3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

Improving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the 3D spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 days after recovery when overall bacterial loads returned to pre-antibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern was resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that bacterial taxa are distributed differently within crypts, with Lactobacilli laying closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

A Contribution to Knowledge of Gyroporus (Gyroporaceae, Boletales) in China: Three New Taxa and Amended Descriptions of Two Previous Species

Some species of Gyroporus (Gyroporaceae, Boletales) in China are investigated on the basis of morphology and molecular phylogenetic analyses. Six Chinese species are recognized in the present study. Among them, G. memnonius, G. porphyreus and G. subglobosus are new to science; G. longicystidiatus and G. paramjitii are previously described; and one ambiguous taxon tentatively named G. cf. castaneus. A key to known species of Gyroporus in China is also provided. A preliminary biogeographical analysis shows that Gyroporus in East Asia and Southeast/South Asia are closely related. Gyroporus longicystidiatus and G. paramjitii are geographically widespread species occurring in East Asia and Southeast/South Asia; G. cf. castaneus is a shared species between East Asia and Europe.

Developing SSR Individual Identification System and Tracking the Geographical Origin of Timber for the Endangered Species Chamaecyparis Formosensis

Chamaecyparis formosensis is an endemic species of Taiwan, threatened from intensive use and illegal felling. An individual identification system for C. formosensis is required to provide scientific evidence for court use and deter illegal felling. In this study, 36 polymorphic simple sequence repeat (SSR) markers were developed. By applying up to 28 non-linkage of the developed markers, it is calculated that the cumulative random probability of identity (CPI) is as low as 1.652×10-12, the combined power of discrimination (CPD) is as high as 0.999999999998348, and the identifiable population size is up to 60 million, which is greater than the known C. formosensis population size in Taiwan. Biogeographical analysis data show that C. formosensis from four geographic areas belong to the same genetic population which can be further divided into three clusters: SY (Eastern Taiwan), HV and GW (Northwestern Taiwan), and MM (Southwestern Taiwan). The developed system was applied to assess the provenance of samples with 88.44% of accuracy rate, and therefore can serve as a pre-screening tool to reduce the range required for comparison. The system developed in this study is a potential crime-fighting tool against illegal felling.

CONTRIBUTION TO A CARTOGRAPHIC AND PHYTOGEOGRAPHIC STUDY OF A LAVATERA MARITIMA MALVACEAEINTHETLEMCENCOAST

This study allowed us to define on the one hand the biogeographical criteria, and on the other hand to develop a cartographic sketch of the physiognomy of Lavatera maritima in our study area. This work is devoted to the biogeographical analysis of Lavatera maritima in the Tlemcen Coast (Rachgoune 1 and 2, Béni-saf1 and 2 Oulhassa and Madrid). The biogeographic distribution shows the dominance of the Mediterranean element. A vegetation map can be viewed in different ways, as a physiognomy map showing the present state of vegetation, or as a land use map. The development of a cartographic test of the distribution of Lavatera maritima in the coast of Tlemcen aims to know the current status and range of this plant species.

Moss-inhabiting diatom communities from Ile Amsterdam (TAAF, southern Indian Ocean)

Background and aims – Despite the ongoing taxonomical revision of the entire (sub)-Antarctic diatom flora, our knowledge on the ecology and community associations of moss-inhabiting diatoms is still rather limited. In the present study, our research aim was to survey the diversity together with the environmental factors structuring the epiphytic moss diatom communities on Ile Amsterdam (TAAF), a small volcanic island in the southern Indian Ocean.Material and methods – A morphology-based dataset and (physico)chemical measurements were used for the ecological and biogeographical analysis of moss-inhabiting diatom flora from Ile Amsterdam. In total, 148 moss samples were examined using light microscopy.Key results – The analysis revealed the presence of 125 diatom taxa belonging to 38 genera. The uniqueness of the Ile Amsterdam diatom flora is mainly reflected by the species composition of the dominant genera Pinnularia, Nitzschia, Humidophila, and Luticola, with a large number of unknown and often new species. This highly specific diatom flora, together with differences in the habitats sampled and the isolated position of the island, resulted in very low similarity values between Ile Amsterdam and the other islands of the Southern Ocean. From a biogeographical point of view, 40% of the taxa have a typical cosmopolitan distribution, whereas 22% of all observed species can be considered endemic to Ile Amsterdam, with another 17% species showing a restricted sub-Antarctic distribution. The NMDS analysis, based on a cluster dendrogram, divides the samples into six main groups. For each group, indicator species were determined. Both environmental data and diatom distributions indicate that apart from elevation, specific conductance, pH, and moisture are the major factors determining the structure of moss-inhabiting diatom communities on Ile Amsterdam.Conclusion – The isolated geographic position and unique climatological and geological features of the island shaped the presence of a unique diatom flora, characterised by many endemic species. The results of the study are of prime importance for further (palaeo-)ecological and biogeographical research.

A phylogenetic and taxonomic assessment of Afrotropical Micracidini (Coleoptera, Scolytinae) reveals a strong diversifying role for Madagascar

Afrotropical bark beetle genera in the tribe Micracidini are revised and an identification key provided. The new classification is based on phylogenetic analyses of five molecular markers (COI, EF-1α, 28S, PABP1, CAD) in combination with morphological characters. Five new genera are erected and one genus synonymized, resulting in a total of 11 valid genera: Lanurgus Eggers, 1920, Traglostus Schedl, 1938, Pseudomicracis Eggers, 1920 (=Saurotocis Wood, 1984 syn. nov.), Phloeocurus Wood, 1984, Afromicracis Schedl, 1959, Dendrochilus Schedl, 1959, Neomicracis Jordal gen. nov., Leiomicracis Jordal gen. nov., Diplotrichus Jordal gen. nov., Pseudolanurgus Jordal gen. nov., Microlanurgus Jordal gen. nov. The following new species are described to be included in the new genera: Leiomicracis aurea Jordal sp. nov., Neomicracis squamigera Jordal sp. nov., both from Tanzania, and Microlanurgus bicolor Jordal sp. nov. and Microlanurgus ater Jordal sp. nov., from Madagascar. The following new synonyms and new combinations are proposed: Afromicracis dubius (Schedl, 1950) (=Afromicracis angolensis Schedl, 1962 syn. nov.), Afromicacis elongatulus (Schedl, 1977) comb. nov.,Afromicracis jasminiae (Schedl 1957) comb. nov. (=Dendrochilus mikaniae Schedl 1957 syn. nov.), Afromicracis robustus (Schedl 1957) comb. nov. (=Dendrochilus arundinarius Schedl 1957 syn. nov., =Hypothenemus bambusae Browne, 1970 syn. nov., =Dendrochilus filum Schedl, 1977 syn. nov.) (all from Dendrochilus), Afromicracis setifer (Schedl 1957) comb. nov. (Mimiocurus), Lanurgus longipilis (Schedl, 1958) comb. nov., Lanurgus pubescens (Schedl, 1961) comb. nov. (both from Traglostus), Diplotrichus catenatus (Schedl, 1953) comb. nov.,Diplotrichus elongatus (Schedl, 1950) comb. nov.,Diplotrichus euphorbia (Schedl, 1961) comb. nov.,Diplotrichus gracilis (Schedl, 1958) comb. nov.,Diplotrichus minor (Schedl, 1950) comb. nov (=Lanurgus frontalis Schedl, 1953 syn. Nov.), Diplotrichus obesus (Schedl, 1953) comb. nov., Diplotrichus pygmaeus (Schedl, 1965) comb. nov., Diplotrichus rugosipes (Schedl, 1961) comb. nov., Diplotrichus subdepressus (Schedl, 1965) comb. nov., Diplotrichus widdringtoniae (Schedl, 1962) comb. nov. (all from Lanurgus), Diplotrichus ignotus (Schedl, 1965) comb. nov. (Pseudomicracis), Pseudolanurgus harunganae (Schedl, 1961) comb. nov. (=Lanurgus cribrellus Schedl, 1965 syn. nov.), Pseudolanurgus bugekeae (Schedl, 1957) comb. nov. (both from Pseudomicracis), Pseudolanurgus minutissimus (Schedl, 1961) comb. nov. (Lanurgus), Pseudomicracis dispar (Schedl, 1961) comb. nov., Pseudomicracis tomicoides (Schedl, 1961) comb. nov. (both from Saurotocis). The following taxa were transferred to genera in other tribes: Acanthotomicus intermedius (Schedl, 1977) comb. nov., Xylocleptes villiersi (Lepesme, 1942) comb. nov. (both from Dendrochilus); Eidophelus agnathus (Schedl, 1942) comb. nov., and Eidophelus ciliatipennis (Schedl, 1979) comb. nov. (all from Miocryphalus). The following five species were included in Karlseniusgen. nov. (Trypophloeini): Karlsenius klainedoxae (Schedl, 1957) comb. nov., Karlsenius nitidum (Schedl, 1965) comb. nov., Karlsenius nigrinum (Schedl, 1957) comb. nov., and Karlsenius attenuatus (Eggers, 1935) comb. nov. (from Miocryphalus), and Karlsenius ghanaensis (Schedl, 1977) comb. nov. (from Eidophelus). A time-tree and biogeographical analysis suggested that Madagascar was colonized only once in Micracidini, from East Africa soon after the origin of the tribe in late Cretaceous. Multiple re-colonisations from Madagascar to the mainland have contributed to further diversification of a tribe which is otherwise highly restricted in geographical distribution.

Mantodea oasis of Palaearctic region: biogeographical analysis of Mantodea in Egypt

Background Egypt forms a home for the highest number of recorded Mantodea species of the Palaearctic Region. The status and ecology of such diversity are far from being completely understood. Main body Through this study, the similarity of Mantodea species composition among Egyptian ecological zones has been examined by using the Sørensen-Dice coefficient, beside the calculation of species richness for each zone. Also, maximum entropy (Maxent) modeling was used to estimate the potential distribution of Mantodea species throughout the country. Three topographical and 19 bioclimatic variables have been used to estimate the current status of all Mantodea species in Egypt. The collected materials of adult mantis have been used to analyze the seasonality of 14 Egyptian common genera. Our results indicated that there was a high faunal similarity between the Western and Eastern deserts, the coastal strip, and the lower Nile valley. The lowest similarity was between Gebel Elba and all other zones. The analysis of habitat suitability of Mantodea in Egypt was fragmentary and focused on different distinct ecological zones. Altitude was the most effective ecological factor that affected Mantodea distribution as a group. Analysis of seasonality data of the common genera of Mantodea indicated that all are found in summer except for Miomantis, Severinia, and Sinaiella. Conclusion Our results can be used as a basis for future studies of the ecology of certain species and conservation of this interesting group in Egypt.