- Erratum: Exploring the microbial community (microflora) associated with ovine Haemonchus contortus (macroflora) field strains. [Journal Article]
- SRSci Rep 2017 09 29; 7(1):12403
- A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper.
A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper.
- Exploring the microbial community (microflora) associated with ovine Haemonchus contortus (macroflora) field strains. [Journal Article]
- SRSci Rep 2017 03 06; 7(1):70
- High-throughput sequencing technology has shown tremendous promise for microbial community composition and diversity. Illumina MiSeq platform was exploited to study the microbial community associated…
High-throughput sequencing technology has shown tremendous promise for microbial community composition and diversity. Illumina MiSeq platform was exploited to study the microbial community associated with the different stages of the life-cycle of ovine Haemonchus contortus field strains using two distinct amplification primer sets (targeting V3-V4, and V5-V7). Scanning electron microscope and polymerase chain reaction coupled with Illumina MiSeq platform were employed to confirm the absence of any parasite surface contamination by intact bacteria or their DNA products. Results showed 48 (V3-V4 tags) and 28 (V5-V7 tags) bacterial genera comprised the microbial flora of H. contortus microbiome. The dominant bacterial genera belonged to Escherichia-Shigella, Pseudomonas and Ochrobactrum, which were shared in all the stages of the parasite life-cycle using V3-V4 and V5-V7 amplicons. Moreover, the parasite microbiome could reflect the external micro-organisms (i.e. micro- and macro-habitats). There is abundant room for further progress in comparing microbiome of different helminths, which has, and will continue to offer considerable potential for better understanding a wide-variety of devastating animal and human diseases.
- European derived Saccharomyces cerevisiae colonisation of New Zealand vineyards aided by humans. [Journal Article]
- FYFEMS Yeast Res 2016; 16(7)
- Humans have acted as vectors for species and expanded their ranges since at least the dawn of agriculture. While relatively well characterised for macrofauna and macroflora, the extent and dynamics o…
Humans have acted as vectors for species and expanded their ranges since at least the dawn of agriculture. While relatively well characterised for macrofauna and macroflora, the extent and dynamics of human-aided microbial dispersal is poorly described. We studied the role which humans have played in manipulating the distribution of Saccharomyces cerevisiae, one of the world's most important microbes, using whole genome sequencing. We include 52 strains representative of the diversity in New Zealand to the global set of genomes for this species. Phylogenomic approaches show an exclusively European origin of the New Zealand population, with a minimum of 10 founder events mostly taking place over the last 1000 years. Our results show that humans have expanded the range of S. cerevisiae and transported it to New Zealand where it was not previously present, where it has now become established in vineyards, but radiation to native forests appears limited.
- Community Structure of Macrobiota and Environmental Parameters in Shallow Water Hydrothermal Vents off Kueishan Island, Taiwan. [Journal Article]
- PlosPLoS One 2016; 11(2):e0148675
- Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters t…
Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution. We determined that positively buoyant vent fluid exhibits a more pronounced negative impact to species on the surface water than on the bottom layer. Species richness increased with horizontal distance from the vent, and continuing for a distance of 2000 m, indicating that the vent fluid may exert a negative impact over several kilometers. The community structure off Kueishan Island displayed numerous transitions along the horizontal gradient, which were broadly congruent with changes in environmental conditions. Combination of variation in Ca2+, Cl-, temperature, pH and depth were revealed to show the strongest correlation with the change in benthic community structure, suggesting multiple factors of vent fluid were influencing the associated fauna. Only the vent crabs of Kueishan Island may have an obligated relationship with vents and inhabit the vent mouths because other fauna found nearby are opportunistic taxa that are more tolerant to acidic and toxic environments.
- Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi. [Journal Article]
- MEMol Ecol 2016; 25(2):630-47
- Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora…
Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the 'generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.
- Evidence for coal forest refugia in the seasonally dry Pennsylvanian tropical lowlands of the Illinois Basin, USA. [Journal Article]
- PPeerJ 2014; 2:e630
- The Moscovian plant macroflora at Cottage Grove southeastern Illinois, USA, is a key example of Pennsylvanian (323-299 Million years ago) dryland vegetation. There is currently no palynological data …
The Moscovian plant macroflora at Cottage Grove southeastern Illinois, USA, is a key example of Pennsylvanian (323-299 Million years ago) dryland vegetation. There is currently no palynological data from the same stratigraphic horizons as the plant macrofossils, leaves and other vegetative and reproductive structures, at this locality. Consequently, reconstructions of the standing vegetation at Cottage Grove from these sediments lack the complementary information and a more regional perspective that can be provided by sporomorphs (prepollen, pollen, megaspores and spores). In order to provide this, we have analysed the composition of fossil sporomorph assemblages in two rock samples taken from macrofossil-bearing inter-coal shale at Cottage Grove. Our palynological data differ considerably in composition and in the dominance-diversity profile from the macrofossil vegetation at this locality. Walchian conifers and pteridosperms are common elements in the macroflora, but are absent in the sporomorph assemblages. Reversely, the sporomorph assemblages at Cottage Grove comprise 17 spore taxa (∼16% and ∼63% of the total assemblages) that are known from the lycopsid orders Isoetales, Lepidodendrales and Selaginallales, while Cottage Grove's macrofloral record fails to capture evidence of a considerable population of coal forest lycopsids. We interpret our results as evidence that the Pennsylvanian dryland glacial landscape at Cottage Grove included fragmented populations of wetland plants living in refugia.
- First Clarkforkian equivalent Land Mammal Age in the latest Paleocene basal Sparnacian facies of Europe: fauna, flora, paleoenvironment and (bio)stratigraphy. [Journal Article]
- PlosPLoS One 2014; 9(1):e86229
- The Paleocene-Eocene Thermal Maximum (PETM) is correlated with the first occurrences of earliest modern mammals in the Northern Hemisphere. The latest Paleocene Clarkforkian North American Land Mamma…
The Paleocene-Eocene Thermal Maximum (PETM) is correlated with the first occurrences of earliest modern mammals in the Northern Hemisphere. The latest Paleocene Clarkforkian North American Land Mammal Age, that has yielded rodents and carnivorans, is the only exception to this rule. However, until now no pre-PETM localities have yielded modern mammals in Europe or Asia. We report the first Clarkforkian equivalent Land Mammal Age in the latest Paleocene deposits of the basal Sparnacian facies at Rivecourt, in the north-central part of the Paris Basin. The new terrestrial vertebrate and macroflora assemblages are analyzed through a multidisciplinary study including sedimentologic, stratigraphic, isotopic, and palynological aspects in order to reconstruct the paleoenvironment and to evaluate biochronologic and paleogeographic implications. The mammals are moderately diverse and not abundant, contrary to turtles and champsosaurs. The macroflora is exceptional in preservation and diversity with numerous angiosperms represented by flowers, fruits, seeds and wood preserved as lignite material, revealing an abundance of Arecaceae, Betulaceae, Icacinaceae, Menispermaceae, Vitaceae and probably Cornaceae. Results indicate a Late Paleocene age based on carbon isotope data, palynology and vertebrate occurrences such as the choristoderan Champsosaurus, the arctocyonid Arctocyon, and the plesiadapid Plesiadapis tricuspidens. However, several mammal species compare better with the earliest Eocene. Among these, the particular louisinid Teilhardimys musculus, also recorded from the latest Paleocene of the Spanish Pyrenees, suggests a younger age than the typical MP6 reference level. Nevertheless, the most important aspect of the Rivecourt fauna is the presence of dental remains of a rodent and a "miacid" carnivoran, attesting to the presence of two modern mammalian orders in the latest Paleocene of Europe. Interestingly, these two groups are also the only modern groups recorded from the latest Paleocene of North America, making Rivecourt the first direct equivalent to the Clarkforkian Land Mammal Age outside of North America.
- Going back to the roots: the microbial ecology of the rhizosphere. [Review]
- NRNat Rev Microbiol 2013; 11(11):789-99
- The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic…
The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.
- Soil ecology of Coccidioides immitis at Amerindian middens in California. [Journal Article]
- AMAppl Microbiol 1974; 27(2):379-88
- Outbreaks of coccidioidomycosis and isolation of Coccidioides immitis have been reported from Amerindian middens. This study was undertaken to determine the most important ecological component(s) for…
Outbreaks of coccidioidomycosis and isolation of Coccidioides immitis have been reported from Amerindian middens. This study was undertaken to determine the most important ecological component(s) for the occurrence of C. immitis at archeological sites. Soils from 10 former Indian villages with no prior history of coccidioidal infection were collected and cultured. The physicochemical properties of the midden soils were compared with nonmidden soils and positive soils. The following theories for the sporadic distribution of the pathogen in the soil of the Lower Sonoran Life Zone were considered: (i) the Larrea tridentata (creosote bush) association, (ii) the preference for saline soils, (iii) isolation near rodent burrows, and (iv) animals as possible agents of dispersal. Results showed that a high percentage of the midden soils contained C. immitis, whereas none of the adjacent, nonmidden soils yielded the fungus. Physicochemical analyses revealed that the dark color and alkaline pH of the midden soils were due to past organic contamination. Repeated isolations were made from soils with low to moderate alkalinity. Alkalinity and sandy texture were consistent features of all soils in this study. However, the lack of any reports of nonsandy infested soils possibly indicates that the sandy texture and alkalinity may be factors in the distribution of this fungus. The organic content, soil parent material, and color were not important in the soil ecology. L. tridentata was not significant in the macroflora at the infested sites surveyed. Samples collected without reference to rodent burrows yielded a high percentage of recoveries. Animals, although not the major natural reservoir, cannot be ignored as possible factors in the ecology of C. immitis.