Endophytic fungi as a promising biocontrol agent to protect wheat from Fusarium graminearum head blight

The search for beneficial endophytes that can be part of a constructed microbial community has increased in recent years. We characterized three endophytic fungi previously isolated from wheat for their in vitro and in planta antagonism toward the Fusarium head blight pathogen, Fusarium graminearum. The endophytes were phylogenetically characterized and shown to be Alternaria destruens, Fusarium commune, and Fusarium oxysporum. Individual fungal endophytes significantly increased seed weight and lowered the accumulation of the mycotoxin deoxynivalenol compared to F. graminearum infected wheat heads without endophyte pretreatment. Investigation into the mechanism of competition in vitro showed that endophytes competitively excluded F. graminearum by pre-emptive colonization and possible inhibition over a distance. Investigations on the use of these endophytes in the field are in progress. Identification of these three endophytes highlights a common quandary in searching for beneficial microbes to use in agriculture: species definitions often do not separate individual isolates’ lifestyles. A greater understanding of the risks in using intraspecies variants for biocontrol is needed and should be examined in the context of the ecology of the individuals being investigated.

Revised species definitions and nomenclature of the blue and purple/rose Cithaerias butterflies (Lepidoptera, Nymphalidae, Satyrinae)

This study reassesses the taxonomic status of Neotropical blue and purple/rose-colored Cithaerias butterflies, thus complementing a previous study of the rose-colored species. Based on comparative study of wing coloration and genitalia morphology, I revise species definitions and the taxonomic status of: Cithaerias andromeda, C. azurina STAT. REV., C. esmeralda STAT. REV., C. bandusia STAT. REV., C. pyropina, and C. songoana STAT. REV. Photographs of adults and illustrations of male and female genitalia are provided for all species. Of particular importance are the genitalia illustrations of male and female C. azurina, presented here for the first time, as well as finding a putative first female of Ecuadorean subspecies C. pyropina julia.

Is Domestication Speciation? The Implications of a Messy Domestication Model in the Holocene

Domestication is one of the fundamental process that has shaped our world in the last 12,000 years. Changes in the morphology, genetics, and behavior of plants and animals have redefined our interactions with our environments and ourselves. However, while great strides have been made towards understanding the mechanics, timing, and localities of domestication, a fundamental question remains at the heart of archaeological and scientific modelling of this process—how does domestication fit into a framework of evolution and natural selection? At the core of this is the ontological problem of what is a species? In this paper, the complicated concepts and constructs underlying ‘species’ and how this can be applied to the process of domestication are explored. The case studies of soybean and proto-indica rice are used to illustrate that our choice of ‘species’ definitions carries with it ramifications for our interpretations, and that care needs to be made when handling this challenging classificatory system.

Photosynthetic Phenomics of Field- and Greenhouse-Grown Amaranths vs. Sensory and Species Delimits

Consumers hesitate to purchase field-grown shoot-tops of amaranths in Sri Lanka, citing the low-cleanliness making growers focus on greenhouse farming. However, the photosynthetic and growth variations in relation to the organoleptic preference of the greenhouse-grown amaranths in comparison to field-grown counterparts have not been studied. Also, the species delimits of the amaranths in Sri Lanka have not been identified, limiting our ability to interpret species-specific production characteristics. Thus, we assessed the common types of amaranths under greenhouse and field conditions. The photosynthesis was measured using a MultispeQ device of the PhotosynQ phenomic platform, which records chlorophyll fluorescence-based parameters. The shoot-tops were harvested and prepared as dishes according to the typical recipe for amaranths in Sri Lanka. The dishes were subjected to an organoleptic assessment for the parameters color, aroma, bitterness, texture, and overall taste. The differences in plant and the shoot-top biomass were also assessed. The markers atpB-rbcL, matk-trnT, and ITS were used to define the species delimits. The field-grown and greenhouse-grown amaranths exhibited species/cultivar-specific photosynthetic variations. The texture and overall taste of the dishes were different among greenhouse and field-grown material. The tasters preferred the texture and the overall taste of the greenhouse-grown shoot-tops. The greenhouse-grown plants also yielded higher shoot-top harvests compared to field-grown counterparts. Out of the tested markers, ITS defines the delimits of amaranth species. The higher organoleptic preference, the appreciable yield levels, unique photosynthetic patterns of the greenhouse-grown amaranths, and species definitions provide the much-needed platform for clean shoot-top production guaranteeing the highest end-user trust.

NEW ARCHAEOBOTANICAL STUDY OF POTTERY FROM THE SUB-NEOLITHIC SITE OF BAZKIV OSTRIV ON THE SOUTHERN BUH RIVER (using Replica-SEM method)

The study of impressions of plants in ancient pottery is one of the traditional methods of archaeobotanical research. Twenty years ago, Halina Pashkevych identified traces of a few cultivated species on the potsherds of the Buh-Dnister culture (BDC) from the Southern Buh River basin based on naked-eye observations (Pashkevich 2000; Kotova 2002). In particular, impressions of grains of Triticum monococcum and Triticum dicoccum were found on the surface of some vessels from the Bazkiv Ostriv site, excavated by Valentyn Danylenko in 1959 (fig. 1). The use of silicone rubber resin to obtain replicas — positive copies of impressions (fig. 2), as well as the use of a scanning electron microscope significantly improved the reliability of specific identifications of traces of plants in recent decades (Ushino, Tagawa 1991; Hisa, Katada 2005). This allows drawing conclusions based on not only grain size and shape but also its anatomically detailed fresh surface, which gets a more reliable result than even the study of charred remains from flotation. Re-identification of impressions on Neolithic vessels from Ukraine using the improved methodology was the goal of a joint Japan-Ukrainian archaeobotanical project, implemented in 2016—2019 (Endo et al. 2017; 2019). Among others, the materials of the Bazkiv Ostriv site were studied. All ceramic finds from the site (701 fragments from 90 vessels including 668 potsherds from 81 BDC vessels and nine fragments from two vessels of the Linear Pottery Culture) were examined. In total, 24 traces identified now or were identified earlier as possible impressions of seeds of plants have been found. The research of them using Replica-SEM method (fig. 3) allowed making only two reliable species definitions. These are impressions of elderberry cf. Sambucus seeds (Bzk-003, Bzk-004) on the surface of vessel 22 of the Skybyntsy type (fig. 4). Another trace was interpreted as a possible impression of the chaff of probable cereal plant doesn’t indefinite for species (Bzk-006). It was recorded on the surface of vessel 1 of the Samchyntsi type (fig. 5). The majority of the rest samples could not be identified even for plants. As a result, none of the observed potsherds from the site, including already published ones as having cereal impressions, contains traces of cultivated plants at present. This conclusion applies to other archaeobotanicaly examined pottery from the BDC monuments too. The absence of farming activity is indirectly evidenced by the complete lack of flint blades sections with characteristic gloss (so-called «sickle inserts») in the flint assemblages of the culture (Haskevych 2003). The absence of changes in the location of the sites in comparison with the previous Mesolithic ones in the region may indicate the preservation of a traditional hunter-fisher-gatherer way of life. So, the influence of neighbour farmer groups there can be traced only in sporadic exchange of prestigious goods, as well as in attempts to imitate the decoration and forms of pottery of the Kriş, Vinča, Szakбlhбt cultures. That is why it would be more correct to call the BDC not Neolithic but Para-Neolithic, or Sub-Neolithic.

Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes

ABSTRACT The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopesticide B. thuringiensis. Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruences, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current species definitions lead to overlapping genomospecies clusters, in which 66.2% of genomes belong to multiple genomospecies at a conventional 95 average nucleotide identity (ANI) genomospecies threshold. A genomospecies threshold of ≈92.5 ANI is shown to reflect a natural gap in genome similarity for the B. cereus group, and medoid genomes identified at this threshold are shown to yield resolvable genomospecies clusters with minimal overlap (six of 2,231 genomes assigned to multiple genomospecies; 0.269%). We thus propose a nomenclatural framework for the B. cereus group which accounts for (i) genomospecies using resolvable genomospecies clusters obtained at ≈92.5 ANI, (ii) established lineages of medical importance using a formal collection of subspecies names, and (iii) heterogeneity of clinically and industrially important phenotypes using a formalized and extended collection of biovar terms. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance; early detection of emerging, high-risk genotypes; and outbreak preparedness. IMPORTANCE Historical species definitions for many prokaryotes, including pathogens, have relied on phenotypic characteristics that are inconsistent with genome evolution. This scenario forces microbiologists and clinicians to face a tradeoff between taxonomic rigor and clinical interpretability. Using the Bacillus cereus group as a model, a conceptual framework for the taxonomic delineation of prokaryotes which reconciles genomic definitions of species with clinically and industrially relevant phenotypes is presented. The nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy that moves beyond arbitrarily set genomospecies thresholds while maintaining congruence with phenotypes and historically important species names.

Appropriate delineation of species for conservation purposes

The first step in conservation management is to delineate groups for separate versus combined management. However, there are many problems with species delineation, including diverse species definitions, lack of standardized protocols, and poor repeatability of delineations. Definitions that are too broad will lead to outbreeding depression if populations are crossed, while those that split excessively may preclude genetic rescue of small inbred populations with low genetic diversity. To minimize these problems, we recommend the use of species concepts based upon reproductive isolation (such as the Biological Species Concept) and advise against the use of Phylogenetic and General Lineage Species Concepts. We provide guidelines as to when taxonomy requires revision and outline protocols for robust species delineations.

Proposal of a taxonomic nomenclature for the Bacillus cereus group which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes

ABSTRACTThe Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus, and biopescticide B. thuringiensis. Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruencies, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes (n = 2,231), we show that current genomospecies definitions lead to overlapping species clusters, and that an average nucleotide identity (ANI) genomospecies threshold of ≈92.5 reflects a natural gap in core genome similarity. We propose a taxonomy for the B. cereus group which accounts for (i) genomospecies using separable species clusters formed at a threshold of ≈92.5 ANI, and (ii) phenotypes relevant to public health and industry. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance, early detection of emerging, high-risk genotypes, and outbreak preparedness. Furthermore, the nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy which moves beyond arbitrarily set genomospecies thresholds, while maintaining congruence with phenotypes and historically important species names.