Uffe N. Nielsen

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

Soil biodiversity and human health

Soil biodiversity is increasingly recognized as providing benefits to human health because it can suppress disease-causing soil organisms and provide clean air, water and food. Poor land-management practices and environmental change are, however, affecting belowground communities globally, and the resulting declines in soil biodiversity reduce and impair these benefits. Importantly, current research indicates that soil biodiversity can be maintained and partially restored if managed sustainably. Promoting the ecological complexity and robustness of soil biodiversity through improved management practices represents an underutilized resource with the ability to improve human health.

Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi‐arid ecosystems

Altered precipitation patterns resulting from climate change will have particularly significant consequences in water-limited ecosystems, such as arid to semi-arid ecosystems, where discontinuous inputs of water control biological processes. Given that these ecosystems cover more than a third of Earths terrestrial surface, it is important to understand how they respond to such alterations. Altered water availability may impact both aboveground and belowground communities and the interactions between these, with potential impacts on ecosystem functioning; however, most studies to date have focused exclusively on vegetation responses to altered precipitation regimes. To synthesize our understanding of potential climate change impacts on dryland ecosystems, we present here a review of current literature that reports the effects of precipitation events and altered precipitation regimes on belowground biota and biogeochemical cycling. Increased precipitation generally increases microbial biomass and fungal:bacterial ratio. Few studies report responses to reduced precipitation but the effects likely counter those of increased precipitation. Altered precipitation regimes have also been found to alter microbial community composition but broader generalizations are difficult to make. Changes in event size and frequency influences invertebrate activity and density with cascading impacts on the soil food web, which will likely impact carbon and nutrient pools. The long-term implications for biogeochemical cycling are inconclusive but several studies suggest that increased aridity may cause decoupling of carbon and nutrient cycling. We propose a new conceptual framework that incorporates hierarchical biotic responses to individual precipitation events more explicitly, including moderation of microbial activity and biomass by invertebrate grazing, and use this framework to make some predictions on impacts of altered precipitation regimes in terms of event size and frequency as well as mean annual precipitation. While our understanding of dryland ecosystems is improving, there is still a great need for longer term in situ manipulations of precipitation regime to test our model.

The future of soil invertebrate communities in polar regions: different climate change responses in the Arctic and Antarctic?

The polar regions are experiencing rapid climate change with implications for terrestrial ecosystems. Here, despite limited knowledge, we make some early predictions on soil invertebrate community responses to predicted twenty-first century climate change. Geographic and environmental differences suggest that climate change responses will differ between the Arctic and Antarctic. We predict significant, but different, belowground community changes in both regions. This change will be driven mainly by vegetation type changes in the Arctic, while communities in Antarctica will respond to climate amelioration directly and indirectly through changes in microbial community composition and activity, and the development of, and/or changes in, plant communities. Climate amelioration is likely to allow a greater influx of non-native species into both the Arctic and Antarctic promoting landscape scale biodiversity change. Non-native competitive species could, however, have negative effects on local biodiversity particularly in the Arctic where the communities are already species rich. Species ranges will shift in both areas as the climate changes potentially posing a problem for endemic species in the Arctic where options for northward migration are limited. Greater soil biotic activity may move the Arctic towards a trajectory of being a substantial carbon source, while Antarctica could become a carbon sink.

The Enigma of Soil Animal Species Diversity Revisited: The Role of Small-Scale Heterogeneity

Background “The enigma of soil animal species diversity” was the title of a popular article by J. M. Anderson published in 1975. In that paper, Anderson provided insights on the great richness of species found in soils, but emphasized that the mechanisms contributing to the high species richness belowground were largely unknown. Yet, exploration of the mechanisms driving species richness has focused, almost exclusively, on above-ground plant and animal communities, and nearly 35 years later we have several new hypotheses but are not much closer to revealing why soils are so rich in species. One persistent but untested hypothesis is that species richness is promoted by small-scale environmental heterogeneity. Methodology/Principal Findings To test this hypothesis we manipulated small-scale heterogeneity in soil properties in a one-year field experiment and investigated the impacts on the richness of soil fauna and evenness of the microbial communities. We found that heterogeneity substantially increased the species richness of oribatid mites, collembolans and nematodes, whereas heterogeneity had no direct influence on the evenness of either the fungal, bacterial or archaeal communities or on species richness of the large and mobile mesostigmatid mites. These results suggest that the heterogeneity-species richness relationship is scale dependent. Conclusions Our results provide direct evidence for the hypothesis that small-scale heterogeneity in soils increase species richness of intermediate-sized soil fauna. The concordance of mechanisms between above and belowground communities suggests that the relationship between environmental heterogeneity and species richness may be a general property of ecological communities.

The ecology of pulse events: insights from an extreme climatic event in a polar desert ecosystem

Climate change is occurring globally, with wide ranging impacts on organisms and ecosystems alike. While most studies focus on increases in mean temperatures and changes in precipitation, there is growing evidence that an increase in extreme events may be particularly important to altering ecosystem structure and function. During extreme events organisms encounter environmental conditions well beyond the range normally experienced. Such conditions may cause rapid changes in community composition and ecosystem states. We present the impact of an extreme pulse event (a flood) on soil communities in an Antarctic polar desert. Taylor Valley, McMurdo Dry Valleys, is dominated by large expanses of dry, saline soils. During the austral summer, melting of glaciers, snow patches and subsurface ice supplies water to ephemeral streams and wetlands. We show how the activation of a non-annual ephemeral stream, Wormherder Creek, and the associated wetland during an exceptional high-flow event alters soil properties and...

Antarctic nematode communities: observed and predicted responses to climate change

The rapidly changing climate in Antarctica is impacting the ecosystems. Since records began, climate changes have varied considerably throughout Antarctica with both positive and negative trends in temperatures and precipitation observed locally. However, over the course of this century a more directional increase in both temperature and precipitation is expected to occur throughout Antarctica. The soil communities of Antarctica are considered simple with most organisms existing at the edge of their physiological capabilities. Therefore, Antarctic soil communities are expected to be particularly sensitive to climate changes. However, a review of the current literature reveals that studies investigating the impact of climate change on soil communities, and in particular nematode communities, in Antarctica are very limited. Of the few studies focusing on Antarctic nematode communities, long-term monitoring has shown that nematode communities respond to changes in local climate trends as well as extreme (or pulse) events. These results are supported by in situ experiments, which show that nematode communities respond to both temperature and soil moisture manipulations. We conclude that the predicted climate changes are likely to exert a strong influence on nematode communities throughout Antarctica and will generally lead to increasing abundance, species richness, and food web complexity, although the opposite may occur locally. The degree to which local communities respond will depend on current conditions, i.e., average temperatures, soil moisture availability, vegetation or more importantly the lack thereof, and the local species pool in combination with the potential for new species to colonize.

Polar lessons learned: Long-term management based on shared threats in Arctic and Antarctic environments

The Arctic and Antarctic polar regions are subject to multiple environmental threats, arising from both local and ex-situ human activities. We review the major threats to polar ecosystems including the principal stressor, climate change, which interacts with and exacerbates other threats such as pollution, fisheries overexploitation, and the establishment and spread of invasive species. Given the lack of progress in reducing global atmospheric greenhouse-gas emissions, we suggest that managing the threats that interact synergistically with climate change, and that are potentially more tractable, is all the more important in the short to medium term for polar conservation. We show how evidence-based lessons learned from scientific research can be shared between the poles on topics such as contaminant mitigation, biosecurity protocols to reduce species invasions, and the regulation of fisheries and marine environments. Applying these trans-polar lessons in tandem with expansion of international cooperation could substantially improve environmental management in both the Arctic and Antarctic.

Belowground Ecology of Scarabs Feeding on Grass Roots: Current Knowledge and Future Directions for Management in Australasia

Many scarab beetles spend the majority of their lives belowground as larvae, feeding on grass roots. Many of these larvae are significant pests, causing damage to crops and grasslands. Damage by larvae of the greyback cane beetle (Dermolepida albohirtum), for example, can cause financial losses of up to AU

DRI-Grass: A New Experimental Platform for Addressing Grassland Ecosystem Responses to Future Precipitation Scenarios in South-East Australia

40 million annually to the Australian sugarcane industry. We review the ecology of some scarab larvae in Australasia, focusing on three subfamilies; Dynastinae, Rutelinae, and Melolonthinae, containing key pest species. Although considerable research on the control of some scarab pests has been carried out in Australasia, for some species, the basic biology and ecology remains largely unexplored. We synthesize what is known about these scarab larvae and outline key knowledge gaps to highlight future research directions with a view to improve pest management. We do this by presenting an overview of the scarab larval host plants and feeding behavior; the impacts of abiotic (temperature, moisture, and fertilization) and biotic (pathogens, natural enemies, and microbial symbionts) factors on scarab larvae and conclude with how abiotic and biotic factors can be applied in agriculture for improved pest management, suggesting future research directions. Several host plant microbial symbionts, such as arbuscular mycorrhizal fungi and endophytes, can improve plant tolerance to scarabs and reduce larval performance, which have shown promise for use in pest management. In addition to this, several microbial scarab pathogens have been isolated for commercial use in pest management with particularly promising results. The entomopathogenic fungus Metarhizium anisopliae caused a 50% reduction in cane beetle larvae while natural enemies such as entomopathogenic nematodes have also shown potential as a biocontrol. Key abiotic factors, such as soil water, play an important role in affecting both scarab larvae and these control agents and should therefore feature in future multi-factorial experiments. Continued research should focus on filling knowledge gaps including host plant preferences, attractive trap crops, and naturally occurring pathogens that are locally adapted, to achieve high efficacy in the field.