The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems.

It is well known that atmospheric concentrations of carbon dioxide (CO2) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO2 and that, primarily as a result of the activities of soil microorganisms, there is a soil-derived respiratory flux of CO2 to the atmosphere that overshadows by tenfold the annual CO2 flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO2 concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro-ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant-derived carbon-utilising microbes, current technologies lack the high-throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant–soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil.

The impact of land-use practices on soil microbes

The extensive use of land resources for food production, fibre for construction, wood pulp for paper, removal for extractive industries, sealing for urban and industrial development and as a receiver (either deliberate or accidental) of polluting substances has wrought huge changes in the chemistry, structure and biology of soils, away from their natural state.

Do arbuscular mycorrhizas or heterotrophic soil microbes contribute toward plant acquisition of a pulse of mineral phosphate?

Aims: We investigated the role of arbuscular mycorrhizal fungi (AMF) and heterotrophic soil microbes in the uptake of phosphorus (P) by Trifolium subterraneum from a pulse. Methods: Plants were grown in sterilised pasture field soil with a realistic level of available P. There were five treatments, two of which involved AMF: 1) unsterilised field soil containing a community of AMF and heterotrophic organisms; 2) Scutellospora calospora inoculum (AMF); 3) microbes added as filtrate from the field soil; 4) microbes added as filtrate from the S. calospora inoculum; 5) no additions, i.e. sterilised field soil. After 11 weeks, plants were harvested: 1 day before (day 0), 1 day after (day 2) and 7 days after (day 8) the pulse of P (10 mg kg−1). Results: There was no difference among treatments in shoot and root dry weight, which increased from day 0 to day 8. At day 0, shoots and roots of plants in the colonised treatments had higher P and lower Mn concentrations. After the pulse, the rate of increase in P concentration in the shoots was slower for the colonised plants, and the root Mn concentration declined by up to 50 % by day 2. Conclusions: Plants colonised by AMF had a lower rate of increase in shoot P concentration after a pulse, perhaps because intraradical hyphae accumulated P and thus reduced its transport to the shoots.

Autoclaving kills soil microbes yet soil enzymes remain active

Biocidal treatment of soil is used to remove or inhibit soil microbial activity, and thus provides insight into the relationship between soil biology and soil processes. Chemical (soil pH, phosphodiesterase, protease) and biological (substrate induced respiration) characteristics of three contrasting soils from tropical savanna ecosystems in north Queensland, Australia were measured in field fresh samples and following autoclaving (121 °C/103 kPa for 30 min on two consecutive days). Autoclaving treatment killed the active soil microbial biomass and significantly decreased protease activity (∼90%) in all three soils. Phosphodiesterase activity in kaolinitic soils also significantly decreased by 78% and 92%. However, autoclave treatment of smectitic soil only decreased phosphodiesterase activity by 4% only. This study demonstrates phosphodiesterase can remain stable in extreme conditions. This might be a characteristic vital to the cycling of phosphorus in shrink–swell clays in Australian tropical savanna ecosystems.

Does repeated burial of skeletal muscle tissue (Ovis aries) in soil affect subsequent decomposition?

The repeated introduction of an organic resource to soil can result in its enhanced degradation. This phenomenon is of primary importance in agroecosystems, where the dynamics of repeated nutrient, pesticide, and herbicide amendment must be understood to achieve optimal yield. Although not yet investigated, the repeated introduction of cadaveric material is an important area of research in forensic science and cemetery planning. It is not currently understood what effects the repeated burial of cadaveric material has on cadaver decomposition or soil processes such as carbon mineralization. To address this gap in knowledge, we conducted a laboratory experiment using ovine (Ovis aries) skeletal muscle tissue (striated muscle used for locomotion) and three contrasting soils (brown earth, rendzina, podsol) from Great Britain. This experiment comprised two stages. In Stage I skeletal muscle tissue (150 g as 1.5 g cubes) was buried in sieved (4.6 mm) soil (10 kg dry weight) calibrated to 60% water holding capacity and allowed to decompose in the dark for 70 days at 22 °C. Control samples comprised soil without skeletal muscle tissue. In Stage II, soils were weighed (100 g dry weight at 60% WHC) into 1285 ml incubation microcosms. Half of the soils were designated for a second tissue amendment, which comprised the burial (2.5 cm) of 1.5 g cube of skeletal muscle tissue. The remaining half of the samples did not receive tissue. Thus, four treatments were used in each soil, reflecting all possible combinations of tissue burial (+) and control (−). Subsequent measures of tissue mass loss, carbon dioxide-carbon evolution, soil microbial biomass carbon, metabolic quotient and soil pH show that repeated burial of skeletal muscle tissue was associated with a significantly greater rate of decomposition in all soils. However, soil microbial biomass following repeated burial was either not significantly different (brown earth, podsol) or significantly less (rendzina) than new gravesoil. Based on these results, we conclude that enhanced decomposition of skeletal muscle tissue was most likely due to the proliferation of zymogenous soil microbes able to better use cadaveric material re-introduced to the soil.

Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions

Volatile organic compounds (VOCs) released by soil microorganisms influence plant growth and pathogen resistance. Yet, very little is known about their influence on herbivores and higher trophic levels. We studied the origin and role of a major bacterial VOC, 2,3-butanediol (2,3-BD), on plant growth, pathogen and herbivore resistance, and the attraction of natural enemies in maize. One of the major contributors to 2,3-BD in the headspace of soil-grown maize seedlings was identified as Enterobacter aerogenes, an endophytic bacterium that colonizes the plants. The production of 2,3-BD by E. aerogenes rendered maize plants more resistant against the Northern corn leaf blight fungus Setosphaeria turcica. On the contrary, E. aerogenes-inoculated plants were less resistant against the caterpillar Spodoptera littoralis. The effect of 2,3-BD on the attraction of the parasitoid Cotesia marginiventris was more variable: 2,3-BD application to the headspace of the plants had no effect on the parasitoids, but application to the soil increased parasitoid attraction. Furthermore, inoculation of seeds with E. aerogenes decreased plant attractiveness, whereas inoculation of soil with a total extract of soil microbes increased parasitoid attraction, suggesting that the effect of 2,3-BD on the parasitoid is indirect and depends on the composition of the microbial community.

WARMING AND CHRONIC HIGH NUTRIENT MANIPULATIONS YIELD DIFFERING LEGACY EFECTS ON THE SOIL MICROBIAL COMMUNITY AND NUTRIENT POOLS IN THE LOW ARCTIC

Climate warming is predicted to increase summer air temperatures in the Arctic, warming soils and enhancing microbial decomposition of soil organic matter. Given the size of the soil carbon stores in the Arctic, even a fraction of its release as CO2 to the atmosphere could result in a positive feedback to climate warming. Fertilizers have been used in the past to quickly increase soil solution nutrients pools to mimic predicted concentrations under climate warming. However, because it may have inadvertent affects on the soil microbial community, fertilizer-induced patterns in microbial decomposition may be unrealistic. This study aimed to better understand the proposed mechanism of enhanced microbial decomposition under nutrient addition and warming treatments to discern whether warming alone is enough to stimulate enhanced microbial decomposition, or if nutrients in excess (i.e. chronic high nutrient additions) are necessary to yield such a response. I investigated the impacts of 10 years of greenhouse summer warming, chronic low nutrient factorial addition (5 g N and 1g P m-2 year-1, respectively), and chronic high nutrient factorial addition (10 g N and 5g P m-2 year-1, respectively) treatments on a mesic birch hummock tundra ecosystem near Daring Lake, NWT, Canada. Soil microbial nutrient pools, soil solution nutrient pools, and microbial community structure were measured in the upper organic, lower organic, and uppermost mineral soil depth intervals of all treatment plots in Spring 2014. Interestingly, the low nutrient additions did not yield any significant trends, yet the warming treatment increased soil bacterial richness suggesting a legacy effect of warming from the previous summers. Enhanced microbial nutrient uptake occurred only in the high nutrient addition treatments, and did not significantly alter soil carbon at least within the ten year period of this experiment. Together, these results and the absence of significant impacts of the low nutrient and greenhouse warming treatments suggests that nutrient and carbon cycling in these low arctic soils may be resilient against climate warming, at least over the initial decades.

The Ecology of Urbanization: A Study of Soil Microbial Community Rosponse

Urbanization is associated with global biodiversity loss of macrophauna and flora through direct and indirect mechanisms, but to date few studies have examined urban soil microbes. Although there are numerous studies on the influence of agricultural management on soil microbial community composition, there has been no global-scale study of human control over urban soil microbial communities. This thesis extends the literature of urban ecology to include soil microbial communities by analyzing soils that are part of the Global Urban Soil Ecology and Education Network (GLUSEEN). Chapter 1 sets the context for urban ecology; Chapters 2 addresses patterns of community assembly, biodiversity loss, and the phylogenetic relationships among community members; Chapter 3 addresses the metabolic pathways that characterize microbial communities existing under different land-uses across varying geographic scales; and Chapter 4 relates Chapter 2 and 3 to one another and to evolutionary theory, tackling assumptions that are particular to microbial ecology.

Chemical and microbiological attributes of an oxisol treated with successive applications of sewage sludge¹

Studies on sewage sludge (SS) have confirmed the possibilities of using this waste as fertilizer and/or soil conditioner in crop production areas. Despite restrictions with regard to the levels of potentially toxic elements (PTE) and pathogens, it is believed that properly treated SS with low PTE levels, applied to soil at adequate rates, may improve the soil chemical and microbiological properties. This study consisted of a long-term field experiment conducted on a Typic Haplorthox (eutroferric Red Latosol) treated with SS for seven successive years for maize production, to evaluate changes in the soil chemical and microbiological properties. The treatments consisted of two SS rates (single and double dose of the crop N requirement) and a mineral fertilizer treatment. Soil was sampled in the 0-0.20 m layer and analyzed for chemical properties (organic C, pH, P, K, Ca, Mg, CEC, B, Cu, Fe, Mn, Zn, Cd, Ni, and Pb) and microbiological properties (basal respiration, microbial biomass activity, microbial biomass C, metabolic quotient, microbial quotient, and protease and dehydrogenase enzyme activities). Successive SS applications to soil increased the macro- and micronutrient availability, but the highest SS dose reduced the soil pH significantly, indicating a need for periodic corrections. The SS treatments also affected soil microbial activity and biomass negatively. There were no significant differences among treatments for maize grain yield. After seven annual applications of the recommended sludge rate, the heavy metal levels in the soil had not reached toxic levels.

Rhizodeposition of organic carbon by plants with contrasting traits for resource acquisition: responses to different fertility regimes

Background and aims Rhizodeposition plays an important role in mediating soil nutrient availability in ecosystems. However, owing to methodological difficulties (i.e., narrow zone of soil around roots, rapid assimilation by soil microbes) fertility-induced changes in rhizodeposition remain mostly unknown. Methods We developed a novel long-term continuous 13C labelling method to address the effects of two levels of nitrogen (N) fertilization on rhizodeposited carbon (C) by species with different nutrient acquisition strategies. Results Fertility-induced changes in rhizodeposition were modulated by root responses to N availability rather than by changes in soil microbial biomass. Differences among species were mostly related to plant biomass: species with higher total leaf and root biomass also had higher total rhizodeposited C, whereas species with lower root biomass had higher specific rhizodeposited C (per gram root mass). Experimental controls demonstrated that most of the biases commonly associated with this type of experiment (i.e., long-term steady-state labelling) were avoided using our methodological approach. Conclusions These results suggest that the amount of rhizodeposited C from plants grown under different levels of N were driven mainly by plant biomass and root morphology rather than microbial biomass. They also underline the importance of plant characteristics (i.e., biomass allocation) as opposed to traits associated with plant resource acquisition strategies in predicting total C rhizodeposition.

Reaping the benefits: science and the sustainable intensification of global agriculture

Food security is one of this century’s key global challenges. By 2050 the world will require increased crop production in order to feed its predicted 9 billion people. This must be done in the face of changing consumption patterns, the impacts of climate change and the growing scarcity of water and land. Crop production methods will also have to sustain the environment, preserve natural resources and support livelihoods of farmers and rural populations around the world. There is a pressing need for the ‘sustainable intensifi cation’ of global agriculture in which yields are increased without adverse environmental impact and without the cultivation of more land. Addressing the need to secure a food supply for the whole world requires an urgent international effort with a clear sense of long-term challenges and possibilities. Biological science, especially publicly funded science, must play a vital role in the sustainable intensifi cation of food crop production. The UK has a responsibility and the capacity to take a leading role in providing a range of scientifi c solutions to mitigate potential food shortages. This will require signifi cant funding of cross-disciplinary science for food security. The constraints on food crop production are well understood, but differ widely across regions. The availability of water and good soils are major limiting factors. Signifi cant losses in crop yields occur due to pests, diseases and weed competition. The effects of climate change will further exacerbate the stresses on crop plants, potentially leading to dramatic yield reductions. Maintaining and enhancing the diversity of crop genetic resources is vital to facilitate crop breeding and thereby enhance the resilience of food crop production. Addressing these constraints requires technologies and approaches that are underpinned by good science. Some of these technologies build on existing knowledge, while others are completely radical approaches, drawing on genomics and high-throughput analysis. Novel research methods have the potential to contribute to food crop production through both genetic improvement of crops and new crop and soil management practices. Genetic improvements to crops can occur through breeding or genetic modifi cation to introduce a range of desirable traits. The application of genetic methods has the potential to refi ne existing crops and provide incremental improvements. These methods also have the potential to introduce radical and highly signifi cant improvements to crops by increasing photosynthetic effi ciency, reducing the need for nitrogen or other fertilisers and unlocking some of the unrealised potential of crop genomes. The science of crop management and agricultural practice also needs to be given particular emphasis as part of a food security grand challenge. These approaches can address key constraints in existing crop varieties and can be applied widely. Current approaches to maximising production within agricultural systems are unsustainable; new methodologies that utilise all elements of the agricultural system are needed, including better soil management and enhancement and exploitation of populations of benefi cial soil microbes. Agronomy, soil science and agroecology—the relevant sciences—have been neglected in recent years. Past debates about the use of new technologies for agriculture have tended to adopt an either/or approach, emphasising the merits of particular agricultural systems or technological approaches and the downsides of others. This has been seen most obviously with respect to genetically modifi ed (GM) crops, the use of pesticides and the arguments for and against organic modes of production. These debates have failed to acknowledge that there is no technological panacea for the global challenge of sustainable and secure global food production. There will always be trade-offs and local complexities. This report considers both new crop varieties and appropriate agroecological crop and soil management practices and adopts an inclusive approach. No techniques or technologies should be ruled out. Global agriculture demands a diversity of approaches, specific to crops, localities, cultures and other circumstances. Such diversity demands that the breadth of relevant scientific enquiry is equally diverse, and that science needs to be combined with social, economic and political perspectives. In addition to supporting high-quality science, the UK needs to maintain and build its capacity to innovate, in collaboration with international and national research centres. UK scientists and agronomists have in the past played a leading role in disciplines relevant to agriculture, but training in agricultural sciences and related topics has recently suffered from a lack of policy attention and support. Agricultural extension services, connecting farmers with new innovations, have been similarly neglected in the UK and elsewhere. There is a major need to review the support for and provision of extension services, particularly in developing countries. The governance of innovation for agriculture needs to maximise opportunities for increasing production, while at the same time protecting societies, economies and the environment from negative side effects. Regulatory systems need to improve their assessment of benefits. Horizon scanning will ensure proactive consideration of technological options by governments. Assessment of benefi ts, risks and uncertainties should be seen broadly, and should include the wider impacts of new technologies and practices on economies and societies. Public and stakeholder dialogue—with NGOs, scientists and farmers in particular—needs to be a part of all governance frameworks.

Rooting theories of plant community ecology in microbial interactions

Predominant frameworks for understanding plant ecology have an aboveground bias that neglects soil micro-organisms. This is inconsistent with recent work illustrating the importance of soil microbes in terrestrial ecology. Microbial effects have been incorporated into plant community dynamics using ideas of niche modification and plant–soil community feedbacks. Here, we expand and integrate qualitative conceptual models of plant niche and feedback to explore implications of microbial interactions for understanding plant community ecology. At the same time we review the empirical evidence for these processes. We also consider common mycorrhizal networks, and propose that these are best interpreted within the feedback framework. Finally, we apply our integrated model of niche and feedback to understanding plant coexistence, monodominance and invasion ecology.

Perfil metagenômico de solo sob cultivo de cana-de-açúcar com perspectiva na produção de bioenergia

Pós-graduação em Microbiologia Agropecuária - FCAV

Eastern Temperate Forests

Human activity in the last century has led to a substantial increase in nitrogen (N) emissions and deposition. This N deposition has reached a level that has caused or is likely to cause alterations to the structure and function of many ecosystems across the United States. One approach for quantifying the level of pollution that would be harmful to ecosystems is the critical loads approach. The critical load is dei ned as the level of a pollutant below which no detrimental ecological effect occurs over the long term according to present knowledge. The objective of this project was to synthesize current research relating atmospheric N deposition to effects on terrestrial and aquatic ecosystems in the United States and to identify empirical critical loads for atmospheric N deposition. The receptors that we evaluated included freshwater diatoms, mycorrhizal fungi and other soil microbes, lichens, herbaceous plants, shrubs, and trees. The main responses reported fell into two categories: (1) biogeochemical, and (2) individual species, population, and community responses. The range of critical loads for nutrient N reported for U.S. ecoregions, inland surface waters, and freshwater wetlands is 1 to 39 kg N ha-1 y-1. This broad range spans the range of N deposition observed over most of the country. The empirical critical loads for N tend to increase in the following sequence for different life forms: diatoms, lichens and bryophytes, mycorrhizal fungi, herbaceous plants and shrubs, trees. The critical loads approach is an ecosystem assessment tool with great potential to simplify complex scientii c information and effectively communicate with the policy community and the public. This synthesis represents the i rst comprehensive assessment of empirical critical loads of N for ecoregions across the United States.