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Humic substances interfere with detection of pathogenic prion protein

Studies examining the persistence of prions (the etiological agent of transmissible spongiform encephalopathies) in soil require accurate quantification of pathogenic prion protein (PrP TSE ) extracted from or in the presence of soil particles. Here, we demonstrate that natural organic matter (NOM) in soil impacts PrP TSE detection by immunoblotting. Methods commonly used to extract PrPTSE from soils release substantial amounts of NOM, and NOM inhibited PrPTSE immunoblot signal. The degree of immunoblot interference increased with increasing NOM concentration and decreasing NOM polarity. Humic substances affected immunoblot detection of prion protein from both deer and hamsters. We also establish that after interaction with humic acid, PrP TSE remains infectious to hamsters inoculated intracerebrally, and humic acid appeared to slow disease progression. These results provide evidence for interactions between PrPTSE and humic substances that influence both accurate measurement of PrP TSE in soil and disease transmission.

Soil Biology and Biochemistry

Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO 2 Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO 2 did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.

Nevada

Soil fluxes of methane, nitrous oxide, and nitric oxide from aggrading forests in coastal Oregon

Soil exchanges of greenhouse and other gases are poorly known for Pacific Northwest forests where gradients in nutrient availability and soil moisture may contribute to large variations in fluxes. Here we report fluxes of methane (CH 4 ), nitrous oxide (N 2 O), and nitric oxide (NO) over multiple seasons from three naturally N-rich, aggrading forests of coastal Oregon, USA. Mean methane uptake rates (3.2 mg CH 4 m −2 d −1 ) were high compared with forests globally, negatively related to water-filled pore space (WFPS), but unrelated to N availability or temperature. Emissions of NO (6.0 μg NO–N m −2 h −1 ) exceeded N 2 O (1.4 μg N 2 O–N m −2 h −1 ), except when WFPS surpassed 55%. Spatial variation in NO fluxes correlated positively with soil nitrate concentrations (which generally exceeded ammonium concentrations, indicating the overall high N status for the sites) and negatively with soil pH, and at one site increased with basal area of N 2 -fixing red alder. Combined NO and N 2 O emissions were greatest from the site with highest annual net N mineralization and lowest needle litterfall C/N. Our findings of high CH 4 uptake and NO/N 2 O ratios generally >1 most likely reflect the high porosity of the andic soils underlying the widespread regenerating forests in this seasonally wet region.

Oregon

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem

Elevated nitrogen (N) deposition due to increased fossil fuel combustion and agricultural practices has altered global carbon (C) cycling. Additions of reactive N to N-limited environments are typically accompanied by increases in plant biomass. Soil C dynamics, however, have shown a range of different responses to the addition of reactive N that seem to be ecosystem dependent. We evaluated the effect of N amendments on biogeochemical characteristics and microbial responses of subalpine forest organic soils in order to develop a mechanistic understanding of how soils are affected by N amendments in subalpine ecosystems. We measured a suite of responses across three years (2011–2013) during two seasons (spring and fall). Following 17 years of N amendments, fertilized soils were more acidic (control mean 5.09, fertilized mean 4.68), and had lower %C (control mean 33.7% C, fertilized mean 29.8% C) and microbial biomass C by 22% relative to control plots. Shifts in biogeochemical properties in fertilized plots were associated with an altered microbial community driven by reduced arbuscular mycorrhizal (control mean 3.2 mol%, fertilized mean 2.5 mol%) and saprotrophic fungal groups (control mean 17.0 mol%, fertilized mean 15.2 mol%), as well as a decrease in N degrading microbial enzyme activity. Our results suggest that decreases in soil C in subalpine forests were in part driven by increased microbial degradation of soil organic matter and reduced inputs to soil organic matter in the form of microbial biomass.

Soil Biology and Biochemistry

Extent of localized tree mortality influences soil biogeochemical response in a beetle-infested coniferous forest

Recent increases in the magnitude and occurrence of insect-induced tree mortality are disruptingevergreen forests globally. To resolve potentially conflicting ecosystem responses, we investigatedwhether surrounding trees exert compensatory effects on biogeochemical signatures following beetleinfestation. To this end, plots were surveyed within a Colorado Rocky Mountain watershed that expe-rienced beetle infestation almost a decade prior and contained a range of surrounding tree mortality(from 9 to 91% of standing trees). Near-surface soil horizons under plot-centered live (green) and beetle-killed (grey) lodgepole pines were sampled over two consecutive summers with variable moistureconditions. Results revealed that soil respiration was 18e28% lower beneath beetle-infested trees andcorrelated to elevated dissolved organic carbon aromaticity. While certain edaphic parameters includingpH and water content were elevated below grey compared to green trees regardless of the mortalityextent within plots, other biogeochemical responses required a higher severity of surrounding mortalityto overcome compensatory effects of neighboring live trees. For instance, C:N ratios under grey treesdeclined with increased severity of surrounding tree mortality, and the proportion of ammonium dis-played a threshold effect with pronounced increases after surrounding tree mortality exceeded ~40%.Overall, the biogeochemical response to tree death was most prominent in the mineral soil horizonwhere tree mortality had the largest affect on carbon recalcitrance and the enrichment of nitrogenspecies. These results can aid in determining when and where nutrient cycles and biogeochemicalfeedbacks to the atmosphere and hydrosphere will be observed in association with this type of ecological disturbance.

Rocky Mountain Watershed

Plant and microbial biomarkers suggest mechanisms of soil organic carbon accumulation in a Mojave Desert ecosystem under elevated CO2

We investigated how properties of soil organic matter (SOM) were altered after 10 years exposure to elevated atmospheric CO 2 concentration ([CO 2 ]) in a Mojave Desert ecosystem, using plant and microbial biomarkers. We focused on roles of Larrea tridentata , the dominant evergreen shrub which form islands of fertility, and biological soil crusts which have extensive cover in plant interspace. Soils to 5 cm in depth were collected under L. tridentata and plant interspace, and biological soil crusts to 0.5 cm in depth under three cover types, Pleuraphis rigida , a C 4 grass, shrubs and plant interspace. Soil organic carboncontents were not significantly different between elevated and ambient [CO 2 ]. However, significantly higher abundance of n -alkanes, a major constituent of foliage wax material, occurred in the elevated compared to ambient [CO 2 ] plots in the soils collected under L. tridentata , but no such difference was found in the soils at plant interspace or the biological soil crusts. There was no significant difference in abundance of microbial phospholipid fatty acids between the CO 2 treatments in the soils of either cover types. However, neutral lipid fatty acid abundance was significantly higher under elevated than ambient [CO 2 ] in the soils under L. tridentata , whereas no such significant difference was observed at plant interspace. These results emphasize important roles of the dominant shrubs in SOM formation under elevated [CO 2 ] in arid ecosystems. Elevated [CO 2 ] stimulated growth of L. tridentata in wet years, and aboveground litter deposition via senescence contributed to SOM formation in islands of fertility. In addition, elevated [CO 2 ] stimulated soil microbial turnover rates in rhizosphere of L. tridentata , which left more soil microbial necromass, a major SOM source. We concluded that responses of dominant shrubs to elevated [CO 2 ] can stimulate SOM formation in arid ecosystems, but biological soil crusts may have limited capacity.

Soil Biology and Biochemistry

Exclusion of small mammals and lagomorphs invasion interact with human-trampling to drive changes in topsoil microbial community structure and function in semiarid Chile

Species losses and additions can disrupt the relationship between resident species and the structure and functioning of ecosystems. Persistent human-trampling, on the other hand, can have similar effects through the disruption of biocrusts on surface soils of semiarid systems, affecting soil stability and fixation of carbon and nitrogen. Here, we tested the interactive and synergistic impacts of the exclusion of native mammalian herbivores and the effects of introduced lagomorphs in a semiarid thorn scrub ecosystem, where soils were subjected to two different trampling intensities (i.e., trampled and non-trampled). We postulated that because of their differential habitat use and fossorial activities, with respect to native small mammals, lagomorphs would have strong negative effects on soil structure, biocrust cover, and biocrust bacterial community structure. Our expectations were that changes in biocrust cover in response to trampling where native mammals were excluded, but exotic lagomorphs were present, will spread their impacts on soil chemical and physical features. To test our hypotheses, we measured changes in soil biogeochemical properties in four experimental plots where lagomorphs (L)/small mammals (SM) were experimentally manipulated to exclude them from the plots (−), or let them be present (+). The experimental combinations monitored were: -L/+SM, -L/-SM, +L/+SM, and +L/-SM. Results showed that human-trampling disturbance interacted with the loss of native small mammals and the presence of non-native lagomorphs to cause large changes on biological (i.e., biocrust cover, bacterial and nifH genes abundance), physical (i.e., soil moisture and soil stability) and chemical (i.e., TC and TN) soil features. The relative impacts of trampling disturbance on biological and physicochemical features were strongly influenced by the presence of non-native lagomorphs. For example, larger decreases in biocrust cover and bacterial abundance were observed in treatments without lagomorphs (-L/+SM; -L/-SM). In turn, losses of biocrust cover, in addition to trampling, determined decreases in soil stability in all treatments. These results suggest that non-native lagomorphs surpass the effects of the loss of native small mammals in reducing soil quality and productivity. Therefore, human-trampling has the potential to convert low disturbed soils, as those observed in non-trampled soils in treatments -L/+SM, -L/-SM into poor soils with low biocrusts cover and concomitant low stability, as observed in +L/+SM; +L/-SM treatments. These findings agree with previous observations that different components of global change act in synergic ways in fragile, water-limited environments. Because biological invasions and soil surface disturbance are becoming widespread in dryland regions globally, understanding the long-term consequences of these interactions is essential.

Fray Jorge National Park

Long-term nitrogen addition shifts the soil nematode community to bacterivore-dominated and reduces its ecological maturity in a subalpine forest

Nitrogen deposition from anthropogenic sources is a global problem that reaches even the most remote ecosystems. Responses belowground vary by ecosystem, and have feedbacks to geochemical processes, including carbon storage. A long-term nitrogen addition study in a subalpine forest has shown carbon loss over time, atypical for a forest ecosystem. Loss of microbial biomass is likely linked to lower soil carbon, but the mechanism behind this is still unknown. One possible explanation is through increased turnover due to grazing by soil fauna. Because nematodes occupy many trophic levels and are sensitive to trophic and environmental changes, assessing their communities helps reveal belowground responses. In this study, we tested the hypothesis that long-term nitrogen fertilization affects nematode community structure and maturity beneath coniferous forests in the Rocky Mountains, indicating a faster cycling, bacterial-driven system. We identified and enumerated nematodes by trophic group and family from experimental plots. Total nematode abundance was 40–96% greater in fertilized plots compared to the control, but richness, diversity, and ecological maturity were lower. The differences in abundance were driven by opportunistic bacterivores (e.g., Rhabditidae) and plant parasites (e.g., Tylenchidae), which made up 23 and 13% of the community in fertilized compared to 7 and 5% in control plots, respectively. Nematode maturity indices showed that the nematode food webwas enriched (indicating high nutrient/resource status) and structured (all trophic levels present, including long-lived predators) in both treatments, but significantly more enriched in the fertilized treatment. Nonmetric multidimensional scaling of the relative abundance of nematode families demonstrated that nematode community composition differed between treatments, driven largely by opportunistic bacterivores (e.g., Rhabditidae) in the fertilized plots. The mechanism of the aboveground–belowground link between nitrogen deposition and nematode community composition is likely through increased microbial turnover, and sustained high-quality food for microbial grazing nematodes.

Soil Biology and Biochemistry

Biological and mineralogical controls over cycling of low molecular weight organic compounds along a soil chronosequence

Low molecular weight organic compounds (LMWOC) represent a small but critical component of soil organic matter (SOM) for microbial growth and metabolism. The fate of these compounds is largely under microbial control, yet outside the cell, intrinsic soil properties can also significantly influence their turnover and retention. Using a chronosequence representing 1200 ka of pedogenic development, we compared physicochemical vs biological controls on the turnover and retention of fast-cycling carbon (C), e.g. glucose (GLU) and p-hydroxybenzoic acid (PHBA). Along the chronosequence, we observed mineralogical gradients whereby amorphous constituents were greatest in intermediate-aged sites, while older sites demonstrated soils with more ordered and less reactive mineralogy. Soil microbial community composition varied along the soil chronosequence and we observed reductions in total biomass and fungal biomass from younger to older sites, but this did not affect the turnover of LMWOC. Microbial utilization of LMWOC was substrate- and soil-dependent; amorphous Fe and Al oxides reduced the respiration of PHBA but respiration from glucose remained less affected. Variation in soil mineralogy did not significantly alter recovery of PHBA within microbial biomass or fungal vs. bacterial biomarkers, suggesting that reduced respiration of the phenolic resulted from direct mineral interaction with ionizable functional groups rather than changes to microbial allocation of PHBA. We conclude patterns of soil carbon storage observed across chronosequences are moderated by mineralogical effects on microbial access to LMWOC, independent of variation in microbial community composition. Keywords: 13C; Glucose; Microbial biomass C; Organo-mineral interactions; p-Hydroxybenzoic acid; Selective dissolution mineralogical analyses

Soil Biology and Biochemistry

Multiple mechanisms determine the effect of warming on plant litter decomposition in a dryland

In drylands, where soil fertility is typically low, plant litter decomposition provides particularly critical carbon and nitrogen inputs into soil. Although climate change is projected to increase the already large global extent of drylands, it is unknown how warmer temperatures will affect core ecosystem processes, such as plant litter decomposition, in these systems. To address this key unknown, we conducted a litterbag study in a long-term dryland warming experiment in southeastern Utah, USA. Unexpectedly, we did not find an overall effect of warming on leaf litter mass loss over time. Instead, our results indicated both positive and negative effects of warming on mass loss which offset one another. In particular, our findings suggested that a warming-induced degradation of biological soil crusts (soil surface community of mosses, lichens, and/or cyanobacteria that live in drylands worldwide) increased soil-litter mixing, thereby accelerating decomposition. Results also suggested that warming-induced decreases in litter moisture slowed decomposition. In addition to assessing mass loss, we found that warming lowered the carbon-to-nitrogen ratio of the decomposing litter. These results showed that warming did not alter the total litter mass-loss rates in this ecosystem, but that decomposition patterns were affected through more nuanced changes to both the biological and physical environment of dryland soils.

Utah

Warming and microbial uptake influence the fate of added soil carbon across a Hawai'ian weathering gradient

Tropical forest soils contain some of the largest carbon (C) stocks on Earth, yet the effects of warming on the fate of fresh C entering tropical soils are still poorly understood. This research sought to understand how the fate of fresh C entering soils is influenced by warming, soil weathering status, and C chemistry. We hypothesized that compounds that are quickly incorporated into microbial biomass (i.e., greater C use efficiency [CUE]) subsequently have longer-term (255 days) retention in soil. We also hypothesized that relatively weathered soils with greater sorptive capacity also retain more fresh C in the short and longer-terms, and that C in these soils is more resistant to weathering loss compared with less weathered soils. We tested these hypotheses by adding two 13 C-labeled compounds (glucose and glycine) to three tropical forest soils from a weathering gradient in Hawai'i, and then incubating soils at ambient (16 °C), +5 °C, and +10 °C for 255 days. We found that 255-day 13 C retention in mineral soil across sites and temperatures was best predicted by two factors: initial retention of 13 C in mineral soil and initial microbial 13 CUE (Adjusted R 2 = 0.78). Carbon compound type influenced 13 C initial retention, with greater glucose- 13 C retention versus glycine- 13 C retention in mineral soils and microbial biomass, corresponding to greater glucose- 13 C retention in soil at 255 days. Warming had a negative longer-term effect on the retention of 13 C only in the least-weathered soil, supporting our hypothesis. These results show that initial retention of fresh C in soils via mineral sorption and microbial uptake is a strong predictor of longer-term retention, indicating that immediate C losses are a major hurdle for soil C storage. Also, retention of fresh C appears most sensitive to warming in less-weathered tropical soils, supporting the idea that mineral sorption may provide some protections against warming. Understanding the interaction between soil sorptive properties and warming for C cycling could improve predictions of forest-climate feedbacks for tropical regions.

Soil Biology and Biochemistry

Mechanisms for retention of low molecular weight organic carbon varies with soil depth at a coastal prairie ecosystem

Though primary sources of carbon (C) to soil are plant inputs (e.g., rhizodeposits), the role of microorganisms as mediators of soil organic carbon (SOC) retention is increasingly recognized. Yet, insufficient knowledge of sub-soil processes complicates attempts to describe microbial-driven C cycling at depth as most studies of microbial-mineral-C interactions focus on surface horizons. We leveraged a well-studied paleo-marine terrace (90 ka) located near Santa Cruz, CA, to characterize the short-term (days to weeks) and intermediate-term (months to years) fate of two low molecular weight organic carbon. compounds at three depths in the soil profile (∼25 cm, A horizon; ∼75 cm A/B transition; and ∼125 cm, B horizon). We employed isotopically-labeled glucose (GLU) and oxalic acid (OXA) to represent two common classes of rhizodeposits: carbohydrates and organic acids. Using a combination of laboratory (9 d) and field (490 d) incubations, we traced the fate of GLU-C and OXA-C through dissolved-, metal-associated-, and microbially-respired CO2 and bulk SOC pools. Our results suggest new SOC retention (i.e., defined as 13C label identified in solid or aqueous fractions) over intermediate time frames (490 d) is correlated with patterns in short-term (9 d) cycling dynamics, which in turn is related to the theoretical efficiency by which microorganisms process each substrate. For all horizons (A, A/B, and B) GLU-C was converted to CO2 more quickly than OXA-C with modeled decomposition rates ∼2–4 times faster for GLU depending on microbial density (higher in A than B horizon). The faster decomposition rates of GLU-C increased fractional recovery (0.399 ± 0.026 to 0.504 ± 0.030 for GLU-C) compared to OXA-C (0.035 ± 0.003 to 0.127 ± 0.010) among all horizons in our field experiment (490 d). Though the overall proportion of GLU-C recovered in solid fractions did not vary significantly with horizon, based on 13C recovered in aqueous fractions the apparent mechanism for retention did. After the 9-d laboratory incubation, fractional recovery for GLU-C among C pools associated with microbial biomass was almost 20× higher than OXA-C (0.192 versus 0.010, respectively across all horizons). More than a year later, 43–46% of GLU-C retained in the field incubation was extractable with a neutral salt (representing a pool of soil C residing within or available to microbial biomass) among A and A/B horizons, while only 6% of retained GLU-C was similarly extractable in the B horizon. Thus, it appears among depths with higher microbial density (A, A/B horizons), anabolic recycling is the most likely process contributing to the persistence of glucose C, whereas abiotic sinks contributed more to intermediate-term stability for GLU-C in the B horizon. By contrast, most OXA-C was lost, presumably as CO2, over the short-term from the A and A/B horizons (fractional recovery: 0.136 ± 0.011 and 0.091 ± 0.002, respectively). However, though substantially lower than GLU-C recovered at the conclusion of our field experiment, the fraction of oxalic acid C retained in the B horizon over both short- (0.72 ± 0.037) and intermediate-time (0.127 ± 0.010) frames was several-fold higher than for overlying horizons. The specific process(es) (e.g., more efficient microbial utilization, metal-organic complexation, direct adsorption to the mineral matrix, etc.) contributing to higher retention for OXA-C at depth are discussed but remain unresolved.

Soil Biology and Biochemistry

The influence of soil development on the depth distribution and structure of soil microbial communities.

Although it has been shown that the interaction of climate and time shape the dynamics of soil organic matter (SOM) storage and preservation in soil, the role of soil microbial communities in this dynamic remains unclear. Microbial communities are present throughout soil profiles and likely play critical roles in SOM and nutrient cycling, however the influence of other factors such as soil development (i.e., age) and the composition SOM on microbial community variation with depth has yet to be quantified. Improving our understanding of the relationship between soil development, soil depth, and microbial communities may provide insight to the critical role they play in cycling and preservation of SOM, as well as more mechanistic predictions of the response of soil communities to change, such as landscape-scale changes in available moisture or temperature regimes. Here we compare soils spanning a soil age by climate gradient (i.e., climo-chronosequence) to better understand the mechanisms which influence soil microbial community structure and the molecular composition of SOM. While we observed little depth-dependence in metrics of microbial community structure (i.e., composition, diversity, dissimilarity) across the range of soil development under a wetter climate, we found significant depth-dependent changes in community metrics under a drier climate, which became more pronounced as soils became older. This shift in bacterial and archaeal community structure and diversity is most apparent below a clay-rich argillic horizon formed in the older, drier soils. The molecular composition of SOM as measured by high resolution mass spectrometry (i.e., FTICR MS) also exhibited similar shifts in composition with soil depth and age. Our results highlight how soil moisture shapes the interaction of soil development, SOM, and microbial community composition. Differences in the moisture regime between our two study sites drives differences in biogeochemical depth gradients and subsequent variation in soil microbes and SOM. This suggests that knowledge of not just the pedogenic trajectory of soil development, but also the spatial position relative to distinct pedogenic features, are important for explaining variations in the depth-dependencies of microbial communities and associated SOM.

California

Controls on denitrification in riparian soils in headwater catchments of a hardwood forest in the Catskill Mountains, U.S.A.

Denitrification in riparian soils is thought to be an important factor that reduces hydrologic export of nitrate from forested and agricultural catchments. A 2-y study to identify the soil factors most closely associated with denitrification in riparian soils in headwater catchments within the Catskill Mountains of New York, included field surveys of surface and subsurface denitrification rates, and an amendment experiment to assess the relative effects of increases in available carbon and substrate NO-/3 on denitrification rates. Denitrification rates were measured by acetylene inhibition during incubation of intact soil cores from eight soil types representing a range of drainage classes. Soil cores were analyzed for organic matter, total P, extractable NO-/3-N and NH+/4-N, organic N, pH, moisture, porosity, and water-filled pore space, to determine which of these factors were most closely associated with denitrification. The distribution of denitrification rates found during the field surveys was highly skewed, with many low or zero values and few high values. Denitrification rates were positively associated with high soil organic matter, total P, and water-filled pore space, and were highest in seep (poorly-drained) soils, toeslope (seasonally-drained) soils, and stream-edge (poorly- to moderately well-drained) soils in which these three soil characteristics were typically high. Denitrification rates in these wet locations were also positively associated with soil NH+/4-N concentration and pH, but not with NO-/3-N concentration, suggesting that the rate of NO-/3 supply (via nitrification or hydrologic transport) was more important than the instantaneous concentration of NO-/3-N in the soils. The amendment experiment indicated that denitrification in soil types studied was most responsive to added glucose alone or with NO-/3. Thus, in these soils, a combination of slow rates of NO-/3 supply and low available carbon appears to limit denitrification. Annual denitrification rates in spring-fed soils (0.74 to 1.43 kg N ha-1 y-1) were up to 5 times greater than in other surface soils, yet these soils accounted for only 1.8% of the catchment's N loss through denitrification because they represent less than 3% of the catchment area. Dry upland soils constituted 71% of the catchment area and accounted for 91% of the catchment's N loss through denitrification. Annual denitrification in the catchment equaled about 65% of stream NO-/3-N and NH+/4-N export and 14% of precipitation NO-/3-N and NH+/4-N inputs. Denitrification appears to be important relative to N input and export in these Catskill catchments.

Soil Biology and Biochemistry