Pilot Valley Basin Microbial Ecology
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB11779 | ENA |
REPOSITORIES: ENA
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Project description:The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.
| S-EPMC3670347 | biostudies-literature
Project description:Diet is a major driver of hominin evolution, but most of the geochemical evidence relies on carbon isotopes (?13C). Here, we report enamel stable calcium isotope (?44/42Ca) values against ?13C values for several hominins and co-existing primates in the Turkana Basin area, circa 4 to 2?Ma. Australopithecus anamensis clusters with mammal browsers, Kenyanthropus platyops is distinct from A. anamensis in foraging into more open environments and the coexisting Theropithecus brumpti encompasses both the grazer and omnivore/carnivore domains. Early Homo is remarkable for its wide distribution in ?44/42Ca values, possibly reflecting omnivorous and opportunistic preferences. Paranthropus boisei is uniquely distributed in the ?13C versus ?44/42Ca iso-space being distinct from all other hominins from the Turkana Basin area as well as from the co-existing Theropithecus oswaldi. Several hypotheses are explored to discuss the unique ?44/42Ca values of Paranthropus boisei including significant differences observed with ?44/42Ca values recently reported for P. robustus from South Africa, questioning the monophyly of this genus.
| S-EPMC7367883 | biostudies-literature
Project description:Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu(2+), was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem.
| S-EPMC3329106 | biostudies-literature
Project description:Herbivores are predicted to evolve appropriate mechanisms to process the plant secondary compounds (PSCs) in their diet and these mechanisms are likely specific to particular suites of PSCs. Changes in diet composition over evolutionary time should select for appropriate alterations in metabolism of the more recent dietary components. We investigated differences in gene expression profiles in the liver with respect to prior ecological and evolutionary experience with PSCs in the desert woodrat, Neotoma lepida. This woodrat species has populations in the Mojave Desert that have switched from feeding on juniper to feeding on creosote at the end of the Holocene as well as populations in the Great Basin Desert that still feed on the ancestral diet of juniper and are naïve to creosote. Juniper and creosote have notable differences in secondary chemistry. Woodrats from the Mojave and Great Basin Deserts were subjected to a fully crossed feeding trial on diets of juniper and creosote after which their livers were analyzed for gene expression. Hybridization of hepatic mRNAs to laboratory rat microarrays resulted in a total of 20,031 genes that met quality control standards. We analyzed differences in large-scale patterns of liver gene expression with respect to GO term enrichment. Diet had a larger effect on gene expression than population membership. However, woodrats with no prior evolutionary experience to the diet upregulated relatively far more genes compared to animals with prior exposure to that diet. This pattern may be the result of naive animal’s attempting to mitigate physiological damage caused by novel PSCs. fully crossed design, two by two feeding trial with two populations of the desert woodrat (Great Basin and Mojave) fed the two diets of juniper and creosote bush
2013-10-18 | E-GEOD-44411 | biostudies-arrayexpress
Project description:We are studying the tree P. euphratica growing in its natural habitat in the Negev desert in Israel. We have used leaf RNA samples from trees growing from four different areas in the desert valley Ein Avdat with contrasting growth conditions, with the primary factor being how much water the trees have access to. Area A trees grow close to a stream. Area B trees are further away from the stream. Area C trees are growing on a slope with no water. Parking place trees grow at a parking place (1km from Area A, B and C) where there is a water irrigation system, and these trees are regularly watered once a week. The control sample in each hybridization is always RNA isolated from a pool of 5 trees from the parking place. The hybridizations are comparing the following: Area A -- parking place Area B -- parking place Area C -- parking place Each hybridization is done with a dye swap and three different biological repeats for a total of 18 hybridizations.
2004-11-30 | E-MEXP-182 | biostudies-arrayexpress
Project description:In deep ocean hypersaline basins, the combination of high salinity, unusual ionic composition and anoxic conditions represents significant challenges for microbial life. We used geochemical porewater characterization and DNA sequencing based taxonomic surveys to enable environmental and microbial characterization of anoxic hypersaline sediments and brines in the Orca Basin, the largest brine basin in the Gulf of Mexico. Full-length bacterial 16S rRNA gene clone libraries from hypersaline sediments and the overlying brine were dominated by the uncultured halophilic KB1 lineage, Deltaproteobacteria related to cultured sulfate-reducing halophilic genera, and specific lineages of heterotrophic Bacteroidetes. Archaeal clones were dominated by members of the halophilic methanogen genus Methanohalophilus, and the ammonia-oxidizing Marine Group I (MG-I) within the Thaumarchaeota. Illumina sequencing revealed higher phylum- and subphylum-level complexity, especially in lower-salinity sediments from the Orca Basin slope. Illumina and clone library surveys consistently detected MG-I Thaumarchaeota and halotolerant Deltaproteobacteria in the hypersaline anoxic sediments, but relative abundances of the KB1 lineage differed between the two sequencing methods. The stable isotopic composition of dissolved inorganic carbon and methane in porewater, and sulfate concentrations decreasing downcore indicated methanogenesis and sulfate reduction in the anoxic sediments. While anaerobic microbial processes likely occur at low rates near their maximal salinity thresholds in Orca Basin, long-term accumulation of reaction products leads to high methane concentrations and reducing conditions within the Orca Basin brine and sediments.
| S-EPMC7173876 | biostudies-literature
Project description:Populations of many shorebird species appear to be declining in North America, and food resources at stopover habitats may limit migratory bird populations. We investigated body condition of, and foraging habitat and diet selection by 4 species of shorebirds in the central Illinois River valley during fall migrations 2007 and 2008 (Killdeer [Charadrius vociferus], Least Sandpiper [Calidris minutilla], Pectoral Sandpiper [Calidris melanotos], and Lesser Yellowlegs [Tringa flavipes]). All species except Killdeer were in good to excellent condition, based on size-corrected body mass and fat scores. Shorebird diets were dominated by invertebrate taxa from Orders Diptera and Coleoptera. Additionally, Isopoda, Hemiptera, Hirudinea, Nematoda, and Cyprinodontiformes contribution to diets varied by shorebird species and year. We evaluated diet and foraging habitat selection by comparing aggregate percent dry mass of food items in shorebird diets and core samples from foraging substrates. Invertebrate abundances at shorebird collection sites and random sites were generally similar, indicating that birds did not select foraging patches within wetlands based on invertebrate abundance. Conversely, we found considerable evidence for selection of some diet items within particular foraging sites, and consistent avoidance of Oligochaeta. We suspect the diet selectivity we observed was a function of overall invertebrate biomass (51.2 ± 4.4 [SE] kg/ha; dry mass) at our study sites, which was greater than estimates reported in most other food selection studies. Diet selectivity in shorebirds may follow tenants of optimal foraging theory; that is, at low food abundances shorebirds forage opportunistically, with the likelihood of selectivity increasing as food availability increases. Nonetheless, relationships between the abundance, availability, and consumption of Oligochaetes for and by waterbirds should be the focus of future research, because estimates of foraging carrying capacity would need to be revised downward if Oligochaetes are truly avoided or unavailable for consumption.
| S-EPMC3445572 | biostudies-literature
Project description:Urban landscapes can present ecological challenges for wildlife species, yet many species survive, and even thrive, near dense human populations. Coyotes (Canis latrans), for example, have expanded their geographic range across North America and, as a result of their adaptability and behavioral flexibility, are now a common occupant of many urban areas in the United States. We investigated the spatial ecology of 27 coyotes fitted with Global Positioning System (GPS) telemetry collars radio-collared in the Cuyahoga Valley, Ohio. Our objectives were to quantify coyote space use, evaluate resource selection, and investigate coyote movement and activity patterns. To measure space use, we estimated home range (95%) and core area (50%) size of coyotes using the adaptive local convex hull (a-LoCoH) method. We found the mean (± SE) home range size of resident coyotes (4.7 ± 1.8 km2) was significantly smaller than ranges of transient coyotes (67.7 ± 89.6 km2). Similarly, mean (± SE) core area size of resident coyotes (0.9 ± 0.6 km2) was significantly smaller than core areas of transient coyotes (11.9 ± 16.7 km2). Home range and core area size of both resident and transient coyotes did not vary by sex, age, or season. For all coyotes, use of natural land cover was significantly greater than use of altered and developed land. When coyotes were using altered and developed land, GPS fixes were most common at night. Coyote movement patterns differed with respect to status, time period, and season; peaking during nighttime hours. A better understanding of coyote space use and movement within anthropogenic landscapes aids management of people, parks, and wildlife by providing the data necessary for research-based management decisions.
| S-EPMC6936805 | biostudies-literature
Project description:Evidence for biotic perchlorate reduction in naturally perchlorate-rich sediments of Pilot Valley Basin, Utah
| PRJEB11780 | ENA
Project description:16S rRNA sequences from desert rodent gut microbiota Raw sequence reads
| PRJNA849280 | ENA