Do soil microbes maximize their growth?

Large regions of temperate forest are subject to elevated atmospheric nitrogen (N) deposition which can affect soil organic matter dynamics by altering mass loss rates, soil respiration, and dissolved organic matter production. At present there is no general model that links these responses to changes in the organization and operation of microbial decomposer communities. Toward that end, we studied the response of litter and soil microbial communities to high levels of N amendment (30 and 80 kg ha(-1) yr(-1)) in three types of northern temperate forest: sugar maple/basswood (SMBW), sugar maple/red oak (SMRO), and white oak/black oak (WOBO). We measured the activity of extracellular enzymes (EEA) involved directly in the oxidation of lignin and humus (phenol oxidase, peroxidase), and indirectly, through the production of hydrogen peroxide (glucose oxidase, glyoxal oxidase). Community composition was analyzed by extracting and quantifying phospholipid fatty acids (PLFA) from soils. Litter EEA responses at SMBW sites diverged from those at oak-bearing sites (SMRO, BOWO), but the changes were not statistically significant. For soil, EEA responses were consistent across forests types: phenol oxidase and peroxidase activities declined as a function of N dose (33-73% and 5-41%, respectively, depending on forest type); glucose oxidase and glyoxal oxidase activities increased (200-400% and 150-300%, respectively, depending on forest type). Principal component analysis (PCA) ordinated forest types and treatment responses along two axes; factor 1 (44% of variance) was associated with phenol oxidase and peroxidase activities, factor 2 (31%) with glucose oxidase. Microbial biomass did not respond to N treatment, but nine of the 23 PLFA that formed >1 mol% of total biomass showed statistically significant treatment responses. PCA ordinated forest types and treatment responses along three axes (36%, 26%, 12% of variance). EEA factors 1 and 2 correlated negatively with PLFA factor 1 ( r = -0.20 and -0.35, respectively, n = 108) and positively with PLFA factor 3 ( r = +0.36 and +0.20, respectively, n = 108). In general, EEA responses were more strongly tied to changes in bacterial PLFA than to changes in fungal PLFA. Collectively, our data suggests that N inhibition of oxidative activity involves more than the repression of ligninase expression by white-rot basidiomycetes.

Cropping management practices influence soil phosphorus (P) availability and soil organic matter (SOM) quality. This chapter summarizes the impact of cropping systems and water management on soil phosphorus status and organic matter characteristics after the first full cycle of the 3-year crop rotations. These data indicated that the 3-year crop rotations impacted more on labile P and organic matter fractions and relevant biochemical parameters (i. e. water extractable P and organic matter, mild modified Morgan soil test P, microbial biomass C and P, phosphatase and urease activities). However, these influences were not always consistent and statistically significant (P = 0.1 or 0.05). Generally, irrigation had a greater influence on stable P and organic matter fractions than crop rotations. Continuous analysis of P and SOM from soils after the completion of the second rotation cycle of the 3-year crop rotations would provide more insights on the improvement of soil fertility and biochemical quality for potato production by crop rotations.

Understanding controls on C stored in soil organic matter (SOM) is of critical importance to models of biospheric C sequestration. Although ecosystem C models assume a strong relationship between plant litter inputs and soil C accumulation, there is little experimental evidence to support this assumption. The Detritus Input and Removal Treatments (DIRT) experiment at Harvard Forest was designed to assess how rates and sources of plant litter inputs control the accumulation and dynamics of organic matter in soils across decadal time scales. Carbon and SOM quantity and quality were measured in O horizon and mineral soil in five treatments: control, double litter, no litter, no roots, and no inputs. After 20 yr of manipulation, doubling litter inputs did not increase bulk soil C or N content, light or heavy fraction pools of C, or measures of labile C. However, the activities of two key enzymes (β‐glucosidase and phosphomonoesterase) increased 30% with litter additions. Exclusion of either aboveground litter or root inputs resulted in sharp declines in O‐horizon C and N but smaller decreases in total mineral soil C and N. However, decreases in light fraction C and soil respiration were significant in removal treatments. Litter exclusion resulted in an 18% decline in total profile mineral soil C, whereas root exclusion resulted in a 9% decline, indicating the importance of aboveground inputs to long‐term C pools. Soil C pools in this forest do not respond linearly or immediately to aboveground or belowground litter inputs, and thus efforts to sequester C by managing productivity and associated litter inputs will probably not result in increased C storage in short time frames.

Low nitrogen (N) availability in the Arctic and Subarctic constrains plant productivity, resulting in low litter inputs to soil. Increased N availability and litter inputs as a result of climate change, therefore, have the potential to impact the functioning of these ecosystems. We examined plant and microbial responses to chronic inorganic N (5 g m−2 year−1) and/or litter (90 g m−2 year−1), supplied during three growing seasons. We also compared the response to more extreme additions, where the total cumulative additions of N (that is, 15 g m−2) and litter (that is, 270 g m−2) were concentrated into a single growth season. Plant productivity was stimulated by N additions and was higher in the extreme addition plots than those with chronic annual additions. Microbial community structure also differed between the chronic and extreme plots, and there was a significant relationship between plant and microbial community structures. Despite differences in microbial structure, the field treatments had no effect on microbial growth or soil C mineralization. However, gross N mineralization was higher in the N addition plots. This led to a lower ratio of soil C mineralization to gross N mineralization, indicating microbial targeting of N-rich organic matter (“microbial N-mining”), likely driven by the increased belowground C-inputs due to stimulated plant productivity. Surprisingly, aboveground litter addition also decreased ratio of soil C mineralization to gross N mineralization. Together, these results suggest that elevated N availability will induce strong responses in tundra ecosystems by promoting plant productivity, driving changes in above- and belowground community structures, and accelerating gross N mineralization. In contrast, increased litter inputs will have subtle effects, primarily altering the ratio between C and N derived from soil organic matter.

Soil nitrate content and organic matter are two important parameters that determine the amount of nitrogen available for plant growth. The goal of this study was to develop soil nitrate and organic matter sensing techniques, since traditional methods of determining soil organic matter and nitrate content are tedious, time-consuming, and expensive. Studies conducted at UC Davis have clearly shown that unmistakable nitrate peaks exist in the mid-infrared (MIR) spectra of soil pastes. In particular, the peak located at 1,390 cm−1 wave number is nitrate sensitive. However, this peak is broad and is influenced by carbonate/bicarbonate and organic matter peaks, which exist in the vicinity of the nitrate peak. Using wavelet analysis, we were able to isolate a single wave number, 1,350 cm−1, at which these interferences were minimal. However, if the soil contained a large amount of carbonates, a second wavelength located at 1,500 cm−1 was necessary to obtain a unique calibration equation. Using the absorbance values at these two wave numbers, nitrate-N concentrations of 14 different soils (6 Californian soils and 8 Israeli ones) could be determined using a single calibration curve with a coefficient of multiple determination (R 2 value) of 0.98. When only six Californian field soils were considered, the calibration equation resulted in an R 2 value of 0.95 with a standard error of 8 ppm. Moreover, preliminary tests indicated that soil organic matter can also be determined using MIR spectral response at two wave numbers (1,383 and 1,452 cm−1). The R 2 value for soil organic matter determination was 0.95 and the standard error was 0.25%. These results indicate that both soil nitrate content and organic matter can be determined using just a few wavelengths in the MIR region with sufficient accuracy for use in site-specific nutrient management.

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

Microbes are the engines for nutrient cycling in the soil, playing an important role in maintaining soil quality and agricultural production, but it is unclear how soil microbial communities respond to continuously mono-cropped cucumber under greenhouse conditions. High-throughput sequencing of the bacterial 16S rRNA and fungal 18S rRNA gene fragments was conducted to compare the variations of microbial communities within greenhouse mono-cropped cucumber systems across 8, 15, and 22 cultivation years with new-build greenhouse of cucumber cultivated just for one season (1 year). Results showed that soil pH and fungal diversity significantly decreased, whereas soil EC, organic matter (OM), and nutrient concentrations (total nitrogen (N), nitrate N (NO3−-N), total and available phosphorus, and potassium) significantly increased when cucumber was mono-cropped for 8 or more years. The mono-cropped cucumber for 8 or more years reduced the relative abundance of the dominant bacterial phyla Actinobacteria, but increased the abundances of Acidobacteria and Firmicutes significantly compared with the cucumber planted for one season. Moreover, the predominant fungal phylum Ascomycota increased significantly with increasing cultivation years of cucumber. Soil OM and NO3−-N are most important factors to drive the variation of soil bacterial community, while soil pH, OM, and NO3−-N markedly responded to the changes of the fungal community in the greenhouse cucumber mono-cropped system. This research provides insights into the response of microbial communities to continuous mono-cropping cucumber, and this has implications on the sustainability of such intensive production systems.

The terrestrial soil organic matter (SOM) pool size depends on the balance between SOM formation and stabilization of decomposing plant litter relative to mineralization as CO2.  Decomposition and mineralization processes are to large extents mediated by microbial decomposer communities. In addition, labile fractions released by decomposing litter can be stabilized in mineral associations (MAOM). High latitude ecosystems are particularly affected by global warming. Increasing temperatures can stimulate litter decomposition and increase nutrient mineralization, thereby increasing nutrient (e.g. nitrogen) availability for plants allowing higher productivity and subsequent plant organic matter inputs. On the other hand, if warming accelerates SOM decomposition stronger than formation processes it can cause large carbon and nutrient losses.Tracing 13C/15N labelled above-ground litter we aimed to disentangle if soil warming changes the balance between litter derived SOM formation through microbial communities, over particulate organic matter (POM) and MAOM stabilization across a decadal geothermal soil warming gradient (from ambient up to +5 °C) in a grassland in Iceland. In addition, we added three levels of inorganic N to disentangle potential direct warming from indirect (over plant feedbacks) effects of increased warming on SOM dynamics.  We found that over the course of two years warming accelerated litter decomposition rates and litter-derived carbon turnover by the microbial community,  and we could recover more litter-derived carbon recovered in particulate organic matter (POM) nor MAOM. Nitrogen additions triggered a faster decomposition of structural above-ground litter compounds, but did not influence carbon turnover in different soil fractions. On the other, hand we found that overall the absolute amount of soil carbon decreased in response to warming. We therefore conclude that direct warming not only increased SOM formation, but also decomposition and mineralization processes, and – at least in the studied grassland – plant inputs may not have counterbalanced warming induced losses.   

Priming effects of Aporrectodea caliginosa on young rhizodeposits and old soil organic matter following wheat straw addition

<p>Permafrost-affected mineral soils store large amounts of the soil organic matter (SOM) in high-latitude regions. These regions are large terrestrial carbon reservoirs and highly vulnerable to the global climate change. Global warming will cause rapid permafrost thaw and potentially accelerate decomposition of SOM. High-latitude regions, such as boreal and arctic ecozones, are regularly affected by wildfires with increasing intensity and frequency caused by global climate change. Wildfires produce pyrogenic organic matter (PyOM) during incomplete combustion of the fuel biomass. Little is known about the cycling of SOM and especially PyOM in permafrost-affected mineral soils, which limits our understanding of potential shifts in cycling and interaction with the soil mineral phase over time.</p><p>Here we study the fate of highly <sup>13</sup>C-labelled (2-3 atm%) ryegrass organic matter and PyOM from the same feedstock (pyrolyzed at 400°C for 4h) during two years of in-situ incubation in boreal forest mineral soils. Soil cores (10 cm length and 6 cm diameter) were buried in the upper 10 cm of mineral soils under continuous and discontinuous to sporadic permafrost conditions at eleven forest locations (with six replicates) in Northern Canada. At the same locations, litter bags (green and rooibos teabags) were buried and soil temperatures were recorded. The soils cores were separated in three depth (0-3, 3-6 and 6-10 cm) to trace the vertical allocation of the applied organic matter. Density and particle fractionations are applied to identify mineral interactions of the ryegrass and pyrolyzed organic matter.</p><p>Preliminary <em>δ</em><sup>13</sup>C results from the soil cores show a more extensive vertical allocation of ryegrass organic matter and PyOM in continuous permafrost-affected soils within the cores. This can be associated to the importance of freeze and thaw cycles for the carbon dynamics of permafrost-affected mineral soils. Tracing the labelled ryegrass organic matter and PyOM offers not only the opportunity to quantify the translocated fraction but also the decomposed proportion of the freshly added organic matter and thus understand short-term carbon dynamics. Preliminary results from the litter bags indicate a larger mass loss of slow cycling woody organic matter (rooibos tea) in discontinuous to sporadic permafrost-affected mineral soils, while larger mass losses of fast cycling organic matter (green tea) were observed in continuous permafrost-affected soils. These initial results indicate a complex cycling of organic matter in soils under different permafrost conditions.</p>

Assessing the spatial distribution of organic matter and total nitrogen in soil is essential for management and optimum utilization of fertilizers. Therefore, the present field experiment was conducted to evaluate the impact of different planting pattern arrangements on the spatial distribution of soil total nitrogen and organic matter content under a maize/soybean strip relay intercropping system. The planting was arranged in a manner such that soil sampling could be done from continuous maize/soybean relay strip intercropping (MS1), maize/soybean relay strip intercropping in rotation (MS2), traditional maize/soybean intercropping (MS3), sole maize (M), sole soybean (S), and fallow land (FL) from 2018 to 2020. The results showed significant variations for soil organic matter and total nitrogen content under different planting pattern arrangements of maize and soybean in the strip relay intercropping system. Across all systems, the highest soil organic matter (29.19 g/kg) and total nitrogen (10.19 g/kg) were recorded in MS2. In contrast, the lowest soil organic matter (1.69 g/kg) and total nitrogen (0.64 g/kg) were observed in FL. Soil organic matter and total nitrogen in MS2 increased by 186.45% and 164.06%, respectively, when compared with FL. Soil organic matter and total nitrogen in MS2 increased by 186.45% and 164.06%, respectively, when compared with FL. Furthermore, under MS2, the spatial distribution of soil organic matter was higher in both maize and soybean crop rows as compared with other cropping patterns, whereas the soil total nitrogen was higher under soybean rows as compared with maize in all other treatment. However, correlation analysis of the treatments showed variations in organic matter content. It can be concluded that different planting patterns can have varying effects on soil organic matter and total nitrogen distribution under the strip relay intercropping system. Moreover, it is recommended from this study that MS2 is a better planting pattern for the strip relay intercropping system, which can increase the spatial distribution of soil organic matter and total nitrogen, thereby improving soil fertility, C:N ratio, and crop production. This study will serve as a foundation towards the scientific usage of chemical fertilizers in agricultural sector.

In many soils, the content and quality of organic matter (OM) control water-stable aggregation, which in turn preserves soil surface integrity. The effects of management practices on soil OM and aggregation remain to be determined for certain soils and climatic conditions. We assessed the effects of eight management systems involving two crop sequences: [barley ( Hordeum vulgare L.) monoculture (M) and barley in rotation (R) with a forage mix of red clover ( Trifolium pratense L.) and timothy ( Phleum pratense L. ‘Champ’)], two fall tillage [moldboard plowing (MP) and chisel plowing (CP)] and two nutrient sources [liquid dairy manure (LDM) and mineral fertilizers (MIN)] on soil aggregation and OM fractions of a silty clay Humic Gleysol. Soil samples from the 0–7.5 cm layer were taken periodically during 7 yr, and the total C and N, microbial biomass C (MBC) and carbohydrate (AHC) contents, alkaline phosphatase activity (APA), and water-stable aggregation were determined. By the 7th yr, initial total C and N contents of the surface soil had increased by 35 and 45%, respectively, in R-CP-LDM. They were slightly increased in R-CP-MIN an d R-MP-LDM, whereas they decreased by an average of 19% in R-MP-MIN and all monoculture plots. Increases in C contents were attributed to higher annual C inputs from forage residues and LDM, less frequent tillage in the rotation, and shallower tillage with CP. The MBC, APA, AHC and aggregation generally responded faster and to a greater degree to conservation management practices than total C and N. Overall, conservation tillage and manure applications resulted in greater improvement in surface soil conditions when used in a rotation system rather than in a monoculture. The rapid rate of changes in soil properties suggests that the surface quality of this cold silty clay soil can be improved relatively quickly with selected management combinations. Key Words: Cropping systems, total soil C, microbial biomass, carbohydrate, alkaline phosphatase, soil aggregation, liquid dairy manure, reducted tillage, rotations

Understanding how photosynthetic carbon is delivered into the soil system through rhizodeposition is of utmost importance in a changing world, as it represents an essential part of carbon cycling in soils. The plant economic space (PES) is a theoretical model representing plant strategies resource acquisition strategies based on two independent trade-offs: (i) resource acquisition vs conservation and (ii) exploration outsourcing (cooperation with mycorrhizal fungi) vs do-it-yourself. The PES is known to be related to a set of chemical and morphological traits, but some physiological traits such as rhizodeposition lack attention because they are harder to measure, while they are crucial for our understanding of resource allocation strategies and their linkages to ecosystem processes. For example, gross rhizodeposition can represent more than 40% of belowground carbon allocation.We aimed to provide more insights on the relationship between rhizodeposition and the two dimensions of the PES, with a focus on the second axis, as arbuscular mycorrhizal fungi (AMF) are supposed to play an essential role of sink in the sink/source model of rhizodeposition. To do so, we grew 15 grassland plant species with contrasting resource acquisition strategies in a 3-month long pot experiment, with or without litter inputs. By means of 13C pulse-labelling, we traced carbon fluxes from recent photosynthates in major pools, including above-and belowground parts of the plant, but also in microbial biomass and microbial functional groups using PLFAs, soil organic matter, and soil respiration. We also measured net and gross nitrogen mineralisation.We hypothesise that (i) rhizodeposition will be strongly link to the fast-slow gradient, fast-growing species being associated with higher rhizodeposition rates, but (ii) rhizodeposition will also show significant relationships with the exploration gradient, as tighter plant-soil biota association – including more AMF colonisation – could promote higher rhizodeposition rate, because of sink mechanisms. Higher rhizodeposition should also be associated (iii) with a shift in microbial community toward functional groups more dependant to plant carbon such as AMF and Gram negative bacteria, as well as (iv) higher soil respiration and nitrogen mineralisation.

Four biochar types, produced by slow pyrolysis of poultry litter (PL) and pine chips (P) at 400 or 500 °C, were added to two adjacent soils with contrasting soil organic matter (SOM) content (8.9 vs. 16.1 g C kg−1). The N mineralization rate was determined during 14‐week incubations and assessments were made of the microbial biomass C, dehydrogenase activity, and the microbial community structure (PLFA‐extraction). The addition of PL biochars increased the net N mineralization (i.e., compared to the control treatment) in both soils, while for treatments with P biochars net N immobilization was observed in both soils. Increasing the pyrolysis temperature of both feedstock types led to a decrease in net N mineralization. The ratio of Bacterial to Fungal PLFA biomarkers also increased with addition of biochars, and particularly in the case of the 500 °C biochars. Next to feedstock type and pyrolysis temperature, SOM content clearly affected the assessed soil biological parameters, viz. net N mineralization or immobilization, MBC and dehydrogenase activity were all greater in the H soil. This might be explained by an increased chance of physical contact between the microbial community activated by SOM mineralization upon incubation and discrete biochar particles. However, when considering the H soil's double C and N content, these responses were disproportionally small, which may be partly due to the L soil's, somewhat more labile SOM. Nonetheless, increasing SOM content and microbial biomass and activity generally appears to result in greater mineralization of biochar. Additionally, higher N mineralization after PL addition to the H soil with lower pH than the L soil can be due to the liming effect of the PL biochars.

Comparative organic geochemistries of soils and marine sediments