Lamb et al. 2006

Lamb EG, Cahill JF, Dale MRT. 2006. A nonlinear regression approach to test for size-dependence of competitive ability. Ecology 87: 1452-1457.

These authors describe a statistical analytical technique, “nonlinear regression”, that potentially provides more information than linear regression techniques including ANCOVA. The basic linear regression formula includes the intercept and the slope as parameters; nonlinear regression adds an exponent parameter. In this paper, these parameters are referred to as k1 (intercept), k2 (slope), and k3 (exponent), in the formula

y = k1 + k2x^k3

where y is the response variable and x is the explanatory variable.

These authors tested their technique on three example datasets from previous studies. The first example is most thoroughly examined, and involves a plant competition experiment. One key feature of all of the example analysis is the dataset must be paired, such that each data point on the x axis corresponds to a partner data point on the y axis. In the plant competition example, individual plants that did not experience competition are paired with individuals that did, because each pair of plants was grown in a communal pot that was treated at the pot level with manipulations such as fertilizer application. The continuous dataset is plant size, measured as the absolute gain in mass over the course of the growing season.

The exponent parameter k3 can take on any value between negative and positive infinity, to describe curves that may be accelerating, saturating, or straight. At values of 1 or -1, k3 is not informative as a parameter, and should be discarded from the model. This analysis is based on a model-building and model-testing technique, where models with various values for the three parameters are tested against null models and each other in an iterative fashion to find the model that best fits the data.

This approach is likely to be useful in the analysis of some of the data collected at Alexandra Fjord in 2009.

Michelsen et al. 1999

Michelsen, A., Graglia, E., Schmidt, I.K., Jonasson, S., Sleep, D., and Quarmby, C. 1999. Differential responses of grass and a dwarf shrub to long-term changes in soil microbial biomass C, N and P following factorial addition of NPK fertilizer, fungicide and labile carbon to a heath. New Phytologist 143(3): 523-538.

These authors measured the responses of two tundra plants, one graminoid and one shrub, to additions of fertilizer, labile carbon, and a fungicide over four years in a heath in subarctic Sweden. The underlying hypothesis is that differences in growth strategy between these two groups of plants would be reflected in their responses to changes in microbial biomass, also measured by these authors.

Molecules inaccessible to plants by virtue of being incorporated into microbial cells in soils dominate their respective pools. For example, in this study, microbial N concentrations were up to 50 times higher than free, inorganic N such as ammonium. Similar ratios were found for C and P. Rapid incorporation of these nutrients into microbes therefore constitutes competition between microbes and plants. Consistent with the variety of ecological and growth strategies that plants have evolved interacting with each other and with the abiotic features, plant strategies impact their interactions with microbes and how they react to such competition.

As predicted, the graminoid Festuca ovina responded rapidly to changes in nutrient levels. Added N from fertilizers led to increased ground cover by this grass, while added labile C, in the form of sugar, led to decreased ground cover, presumably due to a rapid increase in microbial biomass and associated increased microbial uptake of soil N and P. In contrast, the shrub Vaccinium uliginosum did not appreciably react to changes in nutrient levels, consistent with a long-view growth strategy and successful escape from severe competition with soil microbes. This may have been mediated by the mycorrhizal associations the shrub has but the graminoid lacks.

This paper, interestingly, does not cite any of the work by Wardle or Nilsson, the authors who severely criticized the earlier work by this research group (Michelsen et al. 1995).

Wardle and Nilsson 1997

Wardle DA, Nilsson M-C. 1997. Microbe-plant competition, allelopathy and arctic plants. Oecologia 109: 291-293.

These authors critique Michelsen et al. (1995), a study that came to several important conclusions regarding the interactions between Arctic plants and the soil microbial communities. This is a very negative review of that paper, in which these authors question almost all of the conclusions of Michelsen et al. (1995).

These authors make two main criticisms. First, they question the measures of soil microbial activity used by the earlier paper. Second, they question the conclusions regarding the allelopathy of Empetrum hermaphroditum. Soil microbial activity was measured by Michelsen et al. (1995) in two ways: soil respiration, and soil ergosterol content. Neither approach is necessarily informative about one of Michelsen et al.’s (1995) main claims, that soil microbial biomass was increased by the addition of plant leaf extracts. There are a number of studies, many of them with Nilsson as a co-author, in which a lack of association between microbial biomass and soil respiration was demonstrated. Furthermore, ergosterol is presented by Michelsen et al. (1995) as an indicator of fungal biomass, but previous work by Newell and colleagues (e.g. Newell and Fallon, 1991; Newell 1992) showed that ergosterol is not a reliable indicator of biomass nor is it useful as a proxy measure of soil fungal activity; the ratio of ergosterol to fungal biomass is highly variable.

From the reference list in this short paper, it appears that Wardle and Nilsson had, by early 1997, completed a considerable body of work regarding the allelopathic and other ecological interactions of E. hermaphroditum in sub-arctic environments. The conclusion by Michelsen et al. (1995) that the chemicals released by this plant have a greater impact on microbial communities than potential surface-plant competitors is not supported by this work by Wardle, Nilsson, and their colleagues.

The conclusion of Michelsen et al. (1995) that currently has the most direct bearing on my own work is that key plant traits often possessed by prostrate shrubs in tundra ecosystems such as a high root: shoot ratio and storage of nutrients such as nitrogen in the roots allow those plants to escape from or outcompete soil microorganisms. This conclusion was not addressed by these authors, but given the devastation inflicted upon the other conclusions, my confidence in the utility of Michelsen et al. (1995) in addressing issues of interactions between Cassiope tetragonal and soil microbial communities has been shaken.

Michelsen et al. 1995

Michelsen A, Schmidt IK, Jonasson S, Dighton J, Jones HE, Callaghan TV. Inhibition of growth, and effects on nutrient uptake of arctic graminoids by leaf extracts – allelopathy or resource competition between plants and microbes? Oecologia 103: 407-418.

These authors conducted an experiment to examine the potential allelopathic effects of plant leaf extracts among a few species of arctic tundra plants. Three arctic/subarctic plants suspected of releasing phytotoxic compounds upon their competitors including Cassiope tetragonal were harvested and their leaves and branches ground up to make leaf extracts. Three species of arctic graminoids (Carex bigelowii, Festuca vivipara, Luzula arcuata) were then treated with these extracts while growing in either sterilized or non-sterilized soil in greenhouses in southern Sweden. All of the graminoids, the soil they grew in, and two of the leaf extract-providing plants came from a montaine subarctic hillside in northern Sweden; the third leaf extract came from Betula pubescens ssp. tortuosa, a birch, were collected from individuals growing near the tree line at 450m altitude near Abisko Scientific Research Station, above the Arctic Circle in a subarctic ecosystem.

The experimental design was factorial, with two soil types (sterilized vs. non-sterilized) and four leaf-extract treatments including a control of distilled water. In addition to growth of the graminoids, measurements were made of the chemicals in the leaf extracts and soils, nutrient uptake by excised roots, soil ergosterol content, and soil respiration. Excised roots take up nutrients in a manner directly correlated to the nutrient-limitation status of the plant; more phosphorus-starved plants, for example, have roots that more rapidly take up phosphorus when offered. Soil ergosterol content is a measure of fungal biomass, while soil respiration was taken as a measure of total microbial activity.

Sterilized soil had higher extractable nutrients, probably as a result of the breakdown of microbial cells during autoclaving. Nitrate levels were negligible, both in soils and in leaf extracts; nitrate was a component of the dilute nutrient water used to maintain the plants while growing. Some mycorrhizae were found, but they covered less than 1% of the roots in non-sterilized soil, and had no impact on other measured parameters.

The highest growth of all three test graminoids was recorded in sterilized soil with no extract added (i.e. distilled water added instead of leaf extract solution). Plants growing under these conditions experienced no inhibition from the materials of other plants, and did not compete with soil microbes for nutrients, at least during the early stages of the experiment before microbes recolonized the sterilized soils. Recolonization was much faster by prokaryotes than by fungi, as measured by the contrast in soil respiration rates and soil ergosterol contents. Recolonization also varied between leaf extract treatments, with a negative correlation between microbial activity and plant growth; strongly growing plants were able to outcompete colonizing microbes, while poorly growing plants were further inhibited by colonizing and rapidly growing microbes.

All three leaf extracts significantly reduced growth of all three graminoid species. However, it is not clear that allelopathy alone was responsible for this effect. The results of this study indicate that competition between plants and microbes also played a major role. In particular, the components of the leaf extracts, especially labile carbon and (in the case of the Betula extract) phosphorus, appeared to stimulate the microbial community, increasing competitive pressure on the plants. Added nitrogen, for example, appears not to have much benefited the plants, as their roots were N-limited when grown in non-sterilized soil even though the leaf extracts included high concentrations of inorganic nitrogen.

The susceptibility of plants to this combined effect of allelopathy and microbial competition probably varies by species. Plant traits of particular importance are probably the root: shoot ratio, in which plants with more robust roots are less harmed, and the storage of nutrients such as nitrogen in plant roots, in which plants with a growth strategy favouring nutrient storage rather than immediate use are less harmed. Such traits appear to be widespread among the dominant plants of the Arctic tundra, including Cassiope tetragonal and probably other prostrate shrubs. Many of these plants may form associations with mycorrhizal fungi, which provide some protection against microbial competition.

This paper is directly relevant to the discussion section of my current-high-priority Pits & Probes manuscript. The patterns of soil respiration and microbial GHG activity under some of the lowland communities are consistent with successful competition against soil microbes by Cassiope tetragonal and possibly Salix arctica plant roots.

This paper was critiqued quite harshly by Wardle and Nilsson (1997).

Moffat et al. 1990

Moffat AJ, Johnston M, Wright JS. 1990. An improved probe for sampling soil atmospheres. Plant and Soil 121: 145-147.

These authors describe a new design of soil gas probe they produced to examine soil O2 levels, especially at landfills and other potentially polluted sites. The design is fairly complex, with moving parts. Essentially, the probe is driven into the soil to the desired depth, and then lifted slightly to create a void below the tip. The top of the probe is then rotated and tapped to open the tip, and a gas sample can be drawn from a tube on the side. These authors tested this probe by measuring O2 concentrations in a column of sand that had been flushed with pure N2; anoxic conditions were recorded in the deeper parts of this column.

Farías et al. 2009

Farías L, Fernández C, Faúndez J, Cornejo M, Alcaman ME. 2009. Chemolithoautotrophic production mediating the cycling of the greenhouse gases N2O and CH4 in an upwelling ecoystem. Biogeosciences 6: 3053-3069.

“Chemolithoautotrophy is the non-photosynthetic biological conversion of C1 molecules (usually CO2 or CH4) into organic matter."

These authors studied the chemolithoautrophic community in the south-eastern Pacific ocean, at a long-term research position on the small continental shelf of Chile. At this position, the water is about 90m deep, and is part of one of the largest and most productive upwelling regions of the world, where productivity is extremely high. For about 70% of the year, surface winds drive upwelling that brings nutrients such as NO3- up to the photic zone, allowing massive planktonic productivity. Some of these plankton are non-photosynthetic prokaryotic autotrophs, using inorganic molecules such as NH4+, NO2-, and HS- as electron donors to drive the energy-intensive process of fixing inorganic carbon, chiefly CO2, as organic matter. These organisms require oxygen as an electron acceptor, thus they are all aerobic organisms and do not thrive in anaerobic environments. Assimilation of CO2 in the dark is the diagnostic signal of the presence of these organisms. Some chemolithoautrophs use CH4 in addition to or instead of CO2, but always under aerobic conditions; anaerobic methanotrophs are outside the scope of this study, and have not been identified in this system.

Nitrous oxide accumulates in these waters, indicative of greater production than consumption. These authors state that N2O reduction can only occur through a single identified pathway, that of total denitrification that takes NO3- or NO2- all the way to N2, and only under extremely limited O2 conditions; they cite Elkins et al. (1978) and Farías et al. (2009). Variation in space and time in dissolved N2O patterns do suggest some consumption is occurring, but in general production outweighs consumption.

Kostina et al. 1994

Kostina NV, Stepanov AL, Umarov MM. 1994. Study of the complex of nitrous oxide-reducing microorganisms in the soil. Eurasian Soil Science 26: 81-87.

These authors extracted microorganisms from a range of soils apparently collected from various places in Russia and produced cultures of organisms capable of reducing nitrous oxide. The only nitrogen source in culture vials was N2O, and conditions were rendered anaerobic by flushing with argon gas.

Most cultures gradually lost their ability to reduce N2O, especially mixed-species cultures. A few pure strains were isolated that did not show this loss, and maintained high levels of activity in storage.

Pseudomonas spp. and Bacillus spp. contributed the vast majority of N2O-reducing activity in all soils, with other groups including Aeromonas spp., Micrococcus spp., Flavobacterium spp., Erwinia spp., and an organism identified as “similar to Corynebacterium” also showing some activity. Neither actinomycetes nor eukaryotes were found in any of the cultures capable of N2O-reduction, indicating this is a physiological process not possessed by these organisms.

This is an English translation of a paper that was probably originally in Russian: Pochvovedeniye 1993 25: 72-76.