use of molecular markers, molecular cytogenetic techniques, and sequencing, which have greatly expanded our knowledge and ability to finely manipulate wheat and alien genomes. Examples will be provided of various types of stable introgressions, including pyramiding of different alien genes/QTL, into the background of bread and durum wheat genotypes, representing valuable materials for both species to respond to the needed novelty in current and future breeding programs. Challenging contexts, such as that inherent to the 4x nature of durum wheat when compared to 6x bread wheat, or created by presence of alien genes affecting segregation of wheat-alien recombinant chromosomes, will also be illustrated. Full article
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Open AccessFeature PaperArticle
Metabarcoding of Environmental DNA Samples to Explore the Use of Uranium Mine Containment Ponds as a Water Source for Wildlife
Diversity 2017, 9(4), 54; doi:10.3390/d9040054 -
Abstract
Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and
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Understanding how anthropogenic impacts on the landscape affect wildlife requires a knowledge of community assemblages. Species surveys are the first step in assessing community structure, and recent molecular applications such as metabarcoding and environmental DNA analyses have been proposed as an additional and complementary wildlife survey method. Here, we test eDNA metabarcoding as a survey tool to examine the potential use of uranium mine containment ponds as water sources by wildlife. We tested samples from surface water near mines and from one mine containment pond using two markers, 12S and 16S rRNA gene amplicons, to survey for vertebrate species. We recovered large numbers of sequence reads from taxa expected to be in the area and from less common or hard to observe taxa such as the tiger salamander and gray fox. Detection of these two species is of note because they were not observed in a previous species assessment, and tiger salamander DNA was found in the mine containment pond sample. We also found that sample concentration by centrifugation was a more efficient and more feasible method than filtration in these highly turbid surface waters. Ultimately, the use of eDNA metabarcoding could allow for a better understanding of the area’s overall biodiversity and community composition as well as aid current ecotoxicological risk assessment work. Full article
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Open AccessArticle
Taxonomic and Metabolite Diversity of Actinomycetes Associated with Three Australian Ascidians
Diversity 2017, 9(4), 53; doi:10.3390/d9040053 -
Abstract
Actinomycetes are known to be the most prolific producers of biologically active metabolites. Here, we investigated the host species-specificity and the related secondary metabolites of actinomycetes that are associated with three different Australian ascidians, namely Symplegma rubra, Aplidium solidum, and Polyclinum
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Actinomycetes are known to be the most prolific producers of biologically active metabolites. Here, we investigated the host species-specificity and the related secondary metabolites of actinomycetes that are associated with three different Australian ascidians, namely Symplegma rubra, Aplidium solidum, and Polyclinum vasculosum. Results indicated that while isolates from the genera Streptomyces and Micromonospora were highly diverse in the ascidian samples, only two culturable actinomycete Operational Taxonomic Units (OTUs) overlapped between all of the ascidians, pointing to some degree of host species-specificity of the isolates and selective acquisition of microbial associates by the host from the surrounding environment. LC-MS/MS profiling of extracts obtained from the ascidians and their actinomycete associates revealed many overlapping ions between hosts and actinomycetes, indicating that these compounds were likely to be synthesised by the microbial associates. Laboratory cultures of the actinomycetes displayed even more diverse metabolomes than those of their ascidian hosts; thus, making ascidian-associated actinomycetes an excellent target for natural product drug discovery and biotechnology. Full article
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Open AccessFeature PaperArticle
Allelic Variants of Glutamine Synthetase and Glutamate Synthase Genes in a Collection of Durum Wheat and Association with Grain Protein Content
Diversity 2017, 9(4), 52; doi:10.3390/d9040052 -
Abstract
Wheat is one of the most important crops grown worldwide. Despite the fact that it accounts for only 5% of the global wheat production, durum wheat (Triticum turgidum L. subsp. durum) is a commercially important tetraploid wheat species, which originated and
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Wheat is one of the most important crops grown worldwide. Despite the fact that it accounts for only 5% of the global wheat production, durum wheat (Triticum turgidum L. subsp. durum) is a commercially important tetraploid wheat species, which originated and diversified in the Mediterranean basin. In this work, the candidate gene approach has been applied in a collection of durum wheat genotypes; allelic variants of genes glutamine synthetase (GS2) and glutamate synthase (GOGAT) were screened and correlated with grain protein content (GPC). Natural populations and collections of germplasms are quite suitable for this approach, as molecular polymorphisms close to a locus with evident phenotypic effects may be closely associated with their character, providing a better physical resolution than genetic mapping using ad hoc constituted populations. A number of allelic variants were detected both for GS2 and GOGAT genes, and regression analysis demonstrated that some variations are positively and significantly related to the GPC effect. Additionally, these genes map into homoeologous chromosome groups 2 and 3, where several authors have localized important quantitative trait loci (QTLs) for GPC. The information outlined in this work could be useful in breeding and marker-assisted selection programs. Full article
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Open AccessReview
Towards the Genomic Basis of Local Adaptation in Landraces
Diversity 2017, 9(4), 51; doi:10.3390/d9040051 -
Abstract
Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions
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Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties. Full article
Open AccessReview
International Instruments for Conservation and Sustainable Use of Plant Genetic Resources for Food and Agriculture: An Historical Appraisal
Diversity 2017, 9(4), 50; doi:10.3390/d9040050 -
Abstract
This paper critically reviews the evolution of concepts and principles that inspired the adoption and enforcement of international instruments related to the conservation, exchange and sustainable use of plant genetic resources for food and agriculture, including agreements, governance and programs. The review spans
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This paper critically reviews the evolution of concepts and principles that inspired the adoption and enforcement of international instruments related to the conservation, exchange and sustainable use of plant genetic resources for food and agriculture, including agreements, governance and programs. The review spans from the pioneering attempts to regulate this matter, to the negotiations that led to the current regulatory framework, covering the creation of the Panel of Experts on Plant Exploration and Introduction of Food and Agriculture Organization (FAO) in 1965, the establishment of the International Board for Plant Genetic Resources (IBPGR) in 1974 and the FAO Commission on Plant Genetic Resources for Food and Agriculture in 1983, the adoption of the International Undertaking in 1983 and, more recently (2001), the International Treaty for Plant Genetic Resources for Food and Agriculture. The conceptual contribution, offered by Prof. Scarascia Mugnozza and other visionary scholars, to the establishment of these international instruments, is highlighted. Full article
Open AccessReview
Symbiotic Microbes from Marine Invertebrates: Driving a New Era of Natural Product Drug Discovery
Diversity 2017, 9(4), 49; doi:10.3390/d9040049 -
Abstract
Invertebrates account for more than 89% of all extant organisms in the marine environment, represented by over 174,600 species (recorded to date). Such diversity is mirrored in (or more likely increased by) the microbial symbionts associated with this group and in the marine
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Invertebrates account for more than 89% of all extant organisms in the marine environment, represented by over 174,600 species (recorded to date). Such diversity is mirrored in (or more likely increased by) the microbial symbionts associated with this group and in the marine natural products (or MNPs) that they produce. Since the early 1950s over 20,000 MNPs have been discovered, including compounds produced by symbiotic bacteria, and the chemical diversity of compounds produced from marine sources has led to them being referred to as "blue gold" in the search for new drugs. For example, 80% of novel antibiotics stemming from the marine environment have come from Actinomycetes, many of which can be found associated with marine sponges, and compounds with anti-tumorigenic and anti-diabetic potential have also been isolated from marine symbionts. In fact, it has been estimated that marine sources formed the basis of over 50% of FDA-approved drugs between 1981 and 2002. In this review, we explore the diversity of marine microbial symbionts by examining their use as the producers of novel pharmaceutical actives, together with a discussion of the opportunities and constraints offered by “blue gold” drug discovery. Full article
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Open AccessCommunication
Duplex Alu Screening for Degraded DNA of Skeletal Human Remains
Diversity 2017, 9(4), 48; doi:10.3390/d9040048 -
Abstract
The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal
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The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400–500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach. Full article
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Open AccessCommunication
An Update on the Invasion of Weakfish Cynoscion regalis (Bloch & Schneider, 1801) (Actinopterygii: Sciaenidae) into Europe
Diversity 2017, 9(4), 47; doi:10.3390/d9040047 -
Abstract
New information on weakfish introduction vectors, its invasive status, distribution, and use as a fishing resource arose after the publication of “The transatlantic introduction of weakfish Cynoscion regalis (Bloch & Schneider, 1801) (Sciaenidae, Pisces) into Europe” by Morais and Teodósio (2016). Currently, the
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New information on weakfish introduction vectors, its invasive status, distribution, and use as a fishing resource arose after the publication of “The transatlantic introduction of weakfish Cynoscion regalis (Bloch & Schneider, 1801) (Sciaenidae, Pisces) into Europe” by Morais and Teodósio (2016). Currently, the first known report of weakfish in Europe dates back to September 2009, with a specimen captured in the Schelde estuary (Belgium/The Netherlands). This fact suggests that weakfish could have been introduced into Europe via multiple and independent ballast water introduction events, and not through a point-source introduction event with subsequent dispersion as previously hypothesized. It is also unlikely that Schelde weakfish migrated southwards to colonize Iberian aquatic ecosystems. Weakfish have established a population in the Gulf of Cádiz region and have already reached an invasive status in the Sado estuary (Portugal). Weakfish were also captured in several other locations along the Portuguese coast, including the Tagus and Mira estuaries at least since 2013 or 2014, and the Ria Formosa lagoon in 2017. Tagus anglers caught weakfish specimens of ~1 kg and ~40 cm in November 2016, which corresponds to fish of 3+ years of age in the native range. The presence of weakfish in the Tagus estuary is still fairly unknown to local anglers. Sado weakfish has already been sold in local fish markets in southern Portugal for 3 to 10 € kg−1. However, we consider that the weakfish sale price is underrated in comparison with other wild species (e.g., meagre, seabass, gilthead seabream). Increasing sale price will convince fishers to use weakfish as a new fishing resource; however, it is necessary to promote the species among consumers and evaluate consumers’ preference in respect to other species. A putative biological threat might turn into a new valuable fishing resource by implementing adequate management solutions. Full article
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Open AccessReview
Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers
Diversity 2017, 9(4), 46; doi:10.3390/d9040046 -
Abstract
Diagnosis of leprosy and tuberculosis in archaeological material is most informative when based upon entire genomes. Ancient DNA (aDNA) is often degraded but amplification of specific fragments also provides reliable diagnoses. Cell wall lipid biomarkers can distinguish ancient leprosy from tuberculosis and DNA
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Diagnosis of leprosy and tuberculosis in archaeological material is most informative when based upon entire genomes. Ancient DNA (aDNA) is often degraded but amplification of specific fragments also provides reliable diagnoses. Cell wall lipid biomarkers can distinguish ancient leprosy from tuberculosis and DNA extraction residues can be utilized. The diagnostic power of combined aDNA and lipid biomarkers is illustrated by key cases of ancient leprosy and/or tuberculosis. Human tuberculosis was demonstrated in a woman and child from Atlit-Yam (~9 ka) in the Eastern Mediterranean and in the 600 BCE Egyptian “Granville” mummy. Both aDNA and lipids confirmed Pleistocene tuberculosis in a ~17 ka bison from Natural Trap Cave, Wyoming. Leprosy is exemplified by cases from Winchester (10th–12th centuries CE) and Great Chesterford (5th–6th centuries CE). A mixed infection from Kiskundorozsma, Hungary (7th century CE) allowed lipid biomarkers to assess the relative load of leprosy and tuberculosis. Essential protocols for aDNA amplification and analysis of mycolic, mycolipenic, mycocerosic acid, and phthiocerol lipid biomarkers are summarized. Diagnoses of ancient mycobacterial disease can be extended beyond the reach of whole genomics by combinations of aDNA amplification and lipid biomarkers, with sole use of the latter having the potential to recognize even older cases. Full article
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Open AccessArticle
Patterns of Spontaneous Nucleotide Substitutions in Grape Processed Pseudogenes
Diversity 2017, 9(4), 45; doi:10.3390/d9040045 -
Abstract
Pseudogenes are dead copies of genes. Owing to the absence of functional constraint, all nucleotide substitutions that occur in these sequences are selectively neutral, and thus represent the spontaneous pattern of substitution within a genome. Here, we analysed the patterns of nucleotide substitutions
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Pseudogenes are dead copies of genes. Owing to the absence of functional constraint, all nucleotide substitutions that occur in these sequences are selectively neutral, and thus represent the spontaneous pattern of substitution within a genome. Here, we analysed the patterns of nucleotide substitutions in Vitis vinifera processed pseudogenes. In total, 259 processed pseudogenes were used to compile two datasets of nucleotide substitutions. The ancestral states of polymorphic sites were determined based on either parsimony or site functional constraints. An overall tendency towards an increase in the pseudogene A:T content was suggested by all of the datasets analysed. Low association was seen between the patterns and rates of substitutions, and the compositional background of the region where the pseudogene was inserted. The flanking nucleotide significantly influenced the substitution rates. In particular, we noted that the transition of G→A was influenced by the presence of C at the contiguous 5′ end base. This finding is in agreement with the targeting of cytosine to methylation, and the consequent methyl-cytosine deamination. These data will be useful to interpret the roles of selection in shaping the genetic diversity of grape cultivars. Full article
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Open AccessCommunication
Evidence of Recent Fine-Scale Population Structuring in South American Puma concolor
Diversity 2017, 9(4), 44; doi:10.3390/d9040044 -
Abstract
Habitat loss and fragmentation are considered the major treats to worldwide biodiversity. Carnivores in particular can be more sensitive to landscape modification due to their low occurrence density and large home ranges. Population structuring of Puma concolor has been already reported as a
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Habitat loss and fragmentation are considered the major treats to worldwide biodiversity. Carnivores in particular can be more sensitive to landscape modification due to their low occurrence density and large home ranges. Population structuring of Puma concolor has been already reported as a consequence of extensive human activities in the North American continent. Here, we investigated the occurrence of fine-scale population structuring in the South American cougar population, contrasting two conservation areas immersed in a highly human-fragmented landscape dominated by the presence of sugar cane monoculture, roads, and urbanization, including a series of dams in the Tietê River which enlarges its water body. Seven microsatellites were amplified using non-invasive DNA obtained from fecal samples. We conducted genetic clustering analyses using Bayesian and factorial components. We also performed genetic differentiation analyses by fixation indices (Fst and Dest). Two genetic clusters represented by individuals from each area were found, indicating the occurrence of gene flow reduction between the areas. The intense human-induced landscape modification—which includes the Tietê River water body enlargement, imposing physical barriers to the movement of the individuals—could explain the gene flow reduction. Increasing connectivity among the preserved areas can mitigate such effects, and the creation of corridors or further management actions such as individual translocation to ensure gene flow in the highly-modified landscape may be essential for maintaining the genetic and demographic health of the species and its long-term persistence. Full article
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Open AccessArticle
Staphylococcus aureus Sequences from Osteomyelitic Specimens of a Pathological Bone Collection from Pre-Antibiotic Times
Diversity 2017, 9(4), 43; doi:10.3390/d9040043 -
Abstract
Staphylococcus aureus is a major pathogen causing osteomyelitis, amongst other diseases, and its methicillin-resistant form (MRSA) in particular poses a huge threat to public health. To increase our knowledge of the origin and evolution of S. aureus, genetic studies of historical microorganisms
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Staphylococcus aureus is a major pathogen causing osteomyelitis, amongst other diseases, and its methicillin-resistant form (MRSA) in particular poses a huge threat to public health. To increase our knowledge of the origin and evolution of S. aureus, genetic studies of historical microorganisms may be beneficial. Thus, the aim of this study was to investigate whether osteomyelitic skeletal material (autopsy specimens collected from the mid 19th century until the 1920s) is suitable for detecting historical S. aureus DNA sequences. We established a PCR-based analysis system targeting two specific genes of S. aureus (nuc and fib). We successfully amplified the historical S. aureusnuc and fib sequences for six and seven pre-antibiotic, osteomyelitic bone specimens, respectively. These results encourage further investigations of historical S. aureus genomes that may increase our understanding of pathogen evolution in relation to anthropogenically introduced antibiotics. Full article
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Open AccessArticle
High Levels of Antibiotic Resistance but No Antibiotic Production Detected Along a Gypsum Gradient in Great Onyx Cave, KY, USA
Diversity 2017, 9(4), 42; doi:10.3390/d9040042 -
Abstract
A preliminary study of antibiotic production and antibiotic resistance was conducted in Great Onyx Cave in Mammoth Cave National Park, KY, to determine if gypsum (CaSO4∙2H2O) affects these bacterial activities. The cave crosses through the width of Flint Ridge,
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A preliminary study of antibiotic production and antibiotic resistance was conducted in Great Onyx Cave in Mammoth Cave National Park, KY, to determine if gypsum (CaSO4∙2H2O) affects these bacterial activities. The cave crosses through the width of Flint Ridge, and passages under the sandstone caprock are dry with different amounts of gypsum. The Great Kentucky Desert hypothesis posits that gypsum limits the distribution of invertebrates in the central areas of Great Onyx Cave. Twenty-four bacterial isolates were cultivated from swabs and soils. Using three methods (soil crumb, soil crumb with indicator bacteria, and the cross-streak method using isolated bacteria) we did not detect any production of antibiotics. Antibiotic resistance was widespread, with all 24 isolates resistant to a minimum of two antibiotics of seven tested, with three isolates resistant to all. Antibiotic resistance was high and not correlated with depth into the cave or the amount of gypsum. The Great Kentucky Desert hypothesis of the negative effects of gypsum seems to have no impact on bacterial activity. Full article
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Open AccessReview
An Overview on Marine Sponge-Symbiotic Bacteria as Unexhausted Sources for Natural Product Discovery
Diversity 2017, 9(4), 40; doi:10.3390/d9040040 -
Abstract
Microbial symbiotic communities of marine macro-organisms carry functional metabolic profiles different to the ones found terrestrially and within surrounding marine environments. These symbiotic bacteria have increasingly been a focus of microbiologists working in marine environments due to a wide array of reported bioactive
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Microbial symbiotic communities of marine macro-organisms carry functional metabolic profiles different to the ones found terrestrially and within surrounding marine environments. These symbiotic bacteria have increasingly been a focus of microbiologists working in marine environments due to a wide array of reported bioactive compounds of therapeutic importance resulting in various patent registrations. Revelations of symbiont-directed host specific functions and the true nature of host-symbiont interactions, combined with metagenomic advances detecting functional gene clusters, will inevitably open new avenues for identification and discovery of novel bioactive compounds of biotechnological value from marine resources. This review article provides an overview on bioactive marine symbiotic organisms with specific emphasis placed on the sponge-associated ones and invites the international scientific community to contribute towards establishment of in-depth information of the environmental parameters defining selection and acquisition of true symbionts by the host organisms. Full article
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Open AccessReview
Thirty Years of Research on Crown-of-Thorns Starfish (1986–2016): Scientific Advances and Emerging Opportunities
Diversity 2017, 9(4), 41; doi:10.3390/d9040041 -
Abstract
Research on the coral-eating crown-of-thorns starfish (CoTS) has waxed and waned over the last few decades, mostly in response to population outbreaks at specific locations. This review considers advances in our understanding of the biology and ecology of CoTS based on the resurgence
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Research on the coral-eating crown-of-thorns starfish (CoTS) has waxed and waned over the last few decades, mostly in response to population outbreaks at specific locations. This review considers advances in our understanding of the biology and ecology of CoTS based on the resurgence of research interest, which culminated in this current special issue on the Biology, Ecology and Management of Crown-of-Thorns Starfish. More specifically, this review considers progress in addressing 41 specific research questions posed in a seminal review by P. Moran 30 years ago, as well as exploring new directions for CoTS research. Despite the plethora of research on CoTS (>1200 research articles), there are persistent knowledge gaps that constrain effective management of outbreaks. Although directly addressing some of these questions will be extremely difficult, there have been considerable advances in understanding the biology of CoTS, if not the proximate and ultimate cause(s) of outbreaks. Moving forward, researchers need to embrace new technologies and opportunities to advance our understanding of CoTS biology and behavior, focusing on key questions that will improve effectiveness of management in reducing the frequency and likelihood of outbreaks, if not preventing them altogether. Full article
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Open AccessArticle
Diversity and Bioactivity of Marine Bacteria Associated with the Sponges Candidaspongia flabellata and Rhopaloeides odorabile from the Great Barrier Reef in Australia
Diversity 2017, 9(3), 39; doi:10.3390/d9030039 -
Abstract
Sponges and their associated microbial communities have sparked much interest in recent decades due on the abundant production of chemically diverse metabolites that in nature serve as functional compounds required by the marine sponge host. These compounds were found to carry therapeutic importance
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Sponges and their associated microbial communities have sparked much interest in recent decades due on the abundant production of chemically diverse metabolites that in nature serve as functional compounds required by the marine sponge host. These compounds were found to carry therapeutic importance for medicinal applications. In the presented study, 123 bacterial isolates from the culture collection of the Australian Institute of Marine Science (AIMS) previously isolated from two different sponge species, namely Candidaspongia flabellata and Rhopaloeides odorabile, originating from different locations on the Great Barrier Reef in Queensland, Australia, were thus studied for their bioactivity. The symbiotic bacterial isolates were first identified using 16S rRNA gene analysis and they were found to belong to five different dominating classes of Domain Bacteria, namely Alphaproteobacteria, Gammaproteobacteria, Flavobacteria, Bacilli and Actinobacteria. Following their taxonomical categorization, the isolates were screened for their antimicrobial activity against human pathogenic microbial reference strains: Escherichia coli (ATCC® BAA-196™), E. coli (ATCC® 13706™), E. coli (ATCC® 25922™), Klebsiella pneumoniae (ATCC® BAA-1705™), Enterococcus faecalis (ATCC® 51575™), Bacillus subtilis (ATCC® 19659™), Staphylococcus aureus (ATCC® 29247™), Candida albicans (ATCC® 10231™) and Aspergillus niger (ATCC® 16888™). Over 50% of the isolates displayed antimicrobial activity against one or more of the reference strains tested. The subset of these bioactive bacterial isolates was further investigated to identify their biosynthetic genes such as polyketide synthase (PKS) type I and non-ribosomal peptide synthetase (NRPS) genes. This was done using polymerase chain reaction (PCR) with degenerate primers that have been previously used to amplify PKS-I and NRPS genes. These specific genes have been reported to be possibly involved in bacterial secondary metabolite production. In 47% of the bacterial isolates investigated, the PKS and NRPS genes were located. Some of the bacterial isolates were found to possess both gene types, which agrees with the previous reported biosynthetic ability of certain sponge-symbiotic bacteria such as the Actinobacteria or Gammaproteobacteria to produce secondary metabolites with antimicrobial activity. All these reported activities further confirm that sponge-symbiotic bacteria hold significant bioactivity with medicinal and biotechnological importance. Full article
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Open AccessReview
NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops
Diversity 2017, 9(3), 38; doi:10.3390/d9030038 -
Abstract
Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses
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Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses and a reduction of several food quality parameters. Next generation sequencing (NGS) technologies are being increasingly used to explore “gene space” and to provide high-resolution profiling of nucleotide variation within germplasm collections. On the other hand, advances in high-throughput phenotyping are bridging the genotype-to-phenotype gap in crop selection. The combination of allelic and phenotypic data points via genome-wide association studies is facilitating the discovery of genetic loci that are associated with key agronomic traits. In this review, we provide a brief overview on the latest NGS-based and phenotyping technologies and on their role to unlocking the genetic potential of vegetable crops; then, we discuss the paradigm shift that is underway in horticultural crop breeding. Full article
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Open AccessReview
Dispersal, Isolation, and Interaction in the Islands of Polynesia: A Critical Review of Archaeological and Genetic Evidence
Diversity 2017, 9(3), 37; doi:10.3390/d9030037 -
Abstract
Integration of archaeology, modern genetics, and ancient DNA holds promise for the reconstruction of the human past. We examine the advances in research on the indigenous peoples of Polynesia to determine: (1) what do archaeological and genetic data (ancient and modern DNA) tell
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Integration of archaeology, modern genetics, and ancient DNA holds promise for the reconstruction of the human past. We examine the advances in research on the indigenous peoples of Polynesia to determine: (1) what do archaeological and genetic data (ancient and modern DNA) tell us about the origins of Polynesians; and, (2) what evidence is there for long-distance travel and contacts between Polynesians and indigenous populations of the Americas? We note that the general dispersal pattern of founding human populations in the remote islands of the Pacific and long-distance interaction spheres continue to reflect well-established models. New research suggests that the formation of an Ancestral Polynesia Culture in Western Polynesia may have involved differential patterns of dispersal followed by significant later migrations. It has also been suggested that the pause between the settlement of Western and Eastern Polynesia was centuries longer than currently thought, followed by a remarkably rapid pulse of island colonization. Long-distance travel between islands of the Pacific is currently best documented through the sourcing of artifacts, while the discovery of admixture of Native American DNA within the genome of the people from Easter Island (Rapa Nui) is strong new evidence for sustained contacts between Polynesia and the Americas. Full article
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Open AccessArticle
In Situ Cultured Bacterial Diversity from Iron Curtain Cave, Chilliwack, British Columbia, Canada
Diversity 2017, 9(3), 36; doi:10.3390/d9030036 -
Abstract
The culturable bacterial diversity from Iron Curtain Cave, Chilliwack, British Columbia, Canada was examined. Sixty five bacterial isolates were successfully cultivated, purified, and identified based on 16S rRNA gene sequencing. Four distinguishable phyla, i.e., Actinobacteria (44.61%), Proteobacteria (27.69%), Firmicutes (20%) and Bacteroidetes (7.69%)
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The culturable bacterial diversity from Iron Curtain Cave, Chilliwack, British Columbia, Canada was examined. Sixty five bacterial isolates were successfully cultivated, purified, and identified based on 16S rRNA gene sequencing. Four distinguishable phyla, i.e., Actinobacteria (44.61%), Proteobacteria (27.69%), Firmicutes (20%) and Bacteroidetes (7.69%) were identified. Arthrobacter (21.53%) was identified as the major genus, followed by Sporosarcina (9.23%), Stenotrophomonas (9.23%), Streptomyces (6.15%), Brevundimonas (4.61%), and Crocebacterium (2.8%). Noteworthy, 12.3% of the population was recognized as unidentified bacteria. The isolates were evaluated for their potential antimicrobial activities against multidrug resistant microbial strains. Two species of the genus Streptomyces exhibited a wide range of antimicrobial activities against multidrug resistance (MDR) strains of Escherichiacoli and Pseudomonas spp. along with non-resistant strains of Staphylococcus aureus and E. coli. However, all of the antimicrobial activities were only observed when the isolates were grown at 8 °C in different media. To the best of our knowledge, this is the first study conducted on the Iron Curtain Cave’s bacterial diversity, and reveals some bacterial isolates that have never been reported from a cave. Bacterial isolates identified with antimicrobial properties demonstrated that the Iron Curtain Cave can be further considered as a potential habitat for antimicrobial agents. Full article
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