Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere.

The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12-24 h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700-1000 µm from the tip. Bacteria accumulated predominantly in confined pore spaces within 200 µm from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.

Canopy coverage, light, and moisture affect thermoregulatory trade-offs in an amphibian breeding habitat.

When amphibians thermoregulate, they face a fundamental trade-off between the ability to maintain activity and an increased rate of dehydration at higher temperatures. Canopy coverage affects both the thermal and hydric conditions of the environment and can therefore influence amphibian thermoregulation. Frogs require proper conditions to thermoregulate to successfully grow, survive, and reproduce. But while we know how canopy and environmental variables typically affect operative temperature, less is known about effects on amphibian water loss rates. In this study, we measure the effect of canopy coverage on the conditions available for thermoregulation at a breeding pond of the California red-legged frog, Rana draytonii. We use agar frog models to estimate the thermal and hydric capacities frogs would experience in locations with different canopy coverage and microhabitats. At each site, we deployed models under four microhabitat treatments: wet/sun, wet/shade, dry/sun, and dry/shade. We modeled how environmental variables affected operative temperature and evaporative water loss from agar frogs. We found positive effects of air temperature, the sun treatment, and reduced canopy cover on operative temperature, and negative direct or indirect effects of these variables on evaporative water loss, consistent with the hypothesized trade-off between thermoregulatory behavior to increase temperature and the increased desiccation risk due to higher water loss. Additionally, our results indicate that the availability of wet microhabitats can allow frogs to reduce water loss, potentially mitigating the risk of desiccation when thermoregulating to achieve higher operative temperatures. Our findings suggest, that with access to proper microhabitats, amphibians can mitigate the fundamental trade-off and receive benefits of thermoregulating at high temperatures.

Distribution of Phlebotomus argentipes Annandale & Brunetti, 1908 in the Anuradhapura district, North Central Sri Lanka.

Background & objectives: Phlebotomus argentipes Annandale & Brunetti, 1908 (Diptera: Psychodidae) is the main vector responsible for the transmission of Leishmania donovani (Laveran & Mesnil, 1903) Ross, 1903 in the subcontinent of India. It is the potential vector of cutaneous leishmaniasis in Sri Lanka. The present study determined ecological factors that influence the abundance of P. argentipes in areas with high disease prevalence in the Anuradhapura district, North Central Sri Lanka. Methods: CDC light traps and yellow sticky traps were used for sampling, and abundance was recorded throughout 12 months with selected environmental parameters namely, relative humidity, wind speed, and temperature. The relationships between the abundance of P. argentipes with mean temperature, % relative humidity, and wind speed were tested with regression analysis. The temporal distribution of the vector population was tested with a time series analysis. Results: The study identified the most preferable microhabitats of P. argentipes: shrubs, unclear areas, gardening areas, wet soil areas with leaf litter, and termite hills. The results indicated that the abundance of P. argentipes was highly dependent on mean temperature (P = 0.00, R2 = 68%), and a high number of P. argentipes was recorded for a low mean temperature range of 24.7-27.3°C. Furthermore, the abundance of P. argentipes exhibited an increasing trend with high humidity levels of 72-88% (P = 0.00, R2 = 91.6%). Interpretation & conclusion: These findings may help predict the temporal variation of the potential vector population with studied ecological parameters and contribute to a successful vector management strategy with thorough knowledge of the behavioral pattern of P. argentipes.

Biogeography of the theileriosis vector, Rhipicephalus appendiculatus under current and future climate scenarios of Zimbabwe.

Climate directly influences the epidemiology of vector-borne diseases at various spatial and temporal scales. Following the recent increased incidences of theileriosis in Zimbabwe, a disease mainly transmitted by Rhipicephalus appendiculatus, we determined lethal temperatures for the species and current and possible future distribution using the machine learning algorithm 'Maxent'. Rhipicephalus appendiculatus larvae had an upper lethal temperature (ULT50) of about 44 ± 0.5 °C and this was marginally higher for nymphs and adults at 46 ± 0.5 °C. Environmental temperatures recorded in selected zonal tick microhabitats were below the determined lethal limits, indicating the ability of the tick to survive these regions. The resultant model under current climatic conditions showed areas with high suitability indices to the eastern, northeastern and southeastern parts of the country, mainly in Masvingo, Manicaland and Mashonaland Central provinces. Future predictions as determined by 2050 climatic conditions indicate a reduction in suitable habitats with the tick receding to presently cooler high elevation areas such as the eastern Highlands of Zimbabwe and a few isolated pockets in the interior of the country. Lowveld areas show low suitability under current climatic conditions and are expected to remain unsuitable in future. Overall, the study shows that R. appendiculatus distribution is constrained by climatic factors and helps identify areas of where occurrence of the species and the disease it transmits is highly likely. This will assist in optimizing disease surveillance and vector management strategies targeted at the species.

Songbird nests on the ground as islands of diversity of ptyctimous mites (Acari: Oribatida) in the primeval Bialowieza Forest (Poland).

Due to specific microclimatic conditions and accumulation of organic matter, bird nests are microhabitats that are often inhabited by various invertebrates, including mites (Acari). We tested whether nests of the ground-nesting passerine Phylloscopus sibilatrix (Bechstein) (Passeriformes: Phylloscopidae) [wood warbler] were associated with an increased local diversity of ptyctimous mites (Acari: Oribatida) on the forest floor in the Bialowieza National Park, East Poland. In 2019-2020, we analysed 150 warbler nests shortly after they had been vacated by the birds, and additionally we sampled mites in leaf litter at 1 and 6 m distances from 21 of the collected nests. We found on average more mite species in nests sampled in 2020 than in nests sampled in 2019. Although the species composition largely overlapped between bird nests and the litter, bird nests contained a greater average number of mite species than litter samples, including species found only - Microtritia minima (Berlese) and Phthiracarus crenophilus Willmann - or mostly - Euphthiracarus cribrarius (Berlese) and Phthiracarus globosus (C.L. Koch) - in bird nests. The results suggest that the presence of bird nests may increase the local diversity of the invertebrate species assemblage.

Cross-habitat distribution pattern of Bacillus communities and their capacities of producing industrial hydrolytic enzymes in Paracel Islands: Habitat-dependent differential contributions of the environment.

Bacillus as a predominant genus of enzyme-producing bacteria presents desirable features to fulfill the vast demand of specific industries, whereas the knowledge of the Bacillus communities and their capacities of producing industrial hydrolytic enzymes across the microhabitats of the Paracel Islands is limited. Herein, a total of 193 culturable Bacillus strains belonging to 19 species were isolated across the microhabitats of seawater, sediment, coral and seagrass, covering 39 stations of the Paracel Islands. Each microhabitat displayed its unique species, while the species of Bacillus paramycoides besides being the dominant species with an abundance of 54.94% also was the only species shared by all microhabitats of the Paracel Islands. Of the Bacillus communities, 97.41% of the isolates exhibited the capacity of producing one-or-more types of enzymes with comparatively higher and broader ranges of enzyme activities, including 163 protease-, 27 cellulase-, 118 alginate lyase-, 140 K-carrageenase- and 158 agarose-producing strains. By the correlation analyses of "Bacillus-environmental factors" and "Enzyme-producing Bacillus-environmental factors", the cross-habitat distribution and enzyme-producing capacity pattern of the Bacillus communities were strongly driven by habitat type, and the environmental factors made habitat-dependent differential contributions to that in the Paracel Islands. It's worth noting that the cellulase-producing strain wasn't detected in seagrass due to its survival strategy to prevent cellulose degradation by inhibiting cellulase-producing bacteria, while coral contained more stable microbial metabolic functions to protect against environmental fluctuations. These findings besides providing large quantities of promising enzyme-producing candidates for specific industrial desires, also facilitate the development and utilization of marine microbial resources and the environmental policy- and/or law-making according to environmental features across the microhabitats of the Paracel Islands.

Lack of specialist nidicoles as a characteristic of mite assemblages inhabiting nests of the ground-nesting wood warbler, Phylloscopus sibilatrix (Aves: Passeriformes).

Bird and mammal nests provide microhabitats that support a range of other species, including invertebrates. However, the variation between communities of nest-dwelling invertebrates in different nests is poorly understood. The major aim of this study was to analyze the assemblage structure of mites from the suborder Uropodina (Acari: Mesostigmata) and from superfamily Crotonioidea (Acari: Oribatida) inhabiting nests of the wood warbler, Phylloscopus sibilatrix (Aves: Passeriformes), located on a forest floor in Bialowieza Forest, in eastern Poland. We also assessed the correlation between the nest material used by the birds with the assemblage structure of Uropodina mites, and compared the results with published studies of the nests of other birds and a mammal (common mole, Talpa europaea), and also with communities of mites inhabiting the soil. The field research was conducted in the strict nature reserve of the Bialowieza National Park, a near-primeval European temperate forest. In 2019, immediately after the breeding period, 69 wood warbler nests and 439 soil samples were collected. Analyses revealed assemblages of Uropodina mites inhabiting the nests that consisted of 14 species, mostly common soil species. Only five species of oribatid mites from superfamily Crotonioidea were present in the nest material. Analyzed nests had a high percentage of tree leaves and grass blades, whereas moss was the least frequent component of the nest material. The Uropodina mites were more abundant in the nests that had greater amounts of grass blades, but similar relationships were insignificant for the nests with varying amounts of tree leaves or moss. The assemblages of Uropodina mites inhabiting wood warbler nests were very similar to those found in soil and nests of the common mole, but they lacked typical nest-dwelling species of Uropodina (i.e., specialized nidicoles).

The Enemy Within: How Does a Bacterium Inhibit the Foraging Aptitude and Risk Management Behavior of Allenby's Gerbils?

AbstractMicrobes inhabiting multicellular organisms have complex, often subtle effects on their hosts. Gerbillus andersoni allenbyi are commonly infected with Mycoplasma haemomuris-like bacteria, which may cause mild nutrient (choline, arginine) deficiencies. However, are there more serious ecological consequences of infection, such as effects on foraging aptitudes and risk management? We tested two alternatives: the nutrient compensation hypothesis (does nutrient deficiency induce infected gerbils to make up for the shortfall by foraging more and taking greater risks?) and (2) the lethargy hypothesis (do sick gerbils forage less, and are they compromised in their ability to detect predators or risky microhabitats?). We compared the foraging and risk management behavior of infected and noninfected gerbils. We experimentally infected gerbils with the bacteria, which allowed us to compare between noninfected, acutely infected (peak infection loads), and chronically infected (low infection loads) individuals. Our findings supported the lethargy hypothesis over the nutrient compensation hypothesis. Infected individuals incurred dramatically elevated foraging costs, including less efficient foraging, diminished "quality" of time spent vigilant, and increased owl predation. Interestingly, gerbils that were chronically infected (lower bacteria load) experienced larger ecological costs than acutely infected individuals (i.e., peak infection loads). This suggests that the debilitating effects of infection occur gradually, with a progressive decline in the quality of time gerbils allocated to foraging and managing risk. These increased long-term costs of infection demonstrate how small direct physiological costs of infection can lead to large indirect ecological costs. The indirect ecological costs of this parasite appear to be much greater than the direct physiological costs.

Uncovering fungal community composition in natural habitat of Ophiocordyceps sinensis using high-throughput sequencing and culture-dependent approaches.

BACKGROUND: The fungal communities inhabiting natural Ophiocordyceps sinensis play critical ecological roles in alpine meadow ecosystem, contribute to infect host insect, influence the occurrence of O. sinensis, and are repertoire of potential novel metabolites discovery. However, a comprehensive understanding of fungal communities of O. sinensis remain elusive. Therefore, the present study aimed to unravel fungal communities of natural O. sinensis using combination of high-throughput sequencing and culture-dependent approaches. RESULTS: A total of 280,519 high-quality sequences, belonging to 5 fungal phyla, 15 classes, 41 orders, 79 families, 112 genera, and 352 putative operational taxonomic units (OTUs) were obtained from natural O. sinensis using high-throughput sequencing. Among of which, 43 genera were identified in external mycelial cortices, Ophiocordyceps, Sebacinia and Archaeorhizomyces were predominant genera with the abundance of 95.86, 1.14, 0.85%, respectively. A total of 66 genera were identified from soil microhabitat, Inocybe, Archaeorhizomyces, unclassified Thelephoraceae, Tomentella, Thelephora, Sebacina, unclassified Ascomycota and unclassified fungi were predominant genera with an average abundance of 53.32, 8.69, 8.12, 8.12, 7.21, 4.6, 3.08 and 3.05%, respectively. The fungal communities in external mycelial cortices were significantly distinct from soil microhabitat. Meanwhile, seven types of culture media were used to isolate culturable fungi at 16 °C, resulted in 77 fungal strains identified by rDNA ITS sequence analysis, belonging to 33 genera, including Ophiocordyceps, Trichoderma, Cytospora, Truncatella, Dactylonectria, Isaria, Cephalosporium, Fusarium, Cosmospora and Paecilomyces, etc.. Among all culturable fungi, Mortierella and Trichoderma were predominant genera. CONCLUSIONS: The significantly differences and overlap in fungal community structure between two approaches highlight that the integration of high-throughput sequencing and culture-dependent approaches would generate more information. Our result reveal a comprehensive understanding of fungal community structure of natural O. sinensis, provide new insight into O. sinensis associated fungi, and support that microbiota of natural O. sinensis is an untapped source for novel bioactive metabolites discovery.

Thermal tolerance and the importance of microhabitats for Andean frogs in the context of land use and climate change.

Global warming is having impacts across the Tree of Life. Understanding species' physiological sensitivity to temperature change and how they relate to local temperature variation in their habitats is crucial to determining vulnerability to global warming. We ask how species' vulnerability varies across habitats and elevations, and how climatically buffered microhabitats can contribute to reduce their vulnerability. We measured thermal sensitivity (critical thermal maximum-CTmax ) of 14 species of Pristimantis frogs inhabiting young and old secondary, and primary forests in the Colombian Andes. Exposure to temperature stress was measured by recording temperature in the understorey and across five microhabitats. We determined frogs' current vulnerability across habitats, elevations and microhabitats accounting for phylogeny and then ask how vulnerability varies under four warming scenarios: +1.5, +2, +3 and +5°C. We found that CTmax was constant across species regardless of habitat and elevation. However, species in young secondary forests are expected to become more vulnerable because of increased exposure to higher temperatures. Microhabitat variation could enable species to persist within their thermal temperature range as long as regional temperatures do not surpass +2°C. The effectiveness of microhabitat buffering decreases with a 2-3°C increase, and is almost null under a 5°C temperature increase. Microhabitats will provide thermal protection to Andean frog communities from climate change by enabling tracking of suitable climates through short distance movement. Conservation strategies, such as managing landscapes by preserving primary forests and allowing regrowth and reconnection of secondary forest would offer thermally buffered microhabitats and aid in the survival of this group.

Para determinar la vulnerabilidad de las especies al calentamiento global es indispensable considerar la tolerancia fisiológica de las especies al cambio de temperatura y las condiciones ambientales a las que están expuestas. En este estudio exploramos la vulnerabilidad de especies a través de diferentes hábitats y altitudes y examinamos si ciertos microhábitats contribuyen a reducir la vulnerabilidad al calentamiento global. Medimos la tolerancia térmica (CTmax ) de catorce especies de ranas Pristimantis en bosques secundarios jóvenes y viejos, y bosques primarios en los Andes tropicales. Registramos la temperatura a la que estas especies están expuestas en el sotobosque así como dentro de cinco microhábitats. Usando CTmax y las temperaturas a las que están expuestas, determinamos la vulnerabilidad de las especies en diferentes hábitats, elevaciones y microhábitats. También preguntamos cómo cambiará esta vulnerabilidad si la temperatura incrementa: 1.5°C, 2°C, 3°C y 5°C. CTmax fue constante en todos los hábitats y elevaciones. Las especies de bosques secundarios jóvenes son más vulnerables pues están expuestas a temperaturas más altas. Al utilizar microhábitats, las especies estarán protegidas si el aumento de temperatura no supera los + 2°C. Todos los microhábitats seguirán proporcionando refugio térmico si la temperatura aumenta 1.5°C, pero esta protección térmica disminuirá si la temperatura aumenta 2-3°C y será casi nula con un aumento de temperatura de 5°C. Los microhábitats proporcionarán protección térmica a la comunidad de ranas de los Andes contra el cambio climático. Estrategias de conservación, como la regeneración natural y la reconexión de bosques secundarios y la preservación de bosques primarios, ayudaría a la supervivencia de las ranas al tener microhábitats que ofrecen refugio térmico.

Microbial diversity and functional response to the redox dynamics of pyrite-rich sediment and the impact of preload surcharge.

Microbial diversity and activities play pivotal biogeochemical roles in a redox-sensitive, pyrite-rich sediment's ecosystem. However, very little is known about the microbial community composition and distribution among the redox zones of pyrite-rich sediment and their response to changes caused by the burial of the sediment beneath compacted fill. In the present work, culture-independent, molecular phylogenetic investigations of the prokaryotic population and its diversity in a naturally occurring pyrite-rich sediment were undertaken to determine the microbial community composition, richness, diversity and distributions among the varying redox zones and their functional response to the imposition of surface surcharge, in the form of compacted fill. It was established that the pyrite-rich sediment is a redox-sensitive environment consisting of microhabitats with distinct and discontinuous physico-chemical characteristics, including DO, pH, Eh, temperature, electrical conductivity and salinity. It is a favourable environment for cyclic transformation of inorganic sulphur compounds and a unique environment for the habitation and growth of various microorganisms. Microbes adapted to the microhabitat and lived together in consortia, in response to their physiological and functional requirements. Microbes involved in the sulphur cycle had their populations concentrated in the oxic zone, while those involved in iron and carbon cycles were prevalent in the anoxic zones. As a result, highly diverse microbial populations occurred in isolated peaks within the sediment. The physico-chemical differences within the sediment changed in response to changes in the sediment redox dynamics. Imposition of the surcharge resulted in significant changes in the pH, temperature, Eh, DO, EC and salinity, reflecting marked re-distribution of the microbial population within the ecosystem. The cable bacteria phenomenon was evident in the sediment studied; however, there were doubt regarding their filamentous occurrence.

Rapid emergence and mechanisms of resistance by U87 glioblastoma cells to doxorubicin in an in vitro tumor microfluidic ecology.

In vitro prediction of the probable rapid emergence of resistance to a drug in tumors could act to winnow out potential candidates for further costly development. We have developed a microfluidic device consisting of ∼500 hexagonal microcompartments that provides a complex ecology with wide ranges of drug and nutrient gradients and local populations. This ecology of a fragmented metapopulation induced the drug resistance in stage IV U87 glioblastoma cells to doxorubicin in 7 d. Exome and transcriptome sequencing of the resistant cells identified mutations and differentially expressed genes. Gene ontology and pathway analyses of the genes identified showed that they were functionally relevant to the established mechanisms of doxorubicin action. Specifically, we identified (i) a frame-shift insertion in the filamin-A gene, which regulates the influx and efflux of topoisomerase II poisons; (ii) the overexpression of aldo-keto reductase enzymes, which convert doxorubicin into doxorubicinol; and (iii) activation of NF-κB via alterations in the nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway from mutations in three genes (CARD6, NSD1, and NLRP13) and the overexpression of inflammatory cytokines. Functional experiments support the in silico analyses and, together, demonstrate the effects of these genetic changes. Our findings suggest that, given the rapid evolution of resistance and the focused response, this technology could act as a rapid screening modality for genetic aberrations leading to resistance to chemotherapy as well as counter selection of drugs unlikely to be successful ultimately.

Sphagnum Species Modulate their Phenolic Profiles and Mycorrhizal Colonization of Surrounding Andromeda polifolia along Peatland Microhabitats.

Sphagnum mosses mediate long-term carbon accumulation in peatlands. Given their functional role as keystone species, it is important to consider their responses to ecological gradients and environmental changes through the production of phenolics. We compared the extent to which Sphagnum phenolic production was dependent on species, microhabitats and season, and how surrounding dwarf shrubs responded to Sphagnum phenolics. We evaluated the phenolic profiles of aqueous extracts of Sphagnum fallax and Sphagnum magellanicum over a 6-month period in two microhabitats (wet lawns versus dry hummocks) in a French peatland. Phenolic profiles of water-soluble extracts were measured by UHPLC-QTOF-MS. Andromeda polifolia mycorrhizal colonization was quantified by assessing the intensity of global root cortex colonization. Phenolic profiles of both Sphagnum mosses were species-, season- and microhabitat- dependant. Sphagnum-derived acids were the phenolics mostly recovered; relative quantities were 2.5-fold higher in S. fallax than in S. magellanicum. Microtopography and vascular plant cover strongly influenced phenolic profiles, especially for minor metabolites present in low abundance. Higher mycorrhizal colonization of A. polifolia was found in lawns as compared to hummocks. Mycorrhizal abundance, in contrast to environmental parameters, was correlated with production of minor phenolics in S. fallax. Our results highlight the close interaction between mycorrhizae such as those colonizing A. polifolia and the release of Sphagnum phenolic metabolites and suggest that Sphagnum-derived acids and minor phenolics play different roles in this interaction. This work provides new insight into the ecological role of Sphagnum phenolics by proposing a strong association with mycorrhizal colonization of shrubs.

Evaluating Movement Patterns and Microhabitat Selection of the Japanese Common Toad (Bufo japonicus formosus) Using Fluorescent Powder Tracking.

Bufo japonicus formosus (Eastern-Japanese common toad) is endemic to Eastern Japan. As with many Japanese amphibians, little is known about its terrestrial life, especially during the nonbreeding season. This species persists even in highly disturbed urban areas where many other amphibian species have already been extirpated. An understanding of how such species use habitats within remnant landscapes may help to inform management strategies for the conservation of urban ecosystems. We examined the nightly movement patterns, distance traveled, movement range, and microhabitat selection of non-breeding adult B. j. formosus at an urbanized site, using fluorescent powder tracking. We evaluated the usefulness of this tracking method through this survey. We found that the nightly distances traveled by these toads varied greatly among individuals and nights. No sexual differences in movement pattern, distance traveled, and movement range were detected. However, body size significantly affected distance traveled and movement range. We found that toads tended to use areas covered with grasses and mosses more frequently than expected, and to avoid paved areas. Fluorescent powder tracking was effective for the elucidation of movement patterns and habitat selection of amphibians. Our results provide useful information for the conservation of amphibians, especially for species inhabiting urbanized areas.

Drought-induced mortality patterns and rapid biomass recovery in a terra firme forest in the Colombian Amazon.

Extreme climatic events affecting the Amazon region are expected to become more frequent under ongoing climate change. In this study, we assessed the responses to the 2010 drought of over 14,000 trees ≥10 cm dbh in a 25 ha lowland forest plot in the Colombian Amazon and how these responses varied among topographically defined habitats, with tree size, and with species wood density. Tree mortality was significantly higher during the 2010-2013 period immediately after the drought than in 2007-2010. The post-drought increase in mortality was stronger for trees located in valleys (+243%) than for those located on slopes (+67%) and ridges (+57%). Tree-based generalized linear mixed models showed a significant negative effect of species wood density on mortality and no effect of tree size. Despite the elevated post-drought mortality, aboveground biomass increased from 2007 to 2013 by 1.62 Mg ha-1  yr-1 (95% CI 0.80-2.43 Mg ha-1  yr-1 ). Biomass change varied among habitats, with no significant increase on the slopes (1.05, 95% CI -0.76 to 2.85 Mg ha-1  yr-1 ), a significant increase in the valleys (1.33, 95% CI 0.37-2.34 Mg ha-1  yr-1 ), and a strong increase on the ridges (2.79, 95% CI 1.20-4.21 Mg ha-1  yr-1 ). These results indicate a high carbon resilience of this forest to the 2010 drought due to habitat-associated and interspecific heterogeneity in responses including directional changes in functional composition driven by enhanced performance of drought-tolerant species that inhabit the drier ridges.

Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum.

PREMISE OF THE STUDY: Populations with phenotypic polymorphism in discrete characters may be good models for investigating genome evolution and speciation. Sphagnum magellanicum Brid. is found throughout the northern hemisphere, and despite considerable variation in morphological characters, it is considered one of the least taxonomically controversial peatmoss species. We have observed two main morphs of the species associated with different microhabitats. Here we investigated the genomic and environmental basis of this intraspecific morphological variation. METHODS: We conducted transplant and common garden experiments to test whether the two morphs are genetically differentiated. We then used RAD-sequencing to quantify the genomic divergence between the morphs and approximate Bayesian computation (ABC) to infer the most likely demographic scenario explaining the genome-wide differentiation of the two morphs. KEY RESULTS: We found that genomic differentiation between the two morphs is unexpectedly high and that several of the differentiated morphological characters have a genetic basis. Using simulation approaches, we found support for a scenario of ancient divergence followed by recent secondary contact. CONCLUSIONS: We show that the two morphs represent the two main genetic clusters previously found worldwide. Our results demonstrate that relatively minor morphological differentiation in a presumed phenotypically plastic peatmoss may be associated with massive divergence across the genome.

Pyrosequencing analysis revealed complex endogenetic microorganism community from natural DongChong XiaCao and its microhabitat.

BACKGROUND: Ophiocordyceps sinensis (DongChong XiaCao (DCXC) in Chinese), a fungal parasite of caterpillars, is a traditional Chinese medicine. Bioactive components isolated from natural DCXC possess a wide range of pharmacological actions. Many efforts have been directed towards isolating the fungi based on culture-dependent methods for investigation of fungal diversity in order to determine the anamorph of natural DCXC and find new medicinal fungi resources, and the results have been varied. RESULTS: In the present study, a total of 44,588 bacterial and 51,584 fungal sequences corresponding to 11,694 and 9297 putative operational taxonomic units (OTU) were respectively identified by a Roche/454-based, high throughput sequence analysis of 16S rRNA genes and ITS regions. The main bacterial groups were Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria and Firmicutes, while the Ascomycota, Basidiomycota and Zygomycota were the main fungal phyla. Proteobacteria presented 68.4, 49.5, 38.9 and 35.6 % of all bacteria in the sclerotia, stromata, external mycelial cortices and soil, respectively. As the main fungi phyla, Ascomycota presented 21.0, 45.6 26.4 and 59.3 % in the sclerotia, stromata, external mycelial cortices and soil, respectively. Bacterial and fungal communities were more diverse in the environmental sample than in the natural DCXC sample. Microbial communities were obviously distinct in each sample. Several novel unclassifiable bacterial (10.41 %) and fungal (37.92 %) species were also detected. CONCLUSIONS: This study revealed an abundant endogenetic fungal and bacterial resources and a variety of genetic information in natural DCXC by high-throughput 454 sequencing technology. Microorganism that had been discovered in natural DCXC will provide sources for screening the new bioactive metabolites and its biotechnological application.

Analysis of rbcL sequences reveals the global biodiversity, community structure, and biogeographical pattern of thermoacidophilic red algae (Cyanidiales).

Thermoacidophilic cyanidia (Cyanidiales) are the primary photosynthetic eukaryotes in volcanic areas. These red algae also serve as important model organisms for studying life in extreme habitats. The global biodiversity and community structure of Cyanidiales remain unclear despite previous sampling efforts. Here, we surveyed the Cyanidiales biodiversity in the Tatun Volcano Group (TVG) area in Taiwan using environmental DNA sequencing. We generated 174 rbcL sequences from eight samples from four regions in the TVG area, and combined them with 239 publicly available rbcL sequences collected worldwide. Species delimita-tion using this large rbcL data set suggested at least 20 Cyanidiales OTUs (operational taxono-mic units) worldwide, almost three times the presently recognized seven species. Results from environmental DNA showed that OTUs in the TVG area were divided into three groups: (i) dominant in hot springs with 92%-99% sequence identity to Galdieria maxima; (ii) largely distributed in drier and more acidic microhabitats with 99% identity to G. partita; and (iii) primarily distributed in cooler microhabitats and lacking identity to known cyanidia species (a novel Cyanidiales lineage). In both global and individual area analyses, we observed greater species diversity in non-aquatic than aquatic habitats. Community structure analysis showed high similarity between the TVG community and West Pacific-Iceland communities, reflecting their geographic proximity to each other. Our study is the first examination of the global species diversity and biogeographic affinity of cyanidia. Additionally, our data illuminate the influence of microhabitat type on Cyanidiales diversity and highlight intriguing questions for future ecological research.

Prevalence of urease in Vibrio parahaemolyticus from the Mississippi Sound.

UNLABELLED: Vibrio parahaemolyticus is a pathogenic marine bacterium that causes food-borne gastroenteritis and, less commonly, wound infections. As is the case for many pathogens, all V. parahaemolyticus strains possess at least one erythrocyte-lysing haemolysin. In addition, many V. parahaemolyticus also possess the enzyme urease. We tested 206 environmental V. parahaemolyticus isolates from Mississippi coastal waters for urease and haemolytic activity using urea agar with added salt and Wagatsuma agar, respectively. The relative abundance of haemolysin-producing V. parahaemolyticus was consistently high throughout the sampling period. In contrast, the number of urease-positive organisms increased from 36% in 2006 to 80% in 2007 and 97% in 2009. We then tested the ability of four strains representing each of the three sample years along with seven other bacterial strains for their ability to grow in seawater urea and raise the pH of this seawater broth. Finally, one of the 4 strains was tested for its ability to form an alkaline microhabitat immediately above its biofilm. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study illustrate that V. parahaemolyticus has the ability to create alkaline microhabitats that could enhance virulence, including virulence from haemolysins. This finding could have both clinical and ecological impact as to how V. parahaemolyticus can modify its habitat.

Elucidating the structure, and composition of bacterial symbionts in the gut regions of wood-feeding termite, Coptotermes formosanus and their functional profile towards lignocellulolytic systems.

The wood-feeding termite, Coptotermes formosanus, presents an efficient lignocellulolytic system, offering a distinctive model for the exploration of host-microbial symbiosis towards lignocellulose degradation. Despite decades of investigation, understanding the diversity, community structure, and functional profiles of bacterial symbionts within specific gut regions, particularly the foregut and midgut of C. formosanus, remains largely elusive. In light of this knowledge gap, our efforts focused on elucidating the diversity, community composition and functions of symbiotic bacteria inhabiting the foregut, midgut, and hindgut of C. formosanus via metagenomics. The termite harbored a diverse community of bacterial symbionts encompassing 352 genera and 26 known phyla, exhibiting an uneven distribution across gut regions. Notably, the hindgut displayed a higher relative abundance of phyla such as Bacteroidetes (56.9%) and Spirochetes (23.3%). In contrast, the foregut and midgut were predominantly occupied by Proteobacteria (28.9%) and Firmicutes (21.2%) after Bacteroidetes. The foregut harbored unique phyla like Candidate phylum_TM6 and Armatimonadetes. At the family level, Porphyromonadaceae (28.1, 40.6, and 53.5% abundance in foregut, midgut, and hindgut, respectively) and Spirochaetaceae (foregut = 9%, midgut = 16%, hindgut = 21.6%) emerged as dominant families in the termite's gut regions. Enriched operational taxonomic units (OTUs) were most abundant in the foregut (28), followed by the hindgut (14), while the midgut exhibited enrichment of only two OTUs. Furthermore, the functional analyses revealed distinct influences of bacterial symbionts on various metabolic pathways, particularly carbohydrate and energy metabolisms of the host. Overall, these results underscore significant variations in the structure of the bacterial community among different gut regions of C. formosanus, suggesting unique functional roles of specific bacteria, thereby inspiring further investigations to resolve the crosstalk between host and microbiomes in individual gut-regions of the termite.