EcoFABs: advancing microbiome science through standardized fabricated ecosystems.

Microbiomes play critical roles in ecosystems and human health, yet in most cases scientists lack standardized and reproducible model microbial communities. The development of fabricated microbial ecosystems, which we term EcoFABs, will provide such model systems for microbiome studies.

Managing Agroecosystems for Soil Microbial Carbon Use Efficiency: Ecological Unknowns, Potential Outcomes, and a Path Forward.

Agricultural systems are increasingly managed for improving soil carbon (C) accumulation. However, there are limits to C returns in agricultural systems that constrain soil C accumulation capacity. Increasing the efficiency of how soil microbes process C is gaining interest as an important management strategy for increasing soil C and is a key feature of soil C dynamics in many new microbial-explicit models.

River channel connectivity shifts metabolite composition and dissolved organic matter chemistry.

Biogeochemical processing of dissolved organic matter (DOM) in headwater rivers regulates aquatic food web dynamics, water quality, and carbon storage. Although headwater rivers are critical sources of energy to downstream ecosystems, underlying mechanisms structuring DOM composition and reactivity are not well quantified. By pairing mass spectrometry and fluorescence spectroscopy, here we show that hydrology and river geomorphology interactively shape molecular patterns in DOM composition.

Within-species trade-offs in plant-stimulated soil enzyme activity and growth, flowering, and seed size.

Soil microbial communities affect species demographic rates of plants. In turn, plants influence the composition and function of the soil microbiome, potentially resulting in beneficial feedbacks that alter their fitness and establishment. For example, differences in the ability to stimulate soil enzyme activity among plant lineages may affect plant growth and reproduction.

Understanding how microbiomes influence the systems they inhabit.

Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field.

Catalytic power of enzymes decreases with temperature: New insights for understanding soil C cycling and microbial ecology under warming.

Most current models of soil C dynamics predict that climate warming will accelerate soil C mineralization, resulting in a long-term CO release and positive feedback to global warming. However, ecosystem warming experiments show that CO loss from warmed soils declines to control levels within a few years. Here, we explore the temperature dependence of enzymatic conversion of polymerized soil organic C (SOC) into assimilable compounds, which is presumed the rate-limiting step of SOC mineralization.

Temperature Sensitivity as a Microbial Trait Using Parameters from Macromolecular Rate Theory.

The activity of soil microbial extracellular enzymes is strongly controlled by temperature, yet the degree to which temperature sensitivity varies by microbe and enzyme type is unclear. Such information would allow soil microbial enzymes to be incorporated in a traits-based framework to improve prediction of ecosystem response to global change. If temperature sensitivity varies for specific soil enzymes, then determining the underlying causes of variation in temperature sensitivity of these enzymes will provide fundamental insights for predicting nutrient dynamics belowground.

Opposing effects of different soil organic matter fractions on crop yields.

Soil organic matter is critical to sustainable agriculture because it provides nutrients to crops as it decomposes and increases nutrient- and water-holding capacity when built up. Fast- and slow-cycling fractions of soil organic matter can have different impacts on crop production because fast-cycling fractions rapidly release nutrients for short-term plant growth and slow-cycling fractions bind nutrients that mineralize slowly and build up water-holding capacity. We explored the controls on these fractions in a tropical agroecosystem and their relationship to crop yields.

Phosphorus mobilizing consortium Mammoth P(™) enhances plant growth.

Phosphorus (P) is a critical nutrient used to maximize plant growth and yield. Current agriculture management practices commonly experience low plant P use efficiency due to natural chemical sorption and transformations when P fertilizer is applied to soils. A perplexing challenge facing agriculture production is finding sustainable solutions to deliver P more efficiently to plants.

Linking microbial community structure and microbial processes: an empirical and conceptual overview.

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection.

Genomics in a changing arctic: critical questions await the molecular ecologist.

Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox.

Increased plant productivity and decreased microbial respiratory C loss by plant growth-promoting rhizobacteria under elevated CO₂.

Increased plant productivity and decreased microbial respiratory C loss can potentially mitigate increasing atmospheric CO₂, but we currently lack effective means to achieve these goals. Soil microbes may play critical roles in mediating plant productivity and soil C/N dynamics under future climate scenarios of elevated CO₂ (eCO₂) through optimizing functioning of the root-soil interface. By using a labeling technique with (13)C and (15)N, we examined the effects of plant growth-promoting Pseudomonas fluorescens on C and N cycling in the rhizosphere of a common grass species under eCO₂.

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed.

For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates.

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils.

The pool of soil organic carbon (SOC) in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity.

Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought?

Both biogeographical and rainfall manipulation studies show that soil water content can be a strong driver of microbial community composition. However, we do not yet know if these patterns emerge because certain bacterial taxa are better able to survive at dry soil moisture regimes or if they are due to other drought-sensitive ecosystem properties indirectly affecting microbial community composition. In this study, we evaluated (1) whether bacterial community composition changed under an 11-year drought manipulation and (2) whether shifts under drought could be explained by variation in the moisture sensitivity of growth among bacterial taxa (moisture niche partitioning).

Predicted responses of arctic and alpine ecosystems to altered seasonality under climate change.

Global climate change is already having significant impacts on arctic and alpine ecosystems, and ongoing increases in temperature and altered precipitation patterns will affect the strong seasonal patterns that characterize these temperature-limited systems. The length of the potential growing season in these tundra environments is increasing due to warmer temperatures and earlier spring snow melt. Here, we compare current and projected climate and ecological data from 20 Northern Hemisphere sites to identify how seasonal changes in the physical environment due to climate change will alter the seasonality of arctic and alpine ecosystems.

High-throughput fluorometric measurement of potential soil extracellular enzyme activities.

Microbes in soils and other environments produce extracellular enzymes to depolymerize and hydrolyze organic macromolecules so that they can be assimilated for energy and nutrients. Measuring soil microbial enzyme activity is crucial in understanding soil ecosystem functional dynamics. The general concept of the fluorescence enzyme assay is that synthetic C-, N-, or P-rich substrates bound with a fluorescent dye are added to soil samples.

Climate change alters ecological strategies of soil bacteria.

The timing and magnitude of rainfall events are expected to change in future decades, resulting in longer drought periods and larger rainfall events. Although microbial community composition and function are both sensitive to changes in rainfall, it is unclear whether this is because taxa adopt strategies that maximise fitness under new regimes. We assessed whether bacteria exhibited phylogenetically conserved ecological strategies in response to drying-rewetting, and whether these strategies were altered by historical exposure to experimentally intensified rainfall patterns.

Carbon-degrading enzyme activities stimulated by increased nutrient availability in Arctic tundra soils.

Climate-induced warming of the Arctic tundra is expected to increase nutrient availability to soil microbes, which in turn may accelerate soil organic matter (SOM) decomposition. We increased nutrient availability via fertilization to investigate the microbial response via soil enzyme activities. Specifically, we measured potential activities of seven enzymes at four temperatures in three soil profiles (organic, organic/mineral interface, and mineral) from untreated native soils and from soils which had been fertilized with nitrogen (N) and phosphorus (P) since 1989 (23 years) and 2006 (six years).

Decoupling of soil nutrient cycles as a function of aridity in global drylands.

The biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems. It has been suggested that the C, N and P cycles could become uncoupled under rapid climate change because of the different degrees of control exerted on the supply of these elements by biological and geochemical processes. Climatic controls on biogeochemical cycles are particularly relevant in arid, semi-arid and dry sub-humid ecosystems (drylands) because their biological activity is mainly driven by water availability.

Rhizosphere stoichiometry: are C : N : P ratios of plants, soils, and enzymes conserved at the plant species-level?

As a consequence of the tight linkages among soils, plants and microbes inhabiting the rhizosphere, we hypothesized that soil nutrient and microbial stoichiometry would differ among plant species and be correlated within plant rhizospheres. We assessed plant tissue carbon (C) : nitrogen (N) : phosphorus (P) ratios for eight species representing four different plant functional groups in a semiarid grassland during near-peak biomass. Using intact plant species-specific rhizospheres, we examined soil C : N : P, microbial biomass C : N, and soil enzyme C : N : P nutrient acquisition activities.