Microbial Substrate Use Research Articles

Alteration of belowground carbon dynamics by nitrogen addition in southern California mixed conifer forests

Nitrogen deposition rates in southern California are the highest in North America and have had substantial effects on ecosystem functioning. We document changes in the belowground C cycle near ponderosa pine trees experiencing experimental nitrogen (N) addition (50 and 150 kg N ha−1 a−1 as slow release urea since 1997) at two end‐member sites along a pollution gradient in the San Bernardino Mountains, California. Despite considerable differences in N deposition between the two sites, we observed parallel changes in microbial substrate use and soil enzyme activity with N addition. Δ14C measurements indicate that the mean age of C respired by the Oa horizon declined 10–15 years with N addition at both sites. N addition caused an increase in cellulolytic enzyme activity at the polluted site and a decrease in ligninolytic enzyme activity at the unpolluted site. Given the likely differences in lignin and cellulose ages, this could explain the difference in the age of microbial respiration with N addition. Measurements of fractionated soil organic matter did not show the same magnitude of changes in response to N addition as were observed for respired C. This lesser response was likely because the soils are mostly composed of C having turnover times of decades to centuries, and 9 years of N amendment were not enough to affect this material. Consequently, Δ14C of respired CO2 provided a more sensitive indicator of the effects of N addition than other methods. Results suggest that enhanced N deposition alone may not result in increased soil C storage in xeric ecosystems.

Atmospheric CO 2 enrichment and nutrient additions to planted soil increase mineralisation of soil organic matter, but do not alter microbial utilisation of plant- and soil C-sources

Plants link atmospheric and soil carbon pools through CO 2 fixation, carbon translocation, respiration and rhizodeposition. Within soil, microbial communities both mediate carbon-sequestration and return to the atmosphere through respiration. The balance of microbial use of plant-derived and soil organic matter (SOM) carbon sources and the influence of plant-derived inputs on microbial activity are key determinants of soil carbon-balance, but are difficult to quantify. In this study we applied continuous 13C-labelling to soil-grown Lolium perenne, imposing atmospheric CO 2 concentrations and nutrient additions as experimental treatments. The relative use of plant- and SOM-carbon by microbial communities was quantified by compound-specific 13C-analysis of phospholipid fatty acids (PLFAs). An isotopic mass-balance approach was applied to partition the substrate sources to soil respiration (i.e. plant- and SOM-derived), allowing direct quantification of SOM-mineralisation. Increased CO 2 concentration and nutrient amendment each increased plant growth and rhizodeposition, but did not greatly alter microbial substrate use in soil. However, the increased root growth and rhizosphere volume with elevated CO 2 and nutrient amendment resulted in increased rates of SOM-mineralisation per experimental unit. As rhizosphere microbial communities utilise both plant- and SOM C-sources, the results demonstrate that plant-induced priming of SOM-mineralisation can be driven by factors increasing plant growth. That the balance of microbial C-use was not affected on a specific basis may suggest that the treatments did not affect soil C-balance in this study.

Microbial use of organic amendments in saline soils monitored by changes in the 13C/ 12C ratio

An incubation experiment was carried out to investigate whether salinity at high pH has negative effects on microbial substrate use, i.e. the mineralization of the amendment to CO 2 and inorganic N and the incorporation of amendment C into microbial biomass C. In order to exploit natural differences in the 13C/ 12C ratio, substrate from two C 4 plants, i.e. highly decomposed and N-rich sugarcane filter cake and less decomposed N-poor maize leaf straw, were added to two alkaline Pakistani soils differing in salinity, which had previously been cultivated with C 3 plants. In soil 1, the additional CO 2 evolution was equivalent to 65% of the added amount in the maize straw treatment and to 35% in the filter cake treatment. In the more saline soil 2, the respective figures were 56% and 32%. The maize straw amendment led to an identical immobilization of approximately 48 μg N g −1 soil over the 56-day incubation in both soils compared with the control soils. In the filter cake treatment, the amount of inorganic N immobilized was 8.5 μg N g −1 higher in soil 1 than in soil 2 compared with the control soils. In the control treatment, the content of microbial biomass C 3-C in soil 1 was twice that in soil 2 throughout the incubation. This fraction declined by about 30% during the incubation in both soils. The two amendments replaced initially similar absolute amounts of the autochthonous microbial biomass C, i.e. 50% of the original microbial biomass C in soil 1 and almost 90% in soil 2. The highest contents of microbial biomass C 4-C were equivalent to 7% (filter cake) and 11% (maize straw) of the added C. In soil 2, the corresponding values were 14% lower. Increasing salinity had no direct negative effects on microbial substrate use in the present two soils. Consequently, the differences in soil microbial biomass contents are most likely caused indirectly by salinity-induced reduction in plant growth rather than directly by negative effects of salinity on soil microorganisms.

Changing microbial substrate use in Arctic tundra soils through a freeze-thaw cycle

Recent research has established that microbial processes in the arctic continue even when soils are frozen, and that cold-season processes can be important in the overall annual carbon and nitrogen cycles. Despite the importance of wintertime soil microbial processes, our understanding of their controls remains extremely poor. We particularly have a poor understanding of how microbial substrate use patterns change as soils freeze: do microbes use the same substrates as during the growing season, only slower, or do they switch to using different substrates? We used a 14C isotope equilibration technique to partition respiration between the actively turning over microbial biomass and products pool and the plant detritus pool in a range of Arctic tundra soils. Microbes showed a step-function shift in their metabolism as soils cool from +2 to +0.5 °C, roughly doubling the contribution of recycling of microbial C to total soil respiration. There was no additional shift in substrate use as soils underwent bulk soil freezing. The above-0 °C substrate shift is important because tundra soils spend a long time at or just below 0 °C as they are freezing in the early winter. The change in substrate use represents a shift from processing N-poor detritus to N-rich microbial products, causing N available for either plant uptake or leaching to be greatest when soils are near 0 °C. This may explain the observed patterns of growing season N immobilization vs. cold-season mineralization that appear common in Arctic tundra ecosystems.

Microbial community composition and substrate use in a highly weathered soil as affected by crop rotation and P fertilization

A better understanding of soil microbial processes is required to improve the synchrony between nutrient release from plant residues and crop demand. Phospholipid fatty acid analysis was used to investigate the effect of two crop rotations (continuous maize and maize–crotalaria rotation) and P fertilization (0 and 50 kg P ha−1 yr−1, applied as triple superphosphate) on microbial community composition in a highly weathered soil from western Kenya. Microbial substrate use in soils from the field experiment was compared in incubation experiments. Higher levels of soil organic matter and microbial biomass in the maize–crotalaria rotation were connected with higher total amounts of phospholipid fatty acids and an increase in the relative abundances of indicators for fungi and gram-negative bacteria. P fertilization changed the community profile only within the continuous maize treatment. The decomposition of glucose, cellulose and three plant residues (all added at 2.5 g C kg−1 soil) proceeded faster in soil from the maize–crotalaria rotation, but differences were mostly transient. Microbial P and N uptake within one week increased with the water-soluble carbon content of added plant residues. More P and N were taken up by the greater microbial biomass in soil from the maize–crotalaria rotation than from continuous maize. Re-mineralization of nutrients during the decline of the microbial biomass increased also with the initial biological activity of the soil, but occurred only for a high quality plant residue within the half year incubation period. Compared to the effect of crop rotation, P fertilization had a minor effect on microbial community composition and substrate use.

Chronic nitrogen enrichment affects the structure and function of the soil microbial community in temperate hardwood and pine forests

We examined how chronic nitrogen (N) enrichment of pine and hardwood forest stands has affected the relative abundance, functional capacity, and activity of soil bacteria and fungi. During Fall 2002 we collected one soil core (5.6 cm diameter; organic horizon plus 10 cm of mineral soil) from each of four 5 m×5 m subplots within the control, low N (5 g N m −2 per year), and high N (15 g N m −2 per year) plots in both the hardwood and pine stands at the Chronic Nitrogen Amendment Study at Harvard Forest. The samples were analyzed for total and active bacterial and fungal biomass, microbial catabolic response profiles, the activities of cellulolytic and ligninolytic enzymes, and total, labile and microbially derived organic carbon (C). Live, fine roots were also collected from the control and low N pine plots and analyzed for ectomycorrhizal fungal community composition and diversity. Active fungal biomass was 27–61% and 42–69% lower in the fertilized compared to control plots in the hardwood and pine stands, respectively. Active bacterial biomass was not greatly affected by N additions, resulting in significantly lower fungal:bacterial biomass ratios in the N-treated plots. This shift in microbial community composition was accompanied by a significant reduction in the activity of phenol oxidase, a lignin-degrading enzyme produced by white-rot fungi. In the pine stand, ectomycorrhizal fungal community diversity was lower in the low N-treated plot than in the control plot. Differences in ectomycorrhizal community structure were also detected between control and fertilized pine plots, including a reduction in those species with the highest relative frequencies in the control community. Finally, N enrichment altered the pattern of microbial substrate use, with the relative response to the addition of carboxylic acids and carbohydrates being significantly lower in the N-treated plots, even after the data were normalized to account for differences in microbial biomass. These patterns are consistent with lower decomposition rates and altered N cycling observed previously at this site.

Chronic nitrogen enrichment affects the structure and function of the soil microbial community in temperate hardwood and pine forests

We examined how chronic nitrogen (N) enrichment of pine and hardwood forest stands has affected the relative abundance, functional capacity, and activity of soil bacteria and fungi. During Fall 2002 we collected one soil core (5.6 cm diameter; organic horizon plus 10 cm of mineral soil) from each of four 5m×5 m subplots within the control, low N (5 g N m−2 per year), and high N (15 g N m−2 per year) plots in both the hardwood and pine stands at the Chronic Nitrogen Amendment Study at Harvard Forest. The samples were analyzed for total and active bacterial and fungal biomass, microbial catabolic response profiles, the activities of cellulolytic and ligninolytic enzymes, and total, labile and microbially derived organic carbon (C). Live, fine roots were also collected from the control and low N pine plots and analyzed for ectomycorrhizal fungal community composition and diversity. Active fungal biomass was 27–61% and 42–69% lower in the fertilized compared to control plots in the hardwood and pine stands, respectively. Active bacterial biomass was not greatly affected by N additions, resulting in significantly lower fungal:bacterial biomass ratios in the N-treated plots. This shift in microbial community composition was accompanied by a significant reduction in the activity of phenol oxidase, a lignin-degrading enzyme produced by white-rot fungi. In the pine stand, ectomycorrhizal fungal community diversity was lower in the low N-treated plot than in the control plot. Differences in ectomycorrhizal community structure were also detected between control and fertilized pine plots, including a reduction in those species with the highest relative frequencies in the control community. Finally, N enrichment altered the pattern of microbial substrate use, with the relative response to the addition of carboxylic acids and carbohydrates being significantly lower in the N-treated plots, even after the data were normalized to account for differences in microbial biomass. These patterns are consistent with lower decomposition rates and altered N cycling observed previously at this site.

Microbial community composition and substrate use in a highly weathered soil as affected by crop rotation and P fertilization

A better understanding of soil microbial processes is required to improve the synchrony between nutrient release from plant residues and crop demand. Phospholipid fatty acid analysis was used to investigate the effect of two crop rotations (continuous maize and maize–crotalaria rotation) and P fertilization (0 and 50 kg P ha−1 yr−1, applied as triple superphosphate) on microbial community composition in a highly weathered soil from western Kenya. Microbial substrate use in soils from the field experiment was compared in incubation experiments. Higher levels of soil organic matter and microbial biomass in the maize–crotalaria rotation were connected with higher total amounts of phospholipid fatty acids and an increase in the relative abundances of indicators for fungi and gram-negative bacteria. P fertilization changed the community profile only within the continuous maize treatment. The decomposition of glucose, cellulose and three plant residues (all added at 2.5 g C kg−1 soil) proceeded faster in soil from the maize–crotalaria rotation, but differences were mostly transient. Microbial P and N uptake within one week increased with the water-soluble carbon content of added plant residues. More P and N were taken up by the greater microbial biomass in soil from the maize–crotalaria rotation than from continuous maize. Re-mineralization of nutrients during the decline of the microbial biomass increased also with the initial biological activity of the soil, but occurred only for a high quality plant residue within the half year incubation period. Compared to the effect of crop rotation, P fertilization had a minor effect on microbial community composition and substrate use.

Decomposition of 14C labelled glucose in a Pb-contaminated soil remediated with synthetic zeolite and other amendments

In an incubation experiment, we assessed the effects of a synthetic zeolite (type 4A) on biomass and community structure of soil microorganisms in a highly Pb-contaminated soil. The effects of zeolite were compared with other amendments that increase soil pH, such as CaCO 3, or improve microbial properties, such as compost. In a separate experiment, the effect of the different amendments on the efficiency of microbial substrate use was determined using 14C labelled glucose. The amendments led to significant increases in pH and decreases in NH 4NO 3-extractable Pb. A 99% decrease in extractable Pb was only observed in the treatments containing CaCO 3. The addition of the synthetic zeolite 4A gave a 69% and that of compost a 10% reduction. The addition of zeolite and CaCO 3 mobilised soil organic matter as indicated by increased contents of CaCl 2 extractable C and increased CO 2 production rates. Microbial biomass C was increased by all amendments, but in most cases it was not significant. Maximum biomass C was measured where the combined amendment zeolite+compost+CaCO 3 was added. The addition of compost, especially when combined with CaCO 3, resulted in an increased ergosterol content. In contrast, the sole addition of synthetic zeolite had a significant depressive effect on the ergosterol content and, thus, on the ergosterol-to-biomass C ratio. The most striking feature of the treatments containing synthetic zeolite was the effect on glucose decomposition. Zeolite increased both incorporation of 14C into microbial biomass and mineralisation to 14CO 2, so that the ∑CO 2- 14C-to-biomass 14C ratio remained unaffected.

Microbial C and N dynamics during mesophilic and thermophilic incubations of ryegrass

Laboratory studies were conducted to determine C and N dynamics during the decomposition of ryegrass straw under mesophilic and thermophilic conditions. A KC of 0.61 was developed for the chloroform-fumigation extraction method to estimate microbial biomass C. These estimates showed that the C and N requirement of the thermophilic biomass was approximately 50% of the mesophilic biomass. There was no relationship between chloroform-fumigation microbial biomass estimates and plating of microorganisms from straw on specific media. Mineralized C was measured as 185 and 210 g kg-1 straw in the 25°C and 50°C treatments, respectively. The efficiency of microbial substrate use, on a total straw basis, was 34 and 28% in the 25°C and 50°C incubations, respectively. The level of soluble C declined more slowly than total C mineralization at both temperatures, indicating that a portion of the labile C was not readily biodegradable. The addition of N decreased the rate of C mineralization at both temperatures. The reduced N requirement of the thermophiles explains why rapid degradation of the high C:N residue occurred without additional N or the need for the addition of a low C:N ratio substrate. Additional inoculum did not affect the decomposition process. We conclude that the promotion of thermophilic biomass activities, through composting for example, may prove useful in upgrading agricultural wastes for introduction into sustainable cropping systems.

Seasonal Carbon Flow and Decomposer Parameter Relationships in a Semiarid Grassland Soil

The microbial activities of soil cores removed from a semiarid grassland at 3—wk intervals from February to November 1972 were evaluated both with and without nutrient enrichments. Control, wetted, and substrate—treated core O2 utilization rates were measured over the first 3 h of incubation to provide information on seasonal changes in microbial substrate use patterns. Relationships between changes in decomposer parameters also were evaluated on a seasonal basis. Unamended soils showed highest microbial activity in the spring, followed by minimum O2 use and CO2 evolution in the dry summer period, the time when H2O additions caused maximum stimulation of O2 utilization with lower (° 0.7) respiratory quotients. Protein use was strongly correlated with field soil H2O content, followed by increased utilization of amino acids suggesting a sequential breakdown process. Glucose, starch, and cellulose use was independent of short—term changes in soil H2O content and appeared related to seasonal changes in plant root carbohydrage reserves, being minimum in summer and maximum in fall, the only time when marked cellulose use occurred. An all—year correlation showed strong relationships between changes in substrate availability, soil H2O content, respiration, and microbial populations, while on a seasonal basis shifts in the parameters controlling decomposer processes were observed. Respiratory quotients became more positive only during the spring period, a trend which was reflected in seasonal matrix correlations.