This paper reviews the current knowledge of microbial processes affecting C sequestration in agroecosystems. The microbial contribution to soil C storage is directly related to microbial community dynamics and the balance between formation and degradation of microbial byproducts. Soil microbes also indirectly influence C cycling by improving soil aggregation, which physically protects soil organic matter (SOM). Consequently, the microbial contribution to C sequestration is governed by the interactions between the amount of microbial biomass, microbial community structure, microbial byproducts, and soil properties such as texture, clay mineralogy, pore-size distribution, and aggregate dynamics. The capacity of a soil to protect microbial biomass and microbially derived organic matter (MOM) is directly and/or indirectly (i.e., through physical protection by aggregates) related to the reactive properties of clays. However, the stabilization of MOM in the soil is also related to the efficiency with which microorganisms utilize substrate C and the chemical nature of the byproducts they produce. Crop rotations, reduced or no-tillage practices, organic farming, and cover crops increase total microbial biomass and shift the community structure toward a more fungal-dominated community, thereby enhancing the accumulation of MOM. A quantitative and qualitative improvement of SOM is generally observed in agroecosystems favoring a fungal-dominated community, but the mechanisms leading to this improvement are not completely understood. Gaps within our knowledge on MOM-C dynamics and how they are related to soil properties and agricultural practices are identified.

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Bacterial and Fungal Contributions to Carbon Sequestration in Agroecosystems

Life on Earth is sustained by a small volume of soil surrounding roots, called the rhizosphere. The soil is where most of the biodiversity on Earth exists, and the rhizosphere probably represents the most dynamic habitat on Earth; and certainly is the most important zone in terms of defining the quality and quantity of the Human terrestrial food resource. Despite its central importance to all life, we know very little about rhizosphere functioning, and have an extraordinary ignorance about how best we can manipulate it to our advantage. A major issue in research on rhizosphere processes is the intimate connection between the biology, physics and chemistry of the system which exhibits astonishing spatial and temporal heterogeneities. This review considers the unique biophysical and biogeochemical properties of the rhizosphere and draws some connections between them. Particular emphasis is put on how underlying processes affect rhizosphere ecology, to generate highly heterogeneous microenvironments. Rhizosphere ecology is driven by a combination of the physical architecture of the soil matrix, coupled with the spatial and temporal distribution of rhizodeposits, protons, gases, and the role of roots as sinks for water and nutrients. Consequences for plant growth and whole-system ecology are considered. The first sections address the physical architecture and soil strength of the rhizosphere, drawing their relationship with key functions such as the movement and storage of elements and water as well as the ability of roots to explore the soil and the definition of diverse habitats for soil microorganisms. The distribution of water and its accessibility in the rhizosphere is considered in detail, with a special emphasis on spatial and temporal dynamics and heterogeneities. The physical architecture and water content play a key role in determining the biogeochemical ambience of the rhizosphere, via their effect on partial pressures of O2 and CO2, and thereby on redox potential and pH of the rhizosphere, respectively. We address the various mechanisms by which roots and associated microorganisms alter these major drivers of soil biogeochemistry. Finally, we consider the distribution of nutrients, their accessibility in the rhizosphere, and their functional relevance for plant and microbial ecology. Gradients of nutrients in the rhizosphere, and their spatial patterns or temporal dynamics are discussed in the light of current knowledge of rhizosphere biophysics and biogeochemistry. Priorities for future research are identified as well as new methodological developments which might help to advance a comprehensive understanding of the co-occurring processes in the rhizosphere.

Rhizosphere: biophysics, biogeochemistry and ecological relevance

Increasing nutrient inputs into terrestrial ecosystems affect not only plant communities but also associated soil microbial communities. Studies carried out in predominantly unmanaged ecosystems have found that increasing nitrogen (N) inputs generally decrease soil microbial biomass; less is known about long-term impacts in managed systems such as agroecosystems. The objective of this paper was to analyze the responses of soil microorganisms to mineral fertilizer using data from long-term fertilization trials in cropping systems. A meta-analysis based on 107 datasets from 64 long-term trials from around the world revealed that mineral fertilizer application led to a 15.1% increase in the microbial biomass (Cmic) above levels in unfertilized control treatments. Mineral fertilization also increased soil organic carbon (Corg) content and our results suggest that Corg is a major factor contributing to the overall increase in Cmic with mineral fertilization. The magnitude of the effect of fertilization on Cmic was pH dependent. While fertilization tended to reduce Cmic in soils with a pH below 5 in the fertilized treatment, it had a significantly positive effect at higher soil pH values. Duration of the trial also affected the response of Cmic to fertilization, with increases in Cmic most pronounced in studies with a duration of at least 20 years. The input of N per se does not seem to negatively affect Cmic in cropping systems. The application of urea and ammonia fertilizers, however, can temporarily increase pH, osmotic potential and ammonia concentrations to levels inhibitory to microbial communities. Even though impacts of fertilizers are spatially limited, they may strongly affect soil microbial biomass and community composition in the short term. Long-term repeated mineral N applications may alter microbial community composition even when pH changes are small. How specific microbial groups respond to repeated applications of mineral fertilizers, however, varies considerably and seems to depend on environmental and crop management related factors.

Long-term effects of mineral fertilizers on soil microorganisms – A review

Nitrous oxide (N2O) is a potent greenhouse gas (GHG) that also depletes stratospheric ozone. Nitrogen (N) fertilizer rate is the best single predictor of N2O emissions from agricultural soils, which are responsible for ∼ 50% of the total global anthropogenic flux, but it is a relatively imprecise estimator. Accumulating evidence suggests that the emission response to increasing N input is exponential rather than linear, as assumed by Intergovernmental Panel on Climate Change methodologies. We performed a metaanalysis to test the generalizability of this pattern. From 78 published studies (233 site-years) with at least three N-input levels, we calculated N2O emission factors (EFs) for each nonzero input level as a percentage of N input converted to N2O emissions. We found that the N2O response to N inputs grew significantly faster than linear for synthetic fertilizers and for most crop types. N-fixing crops had a higher rate of change in EF (ΔEF) than others. A higher ΔEF was also evident in soils with carbon >1.5% and soils with pH <7, and where fertilizer was applied only once annually. Our results suggest a general trend of exponentially increasing N2O emissions as N inputs increase to exceed crop needs. Use of this knowledge in GHG inventories should improve assessments of fertilizer-derived N2O emissions, help address disparities in the global N2O budget, and refine the accuracy of N2O mitigation protocols. In low-input systems typical of sub-Saharan Africa, for example, modest N additions will have little impact on estimated N2O emissions, whereas equivalent additions (or reductions) in excessively fertilized systems will have a disproportionately major impact.

https://www.pnas.org/content/pnas/111/25/9199.full.pdf

Global metaanalysis of the nonlinear response of soil nitrous oxide (N2O) emissions to fertilizer nitrogen

Antibiotic resistance gene abundances associated with antibiotics and heavy metals in animal manures and agricultural soils adjacent to feedlots in Shanghai; China.

The relationship between the fungal: bacterial biomass ratio and the metabolic quotient (qCO2) was studied in three different soils. In addition, the effect of the fungal: bacterial biomass ratio on the relationship between CO2 evolution and the size of the soil microbial biomass was examined. Soil samples were collected from three experimental fields amended with various organic materials (Yatsugatake, Ibaraki, and Tochigi fields). The range of the fungal:bacterial biomass ratio in the Yatsugatake and Ibaraki fields was small (1.54–2.24 and 1.11–1.71, respectively), but it was large in the Tochigi field (1.18–3.75). We found a high negative correlation between this ratio and the metabolic quotient (qCO2=2.10−0.361 (fungal:bacterial biomass ratio), R=−0.851, P<0.01) in the Tochigi field. Therefore, we suggest tha qCO2 decreases with an increase in the fungal:bacterial biomass ratio, which may be due to a higher efficiency of substrate C use by fungal flora in comparison with bacterial flora. In the Yatsugatake and Ibaraki fields, there was a high positive correlation between CO2 evolution and total microbial biomass. In contrast, no correlation was observed between these two parameters in the Tochigi field, probably reflecting the wide range of values for the fungal:bacterial biomass ratio. From the results obtained, we suggest that the fungal: bacterial biomass ratio is an important factor regulating the relationship between CO2 evolution and the size of the microbial biomass.

Effect of fungal to bacterial biomass ratio on the relationship between CO2 evolution and total soil microbial biomass

To evaluate spatial variability of nitrous oxide (N 2 O) emissions and to elucidate their determining factors on a field-scale basis, N 2 O fluxes and various soil properties were evaluated in a 100- x 100-m onion (Allium cepa L.) field. Nitrous oxide fluxes were determined by a closed chamber method from the one-hundred 10- x 10-m plots. Physical (e.g., bulk density and water content), chemical (e.g., total N and pH), and biological (e.g., microbial biomass C and N) properties were determined from surface soil samples (0-0.1 m) of each plot. Geostatistical analysis was performed to examine spatial variability of both N 2 O fluxes and soil properties. Multivariate analysis was also conducted to elucidate relationships between soil properties and observed fluxes. Nitrous oxide fluxes were highly variable (average 331 μg N m -2 h -1 , CV 217%) and were log-normally distributed. Log-transformed N 2 O fluxes had moderate spatial dependence with a range of >75 m. High N 2 O fluxes were observed at sites with relatively low elevation. Multivariate analysis indicated that an organic matter factor and a pH factor of the principal component analysis were the main soil-related determining factors of log-transformed N 2 O fluxes. By combining multivariate analysis with geostatistics, a map of predicted N 2 O fluxes closely matched the spatial pattern of measured fluxes. The regression equation based on the soil properties explained 56% of the spatially structured variation of the log-transformed N 2 O fluxes. Site-specific management to regulate organic matter content and water status of a soil could be a promising means of reducing N 2 O emissions from agricultural fields.

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Spatial variability of nitrous oxide emissions and their soil-related determining factors in an agricultural field.

Effect of vegetations and temperature on microbial biomass carbon and metabolic quotients of temperate volcanic forest soils

An experiment was conducted to examine the accumulation and mobility of heavy metals (Zn and Cu) at different depths in three types of arable soils (Brown Lowland soil, Andosol, and Brown Forest soil) amended with cattle and pig farmyard manures for 5 years Nitric-perchloric acid digestion was performed for the determination of the total amounts of heavy metals, and 01 M hydrochloric acid extraction was performed for the determination of the amounts of soluble heavy metals Results of the soil analysis indicated that pig farmyard manure application resulted in serious contamination of arable soils with Zn and potentially Cu Especially, the Brown Forest soil displayed a high ability to accumulate heavy metals on the soil surface Total-Zn concentration in surface soils was considerably affected by the holding capacity of soluble-Zn traction Although the Andosol amended with pig farmyard manure showed higher concentrations of heavy metals related to the higher ability of retention on a weight basis, the

Accumulation of Zinc and Copper in an Arable Field after Animal Manure Application

A field experiment was conducted to determine N2O concentrations in the soil profile and emissions as influenced by the application of N fertilizers and manure in a typical Japanese Andisol, which had been under a rotation of oat and carrot for the previous 3 years. The treatments include ammonium sulphate (AS), controlled-release fertilizer (CRF) and cattle manure (CM) in addition to a control; all the fertilizers were applied either at 150 kg N ha–1 or 300 kg N ha–1 at the time of sowing carrot. N2O emissions from the soil surface were measured with closed-chamber techniques, while N2O concentrations in the soil profile were measured using stainless steel sampling probes inserted into the soil at depths of 10, 20, 40, 60, 80 and 100 cm. Moreover, soil water potential, soil temperature and rainfall data were also recorded. The results indicated that N2O concentrations in the soil profile were always greater than in the atmosphere, ranging from 0.36 µl N2O-N l–1 to 5.3 µl N2O-N l–1. The relatively large accumulation of N2O in the lower profiles may be a significant source for N2O flux. Taking the changes of soil mineral N into consideration, most emissions of N2O were probably produced from nitrification. The accumulation of N2O in the soil profile and emissions to the atmosphere were differently influenced by the amendments of N fertilizers and manure, being consistently higher in CRF than in CM and AS treatments at the corresponding application rates, but no significant difference existed with respect to the various N sources.

Kazunori Sakamoto

Papers

Effect of fungal to bacterial biomass ratio on the relationship between CO2 evolution and total soil microbial biomass

Spatial variability of nitrous oxide emissions and their soil-related determining factors in an agricultural field.

Effect of vegetations and temperature on microbial biomass carbon and metabolic quotients of temperate volcanic forest soils

Accumulation of Zinc and Copper in an Arable Field after Animal Manure Application

Nitrous oxide concentrations in an Andisol profile and emissions to the atmosphere as influenced by the application of nitrogen fertilizers and manure