A sensitive genetic-based detection capability for Didymosphenia geminata

It is now well recognized that the increase in global transportation over the last two decades has brought with it an increased potential for the introduction of unwanted microorganisms (aquatic or terrestrial) that may have drastic effects on human and ecosystem health and agriculture. We have developed and validated a unique genetic fingerprinting tool for D. geminata. In concert, we developed field collection and preservation techniques specific for D. geminata along with genetic-based procedures that can now reliably detect D. geminate from a complex environmental community with a high degree of sensitivity. Recent work (Phase 2) has shown that the described methods will provide detection levels from <1 – 10,000 cells ml-1. We contend that the genetic based detection approaches used in this study offer great promise to meet the increasing demands to monitor the global threat from invasive micro-organisms

Field guide for didymo DNA sample collection

This protocol is designed for work in two-person teams for both safety and to maximise sample integrity

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments

Co- variation in soil biodiversity and biogeochemistry in northern and southern Victoria Land, Antarctica

Data from six sites in Victoria Land (72–77°S) investigating co-variation in soil communities (microbial and invertebrate) with biogeochemical properties showthe influence of soil properties on habitat suitability varied among local landscapes as well as across climate gradients. Species richness of metazoan invertebrates (Nematoda, Tardigrada and Rotifera) was similar to previous descriptions in this region, though identification of three cryptic nematode species of Eudorylaimus through DNA analysis contributed to the understanding of controls over habitat preferences for individual species. Denaturing Gradient Gel Electrophoresis profiles revealed unexpectedly high diversity of bacteria. Distribution of distinct bacterial communities was associated with specific sites in northern and southern Victoria Land, as was the distribution of nematode and tardigrade species. Variation in soil metazoan communities was related to differences in soil organic matter, while bacterial diversity and community structure were not strongly correlated with any single soil property. There were no apparent correlations between metazoan and bacterial diversity, suggesting that controls over distribution and habitat suitability are different for bacterial and metazoan communities. Our results imply that top-down controls over bacterial diversity mediated by their metazoan consumers are not significant determinants of bacterial community structure and biomass in these ecosystems

Perceived internal depth in rotating and translating objects

Previous research has indicated that observers use differences between velocities and ratios of velocities to judge the depth within a moving object, although depth cannot in general be determined from these quantities. In four experiments we examined the relative effects of velocity difference and velocity ratio on judged depth within a transparent object that was rotating about a vertical axis and translating horizontally, examined the effects of the velocity difference for pure rotations and pure translations, and examined the effect of the velocity difference for objects that varied in simulated internal depth. Both the velocity difference and the velocity ratio affected judged depth, with difference having the larger effect. The effect of velocity difference was greater for pure rotations than for pure translations. Simulated depth did not affect judged depth unless there was a corresponding change in the projected width of the object. Observers appear to use the velocity difference, the velocity ratio, and the projected width of the object heuristically to judge internal object depth, rather than using image information from which relative depth could potentially be recovered

Rapid microbial dynamics in response to an induced wetting event in Antarctic Dry Valley Soils

The cold deserts of the McMurdo Dry Valleys (MDV), Antarctica, host a high level of microbial diversity. Microbial composition and biomass in arid vs. ephemerally wetted regions are distinctly different, with wetted communities representing hot spots of microbial activity that are important zones for biogeochemical cycling. While climatic change is likely to cause wetting in areas not historically subject to wetting events, the responses of microorganisms inhabiting arid soils to water addition is unknown. The purpose of this study was to observe how an associated, yet non-wetted microbial community responds to an extended addition of water. Water from a stream was diverted to an adjacent area of arid soil with changes in microbial composition and activities monitored via molecular and biochemical methods over 7 weeks. The frequency of genetic signatures related to both prokaryotic and eukaryotic organisms adapted to MDV aquatic conditions increased during the limited 7 week period, indicating that the soil community was transitioning into a typical “high-productivity” MDV community. This work is consistent with current predictions that MDV microbial communities in arid regions are highly sensitive to climate change, and further supports the notion that changes in community structure and associated biogeochemical cycling may occur much more rapidly than predicted

Stand Establishment and Persistence of Perennial Cool-Season Grasses in the Intermountain West and the Central and Northern Great Plains

The choice of plant materials is an important component of revegetation following disturbance. To determine the utility and effectiveness of various perennial grass species for revegetation on varied landscapes, a meta analysis was used to evaluate the stand establishment and persistence of 18 perennial cool-season grass species in 34 field studies in the Intermountain and Great Plains regions of the United States under monoculture conditions. Combined across the 34 studies, stand establishment values ranged from 79% to 43% and stand persistence values ranged from 70% to 0%. Intermediate wheatgrass (Thinopyrum intermedium [Host] Barkworth & D. R. Dewey), tall wheatgrass (Thinopyrum ponticum [Podp.] Z.-W. Liu & R.-C. Wang), crested wheatgrass (Agropyron spp.), Siberian wheatgrass (Agropyron fragile [Roth] P. Candargy), and meadow brome (Bromus riparius Rehmann) possessed the highest stand establishment (≥69%). There were no significant differences among the 12 species with the largest stand persistence values. Basin wildrye (Leymus cinereus (Scribn. & Merr.) A. Love), Altai wildrye (Leymus angustus [Trin.] Pilg.), slender wheatgrass (Elymus trachycaulus [Link] Gould ex Shinners), squirreltail (Elymus spp.), and Indian ricegrass (Achnatherum hymenoides [Roem. & Schult.] Barkworth) possessed lower stand persistence (≤32%) than the majority of the other species, and Indian ricegrass (0%) possessed the lowest stand persistence of any of the species. Correlations between environmental conditions and stand establishment and persistence showed mean annual study precipitation to have the most consistent, although moderate effect (r=~0.40) for establishment and persistence. This relationship was shown by the relatively poor stand establishment and persistence of most species at sites receiving less than 310 mm of annual precipitation. These results will be a tool for land managers to make decisions concerning the importance of stand establishment, stand persistence, and annual precipitation for revegetation projects on disturbed sites

Bringing Antarctica to the lab: a polar desert environmental chamber to study the response of Antarctic microbial communities to climate change

Polar deserts contain unique and sensitive communities responsive to climate-associated habitat changes. However, unlike temperate desert ecosystems, characterizing and predicting the responses of polar ecosystems to environmental change remains a significant challenge due to logistical constraints. Here we aim to demonstrate the use of a custom-designed Polar Desert Environmental Chamber (PDEC) to perform off-continent experimental ecological research. We did so by characterizing the structure and composition of arid edaphic bacterial communities collected from the McMurdo Dry Valleys during a simulated wetting event. The results were discussed in light of previous field observations. Rapid structural and compositional changes were observed during wetting and re-drying treatments. Those were driven by changes in the relative abundance of coexisting taxa, which fluctuated asynchronously over time in response to the treatments. While selection was the main ecological factor influencing communities during dry conditions or the initial wetting, with prolonged exposure to wetness, neutral processes began to drive community assembly. Ultimately, these observations reflect different adaptative responses from microbial taxa to water stress, which can be argued as beneficial to increasing resilience in polar deserts. Our findings demonstrate that experiments conducted in PDEC provide valuable contextual data on community response to environmental change and can accelerate our ability to assess biological thresholds to change within polar desert ecosystems. We advocate that, with careful consideration of key emulated environmental attributes, laboratory-based Antarctic research can complement fieldwork to achieve a nuanced and evidence-based understanding of the ecology of Antarctica’s ice-free regions

Geochemically defined space-for-time transects successfully capture microbial dynamics along lacustrine chronosequences in a polar desert

The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity