Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples

Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages.     

GM-CSF is not essential for optimal fertility or for weight control

Independent studies with GM-CSF−/− mice have concluded that GM-CSF is necessary for normal reproductive outcome and for the maintenance of normal weight. In contrast to the literature we report that GM-CSF−/− and wild type (C57Bl/6) mice over a continuous 12 month period had similar litter size and neonatal survival. Likewise, unlike a literature observation, for the two mouse strains both male and female mice had similar weight gain when fed on a normal chow diet and monitored until 30 weeks of age. It is concluded that GM-CSF is not necessary for an optimal fertility outcome or for normal weight maintenance during development.     

Global assessment of experimental climate warming on tundra vegetation: heterogeneity over space and time

Understanding the sensitivity of tundra vegetation to climate warming is critical to forecasting future biodiversity and vegetation feedbacks to climate. In situ warming experiments accelerate climate change on a small scale to forecast responses of local plant communities. Limitations of this approach include the apparent site-specificity of results and uncertainty about the power of short-term studies to anticipate longer term change. We address these issues with a synthesis of 61 experimental warming studies, of up to 20 years duration, in tundra sites worldwide. The response of plant groups to warming often differed with ambient summer temperature, soil moisture and experimental duration. Shrubs increased with warming only where ambient temperature was high, whereas graminoids increased primarily in the coldest study sites. Linear increases in effect size over time were frequently observed. There was little indication of saturating or accelerating effects, as would be predicted if negative or positive vegetation feedbacks were common. These results indicate that tundra vegetation exhibits strong regional variation in response to warming, and that in vulnerable regions, cumulative effects of long-term warming on tundra vegetation - and associated ecosystem consequences - have the potential to be much greater than we have observed to date.     

Selection of nontarget arthropod taxa for field research on transgenic insecticidal crops: using empirical data and statistical power

One of the possible adverse effects of transgenic insecticidal crops is the unintended decline in the abundance of nontarget arthropods. Field trials designed to evaluate potential nontarget effects can be more complex than expected because decisions to conduct field trials and the selection of taxa to include are not always guided by the results of laboratory tests. Also, recent studies emphasize the potential for indirect effects (adverse impacts to nontarget arthropods without feeding directly on plant tissues), which are difficult to predict because of interactions among nontarget arthropods, target pests, and transgenic crops. As a consequence, field studies may attempt to monitor expansive lists of arthropod taxa, making the design of such broad studies more difficult and reducing the likelihood of detecting any negative effects that might be present. To improve the taxonomic focus and statistical rigor of future studies, existing field data and corresponding power analysis may provide useful guidance. Analysis of control data from several nontarget field trials using repeated-measures designs suggests that while detection of small effects may require considerable increases in replication, there are taxa from different ecological roles that are sampled effectively using standard methods. The use of statistical power to guide selection of taxa for nontarget trials reflects scientists' inability to predict the complex interactions among arthropod taxa, particularly when laboratory trials fail to provide guidance on which groups are more likely to be affected. However, scientists still may exercise judgment, including taxa that are not included in or supported by power analyses.     

Long‐term dynamics of bird diversity in forest and suburb: decay,turnover or homogenization?

Aim Urbanization and deforestation are important drivers of biodiversity change. However, long‐term changes in faunal communities within urbanizing regions are poorly understood. We investigated how well observed community changes in both space and time agree with expectations based on current paradigms in urban ecology. Location Greater Brisbane region, Australia. Methods We compared bird assemblages in two time‐periods 15 years apart, at multiple sites in remnant forest and residential suburbs across an urbanizing landscape. Differences in assemblage composition, species abundances and functional groupings were assessed within and between habitats. Results Compared with forest, suburbs in both time‐periods had over twice the total bird abundance, a different species composition, greater between‐site community similarity, a greater proportion of non‐native species and greater dominance by large‐bodied species. These differences corresponded with changes in sites whose habitat was converted from forest to suburb. Between time‐periods, abundances of 58% of suburban species changed significantly compared with those of 11% in forest. Increaser species outnumbered decreasers in suburbs, with the reverse in forest. Abundance of small‐bodied birds decreased 70% in suburbs and 20% in forest. Broad‐spectrum competitors and nest predators were common among suburban increasers. Among invasive species, the number of increasers was counterbalanced by decreasers. Both site‐scale species richness and between‐site community similarity increased to a small extent in both habitats. Main conclusions Species composition and ecological function of suburban bird communities were very dynamic. Suburban assemblages were neither a subset of forest species nor an increasingly non‐native compilation. Communities in large forest patches were comparatively stable. The notion of habitat‐specific species turnover better characterizes the nature of most changes than either species decline or homogenization, even though both of these were evident. There is considerable scope for careful urban planning, focused on both among‐ and within‐habitat variety, to sustain bird diversity in urbanizing landscapes.     

Relative feeding and development of armyworm on switchgrass and corn, and its potential effects on switchgrass grown for biomass

To help assess the potential for damage by armyworms [Mythimna (Pseudaletia) unipuncta (Haworth) (Lepidoptera: Noctuidae)] to switchgrass (Panicum virgatum L.) and surrounding crops, survival and development were evaluated for larvae reared on leaves of switchgrass, corn (Zea mays L.), and miscanthus (Miscanthus x giganteus Greef and Deuter ex Hodkinson and Renvoize). Additional tests assessed the relationship between leaf position and the concentration of saponins (plant compounds which can provide protection from insect herbivores) and examined the effect of defoliation on switchgrass dry mass. Survival to adulthood was similar when larvae were reared on field-grown leaves of switchgrass and corn. However, lower larval mass (10 d) and delayed development of M. unipuncta (to pupation, adult emergence) suggest switchgrass is an inferior host relative to corn. When fed field-grown miscanthus, no larvae survived 10 d. Few differences were noted between switchgrass and corn grown under controlled (laboratory) conditions, but M. unipuncta survival seemed to decline rapidly when larvae were fed the fourth and fifth leaves of switchgrass. Switchgrass leaf samples collected from different leaf positions and stages of tiller maturity showed up to 10-fold differences in the concentration of the saponin protodioscin, with the greatest concentrations in the fourth and fifth leaves. However, other saponins showed an opposite pattern, indicating the role of protodioscin on insect development should be tested in isolation (e.g., by addition of the purified compound to an artificial diet). Defoliation trials indicated that extremely high M. unipuncta populations may be necessary to cause any significant reduction in switchgrass biomass. Collectively, results suggest M. unipuncta may not present a significant risk to biomass production in switchgrass, but that the spring emergence of switchgrass provides an alternate host for M. unipuncta before colonizing annual food and feed crops.     

Adult activity and oviposition of corn rootworms,Diabrotica spp. (Coleoptera: Chrysomelidae), in Miscanthus,corn and switchgrass

The ability of the biomass crop Miscanthus (Miscanthus × giganteus Greef and Deuter ex Hodkinson and Renvoize) to support larval development for both United States and European populations of the western corn rootworm, Diabrotica virgifera virgifera LeConte, suggests an avenue for interactions with corn (Zea mays L.). To provide context to survival of D. v. virgifera on Miscanthus, adult activity and oviposition of Diabrotica spp. were monitored in central Illinois in 2010–2011 in Miscanthus, corn and switchgrass (Panicum virgatum L.). For D. v. virgifera, vial traps within corn plots captured 3–10 times as many adults as in Miscanthus or switchgrass, while soil samples showed females laid approximately 10 times as many eggs in corn as in the perennial grasses. Adult southern corn rootworms, Diabrotica undecimpunctata howardi Barber, were the most abundant species in 2010 and clearly preferred switchgrass as an adult habitat, with vial traps in switchgrass capturing 5–10 times as many D. u. howardi as those in corn or Miscanthus. Based on the small production areas for Miscanthus and switchgrass (and low use of both by D. v. virgifera), it seems likely that there are no current impacts of these perennial grasses on pest status of Diabrotica spp. in corn or other crops. However, adaptations by Diabrotica spp. to pest management practices suggest they could be a source for interactions between biomass and food or feed crops. Early‐season soil samples did not recover eggs of D. u. howardi, but their use of switchgrass as an adult habitat suggests additional research in areas where switchgrass may be grown near peanuts, alfalfa or other hosts may be needed. Also, investigation of other candidate bioenergy crops known to support Diabrotica spp. larval development is needed to better understand the possible effects of a changing agricultural landscape on corn rootworms.