Estimating taxon-specific population dynamics in diverse microbial communities

Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon- specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortal- ity, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes

Predicting soil carbon loss with warming

Journal ArticleThis is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.ARISING FROM: T. W. Crowther et al. Nature 540, 104–108 (2016); doi:10.1038/nature2015

Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential

In the age of big data, soil data are more available and richer than ever, but – outside of a few large soil survey resources – they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight. Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators. Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication. We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices. Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century

Phylogenetic organization of bacterial activity.

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism\u27s ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.The ISME Journal advance online publication, 4 March 2016; doi:10.1038/ismej.2016.28

Bioavailability of Macro and Micronutrients Across Global Topsoils: Main Drivers and Global Change Impacts

Understanding the chemical composition of our planet\u27s crust was one of the biggest questions of the 20th century. More than 100 years later, we are still far from understanding the global patterns in the bioavailability and spatial coupling of elements in topsoils worldwide, despite their importance for the productivity and functioning of terrestrial ecosystems. Here, we measured the bioavailability and coupling of thirteen macro- and micronutrients and phytotoxic elements in topsoils (3–8 cm) from a range of terrestrial ecosystems across all continents (∼10,000 observations) and in response to global change manipulations (∼5,000 observations). For this, we incubated between 1 and 4 pairs of anionic and cationic exchange membranes per site for a mean period of 53 days. The most bioavailable elements (Ca, Mg, and K) were also amongst the most abundant in the crust. Patterns of bioavailability were biome-dependent and controlled by soil properties such as pH, organic matter content and texture, plant cover, and climate. However, global change simulations resulted in important alterations in the bioavailability of elements. Elements were highly coupled, and coupling was predictable by the atomic properties of elements, particularly mass, mass to charge ratio, and second ionization energy. Deviations from the predictable coupling-atomic mass relationship were attributed to global change and agriculture. Our work illustrates the tight links between the bioavailability and coupling of topsoil elements and environmental context, human activities, and atomic properties of elements, thus deeply enhancing our integrated understanding of the biogeochemical connections that underlie the productivity and functioning of terrestrial ecosystems in a changing world

Temperature sensitivity of bacterial growth in a hot desert soil with large temperature fluctuations

Hot desert ecosystems are characterized by high soil temperatures with large fluctuations annually and diurnally. Thus, one could hypothesize that not only the microbial community would be adapted to high temperatures, but also have a large temperature range conducive for growth. We determined the temperature sensitivity of the soil bacterial community from the Chihuahuan Desert, Big Bend National Park, Texas, USA, using leucine incorporation as a proxy for bacterial growth. Soil samples were taken during early spring and mid-summer from the surface (0-5 cm) and deeper (15-20 cm) soil layers. Mean winter soil temperature preceding the spring samples was 15 degrees C and in summer 36 degrees C at both depths, but with larger amplitude in the top soil than deeper down. T-min was significantly lower in the top 0-5 cm than at 15-20 cm, -1.2 and 0.0 degrees C, respectively. T-opt also was higher in the top soil than deeper down, 42.9 and 41.4 degrees C, respectively, resulting in a larger temperature range for growth (T-opt - T-min) in the top soil reflecting the larger temperature fluctuations in this layer. There were no significant differences in cardinal temperatures for bacterial growth in soils sampled in early spring and mid-summer despite large seasonal differences in temperatures, showing that long periods of colder temperatures was less important than periods of high temperatures as selection pressure for temperature sensitivity. Comparing with earlier results from Antarctic soils (Rinnan et al., 2009), which in contrast represent an extremely low temperature environment, we suggest that the range of temperature cardinal temperatures for soil bacterial communities globally varies from around -15 to 0 degrees C for T-min and 25 to 45 degrees C for T-opt. (C) 2013 Elsevier Ltd. All rights reserved

Comparing temperature sensitivity of bacterial growth in Antarctic marine water and soil

The western Antarctic Peninsula is an extreme low temperature environment that is warming rapidly due to global change. Little is known, however, on the temperature sensitivity of growth of microbial communities in Antarctic soils and in the surrounding oceanic waters. This is the first study that directly compares temperature adaptation of adjacent marine and terrestrial bacteria in a polar environment. The bacterial communities in the ocean were adapted to lower temperatures than those from nearby soil, with cardinal temperatures for growth in the ocean being the lowest so far reported for microbial communities. This was reflected in lower minimum (Tmin) and optimum temperatures (Topt) for growth in water (−17 and +20°C, respectively) than in soil (−11 and +27°C), with lower sensitivity to changes in temperature (Q10; 0–10°C interval) in Antarctic water (2.7) than in soil (3.9). This is likely due to the more stable low temperature conditions of Antarctic waters than soils, and the fact that maximum in situ temperatures in water are lower than in soils, at least in summer. Importantly, the thermally stable environment of Antarctic marine water makes it feasible to create a single temperature response curve for bacterial communities. This would thus allow for calculations of temperature-corrected growth rates, and thereby quantifying the influence of factors other than temperature on observed growth rates, as well as predicting the effects of future temperature increases on Antarctic marine bacteria

Seasonal microbial and nutrient responses during a 5-year reduction in the daily temperature range of soil in a Chihuahuan Desert ecosystem

High daily temperature range of soil (DTRsoil) negatively affects soil microbial biomass and activity, but its interaction with seasonal soil moisture in regulating ecosystem function remains unclear. For our 5-year field study in the Chihuahuan Desert, we suspended shade cloth 15 cm above the soil surface to reduce daytime temperature and increase nighttime soil temperature compared to unshaded plots, thereby reducing DTRsoil (by 5 ºC at 0.2 cm depth) without altering mean temperatures. Microbial biomass production was primarily regulated by seasonal precipitation with the magnitude of the response dependent on DTRsoil. Reduced DTRsoil more consistently increased microbial biomass nitrogen (MBN; +38 %) than microbial biomass carbon (MBC) with treatment responses being similar in spring and summer. Soil respiration depended primarily on soil moisture with responses to reduced DTRsoil evident only in wetter summer soils (+53 %) and not in dry spring soils. Reduced DTRsoil had no effect on concentrations of dissolved organic C, soil organic matter (SOM), nor soil inorganic N (extractable NO3 −–N + NH4 +–N). Higher MBN without changes in soil inorganic N suggests faster N cycling rates or alternate sources of N. If N cycling rates increased without a change to external N inputs (atmospheric N deposition or N fixation), then productivity in this desert system, which is N-poor and low in SOM, could be negatively impacted with continued decreases in daily temperature range. Thus, the future N balance in arid ecosystems, under conditions of lower DTR, seems linked to future precipitation regimes through N deposition and regulation of soil heat load dynamics

Reductions in daily soil temperature variability increase soil microbial biomass C and decrease soil N availability in the Chihuahuan Desert : potential implications for ecosystem C and N fluxes

Maximum and minimum soil temperatures affect belowground processes. In the past 50 years in arid regions, measured reductions in the daily temperature range of air (DTR air) most likely generated similar reductions in the unmeasured daily temperature range of soil (DTR soil). However, the role of DTR soil in regulating microbial and plant processes has not been well described. We experimentally reduced DTR soil in the Chihuahuan Desert at Big Bend National Park over 3 years. We used shade cloth that effectively decreased DTR soil by decreasing daily maximum temperature and increasing nighttime minimum temperature. A reduction in DTR soil generated on average a twofold increase in soil microbial biomass carbon, a 42% increase in soil CO 2 efflux and a 16% reduction in soil NO 3 --N availability; soil available NH 4 +-N was reduced by 18% in the third year only. Reductions in DTR soil increased soil moisture up to 15% a few days after a substantial rainfall. Increased soil moisture contributed to higher soil CO 2 efflux, but not microbial biomass carbon, which was significantly correlated with DTR soil. Net photosynthetic rates at saturating light (A sat) in Larrea tridentata were not affected by reductions in DTR soil over the 3 year period. Arid ecosystems may become greater sources of C to the atmosphere with reduced DTR soil, resulting in a positive feedback to rising global temperatures, if increased C loss is not eventually balanced by increased C uptake. Ultimately, ecosystem models of N and C fluxes will need to account for these temperature-driven processes