Composition and metabolism of microbial communities in soil pores.

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

Distribution of Mn Oxidation States in Grassland Soils and Their Relationships with Soil Pores.

Manganese (Mn) is known to be an active contributor to processing and cycling of soil organic carbon (C), yet the exact mechanisms behind its interactions with C are poorly understood. Plant diversity in terrestrial ecosystems drives feedback links between plant C inputs and soil pores, where the latter, in turn, impact the redox environment and Mn. This study examined associations between soil pores (>36 µm Ø) and Mn within intact soils from two grassland ecosystems, after their >6-year implementation in a replicated field experiment. We used µ-XRF imaging and XANES spectroscopy to explore spatial distribution patterns of Mn oxidation states, combined with X-ray computed microtomography and 2D zymography. A high plant diversity system (restored prairie) increased soil C and modified spatial distribution patterns of soil pores as compared to a single species system (monoculture switchgrass). In switchgrass, the abundance of oxidized and reduced Mn oxidation states varied with distance from pores consistently with anticipated O2 diffusion, while in the soil from restored prairie, the spatial patterns suggested that biological activity played a greater role in influencing Mn distributions. Based on the findings, we propose a hypothesis that Mn transformations promote C gains in soils of high plant diversity grasslands.

Cover crop influence on pore size distribution and biopore dynamics: Enumerating root and soil faunal effects.

Pore structure is a key determinant of soil functioning, and both root growth and activity of soil fauna are modified by and interact with pore structure in multiple ways. Cover cropping is a rapidly growing popular strategy for improving agricultural sustainability, including improvements in pore structure. However, since cover crop species encompass a variety of contrasting root architectures, they can have disparate effects on formation of soil pores and their characteristics, thus on the pore structure formation. Moreover, utilization of the existing pore systems and its modification by new root growth, in conjunction with soil fauna activity, can also vary by cover crop species, affecting the dynamics of biopores (creation and demolition). The objectives of this study were (i) to quantify the influence of 5 cover crop species on formation and size distribution of soil macropores (>36 µm Ø); (ii) to explore the changes in the originally developed pore architecture after an additional season of cover crop growth; and (iii) to assess the relative contributions of plant roots and soil fauna to fate and modifications of biopores. Intact soil cores were taken from 5 to 10 cm depth after one season of cover crop growth, followed by X-ray computed micro-tomography (CT) characterization, and then, the cores were reburied for a second root growing period of cover crops to explore subsequent changes in pore characteristics with the second CT scanning. Our data suggest that interactions of soil fauna and roots with pore structure changed over time. While in the first season, large biopores were created at the expense of small pores, in the second year these biopores were reused or destroyed by the creation of new ones through earthworm activities and large root growth. In addition, the creation of large biopores (>0.5 mm) increased total macroporosity. During the second root growing period, these large sized macropores, however, are reduced in size again through the action of soil fauna smaller than earthworms, suggesting a highly dynamic equilibrium. Different effects of cover crops on pore structure mainly arise from their differences in root volume, mean diameter as well as their reuse of existing macropores.

Empirical Evidence for the Potential Climate Benefits of Decarbonizing Light Vehicle Transport in the U.S. with Bioenergy from Purpose-Grown Biomass with and without BECCS.

Climate mitigation scenarios limiting global temperature increases to 1.5 °C rely on decarbonizing vehicle transport with bioenergy production plus carbon capture and storage (BECCS), but climate impacts for producing different bioenergy feedstocks have not been directly compared experimentally or for ethanol vs electric light-duty vehicles. A field experiment at two Midwest U.S. sites on contrasting soils revealed that feedstock yields of seven potential bioenergy cropping systems varied substantially within sites but little between. Bioenergy produced per hectare reflected yields: miscanthus > poplar > switchgrass > native grasses ≈ maize stover (residue) > restored prairie ≈ early successional. Greenhouse gas emission intensities for ethanol vehicles ranged from 20 to -179 g CO2e MJ-1: maize stover ≫ miscanthus ≈ switchgrass ≈ native grasses ≈ poplar > early successional ≥ restored prairie; direct climate benefits ranged from ∼80% (stover) to 290% (restored prairie) reductions in CO2e compared to petroleum and were similar for electric vehicles. With carbon capture and storage (CCS), reductions in emission intensities ranged from 204% (stover) to 416% (restored prairie) for ethanol vehicles and from 329 to 558% for electric vehicles, declining 27 and 15%, respectively, once soil carbon equilibrates within several decades of establishment. Extrapolation based on expected U.S. transportation energy use suggests that, once CCS potential is maximized with CO2 pipeline infrastructure, negative emissions from bioenergy with CCS for light-duty electric vehicles could capture >900 Tg CO2e year-1 in the U.S. In the future, as other renewable electricity sources become more important, electricity production from biomass would offset less fossil fuel electricity, and the advantage of electric over ethanol vehicles would decrease proportionately.

Field-scale experiments reveal persistent yield gaps in low-input and organic cropping systems.

Knowledge of production-system performance is largely based on observations at the experimental plot scale. Although yield gaps between plot-scale and field-scale research are widely acknowledged, their extent and persistence have not been experimentally examined in a systematic manner. At a site in southwest Michigan, we conducted a 6-y experiment to test the accuracy with which plot-scale crop-yield results can inform field-scale conclusions. We compared conventional versus alternative, that is, reduced-input and biologically based-organic, management practices for a corn-soybean-wheat rotation in a randomized complete block-design experiment, using 27 commercial-size agricultural fields. Nearby plot-scale experiments (0.02-ha to 1.0-ha plots) provided a comparison of plot versus field performance. We found that plot-scale yields well matched field-scale yields for conventional management but not for alternative systems. For all three crops, at the plot scale, reduced-input and conventional managements produced similar yields; at the field scale, reduced-input yields were lower than conventional. For soybeans at the plot scale, biological and conventional managements produced similar yields; at the field scale, biological yielded less than conventional. For corn, biological management produced lower yields than conventional in both plot- and field-scale experiments. Wheat yields appeared to be less affected by the experimental scale than corn and soybean. Conventional management was more resilient to field-scale challenges than alternative practices, which were more dependent on timely management interventions; in particular, mechanical weed control. Results underscore the need for much wider adoption of field-scale experimentation when assessing new technologies and production-system performance, especially as related to closing yield gaps in organic farming and in low-resourced systems typical of much of the developing world.

Long-term nitrous oxide fluxes in annual and perennial agricultural and unmanaged ecosystems in the upper Midwest USA.

Differences in soil nitrous oxide (N2 O) fluxes among ecosystems are often difficult to evaluate and predict due to high spatial and temporal variabilities and few direct experimental comparisons. For 20 years, we measured N2 O fluxes in 11 ecosystems in southwest Michigan USA: four annual grain crops (corn-soybean-wheat rotations) managed with conventional, no-till, reduced input, or biologically based/organic inputs; three perennial crops (alfalfa, poplar, and conifers); and four unmanaged ecosystems of different successional age including mature forest. Average N2 O emissions were higher from annual grain and N-fixing cropping systems than from nonleguminous perennial cropping systems and were low across unmanaged ecosystems. Among annual cropping systems full-rotation fluxes were indistinguishable from one another but rotation phase mattered. For example, those systems with cover crops and reduced fertilizer N emitted more N2 O during the corn and soybean phases, but during the wheat phase fluxes were ~40% lower. Likewise, no-till did not differ from conventional tillage over the entire rotation but reduced emissions ~20% in the wheat phase and increased emissions 30-80% in the corn and soybean phases. Greenhouse gas intensity for the annual crops (flux per unit yield) was lowest for soybeans produced under conventional management, while for the 11 other crop × management combinations intensities were similar to one another. Among the fertilized systems, emissions ranged from 0.30 to 1.33 kg N2 O-N ha-1  yr-1 and were best predicted by IPCC Tier 1 and ΔEF emission factor approaches. Annual cumulative fluxes from perennial systems were best explained by soil NO3- pools (r2  = 0.72) but not so for annual crops, where management differences overrode simple correlations. Daily soil N2 O emissions were poorly predicted by any measured variables. Overall, long-term measurements reveal lower fluxes in nonlegume perennial vegetation and, for conservatively fertilized annual crops, the overriding influence of rotation phase on annual fluxes.

Topography Mediates the Influence of Cover Crops on Soil Nitrate Levels in Row Crop Agricultural Systems.

Supplying adequate amounts of soil N for plant growth during the growing season and across large agricultural fields is a challenge for conservational agricultural systems with cover crops. Knowledge about cover crop effects on N comes mostly from small, flat research plots and performance of cover crops across topographically diverse agricultural land is poorly understood. Our objective was to assess effects of both leguminous (red clover) and non-leguminous (winter rye) cover crops on potentially mineralizable N (PMN) and [Formula: see text] levels across a topographically diverse landscape. We studied conventional, low-input, and organic managements in corn-soybean-wheat rotation. The rotations of low-input and organic managements included rye and red clover cover crops. The managements were implemented in twenty large undulating fields in Southwest Michigan starting from 2006. The data collection and analysis were conducted during three growing seasons of 2011, 2012 and 2013. Observational micro-plots with and without cover crops were laid within each field on three contrasting topographical positions of depression, slope and summit. Soil samples were collected 4-5 times during each growing season and analyzed for [Formula: see text] and PMN. The results showed that all three managements were similar in their temporal and spatial distributions of NO3-N. Red clover cover crop increased [Formula: see text] by 35% on depression, 20% on slope and 32% on summit positions. Rye cover crop had a significant 15% negative effect on [Formula: see text] in topographical depressions but not in slope and summit positions. The magnitude of the cover crop effects on soil mineral nitrogen across topographically diverse fields was associated with the amount of cover crop growth and residue production. The results emphasize the potential environmental and economic benefits that can be generated by implementing site-specific topography-driven cover crop management in row-crop agricultural systems.

Protection of soil carbon within macro-aggregates depends on intra-aggregate pore characteristics.

Soil contains almost twice as much carbon (C) as the atmosphere and 5-15% of soil C is stored in a form of particulate organic matter (POM). Particulate organic matter C is regarded as one of the most labile components of the soil C, such that can be easily lost under right environmental settings. Conceptually, micro-environmental conditions are understood to be responsible for protection of soil C. However, quantitative knowledge of the specific mechanisms driving micro-environmental effects is still lacking. Here we combined CO2 respiration measurements of intact soil samples with X-ray computed micro-tomography imaging and investigated how micro-environmental conditions, represented by soil pores, influence decomposition of POM. We found that atmosphere-connected soil pores influenced soil C's, and especially POM's, decomposition. In presence of such pores losses in POM were 3-15 times higher than in their absence. Moreover, we demonstrated the presence of a feed-forward relationship between soil C decomposition and pore connections that enhance it. Since soil hydrology and soil pores are likely to be affected by future climate changes, our findings indicate that not-accounting for the influence of soil pores can add another sizable source of uncertainty to estimates of future soil C losses.

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.

Forms and functions of meso and micro-niches of carbon within soil aggregates.

Soil aggregates include sand/silt/clay, water, ion and organic matter contents combined with natural dry/wet (D/W) cycling alters both the formation and function of intra-aggregate pore continuity, connectivity, dead-end storage volumes, and tortuosity. Surface aggregates in the 0-5 cm depths of most soils experience from 34 to 57 D/W cycles that exceed differences in water contents >10%. Both the rates of drying or wetting, (intensity) and the D/W range of soil water contents (severity) alter the transport of water, C and N through micro and mesofaunal habitats among multiple size domains. This report identifies micro-niche locations of accumulating soil C within soil aggregate regions that may affect nematode residence sites and migration pathways. Recent advances in X-ray microtomography enable the examination of intact pore networks within soil aggregates at resolutions as small as 4 microns. Geostatistical and multi-fractal methods provide concise characteristics of pore spatial distributions within the aggregates and are useful for comparing these alterations among soils. Aggregates subjected to multiple D/W cycles developed greater spatial correlations that parallel increases in the (13)C sorption within aggregate interiors were compared with locations of soil microbial communities. Past research indicates microbial activities within the soil aggregate matrix are spatially heterogeneous due to complex pore geometries within aggregates. Illumination of the "blackbox" interiors of soil aggregates includes a discussion of natural and anthropogenic alterations of solution flow and carbon sequestration by soil aggregates containing biophysical gradients.

TB-infected deer are more closely related than non-infected deer.

Identifying mechanisms of pathogen transmission is critical to controlling disease. Social organization should influence contacts among individuals and thus the distribution and spread of disease within a population. Molecular genetic markers can be used to elucidate mechanisms of disease transmission in wildlife populations without undertaking detailed observational studies to determine probable contact rates. Estimates of genealogical relationships within a bovine tuberculosis-infected white-tailed deer (Odocoileus virginianus) population indicated that infected deer were significantly more closely related than non-infected deer suggesting that contact within family groups was a significant mechanism of disease transmission. Results demonstrate that epidemiological models should incorporate aspects of host ecology likely to affect the probability of disease transmission.

Biodegrader metabolic expansion during polyaromatic hydrocarbons rhizoremediation.

Root-microbe interactions are considered to be the primary process of polyaromatic hydrocarbon (PAH) phytoremediation, since bacterial degradation has been shown to be the dominant pathway for environmental PAH dissipation. However, the precise mechanisms driving PAH rhizostimulation symbiosis remain largely unresolved. In this study, we assessed PAH degrading bacterial abundance in contaminated soils planted with 18 different native Michigan plant species. Phenanthrene metabolism assays suggested that each plant species differentially influenced the relative abundance of PAH biodegraders, though they generally were observed to increase heterotrophic and biodegradative cell numbers relative to unplanted soils. Further study of >1800 phenanthrene degrading isolates indicated that most of the tested plant species stimulated biodegradation of a broader range of PAH compounds relative to the unplanted soil bacterial consortia. These observations suggest that a principal contribution of planted systems for PAH bioremediation may be via expanded metabolic range of the rhizosphere bacterial community.