Predominant bacterial and fungal assemblages in agricultural soils during a record drought/heat wave and linkages to enzyme activities of biogeochemical cycling

Identification of microbial assemblages predominant under natural extreme climatic events will aid in our understanding of the resilience and resistance of microbial communities to climate change. From November 2010 to August 2011, the Southern High Plains (SHP) of Texas, USA, received only 39.6 mm of precipitation (vs. the historical average of 373 mm) and experienced the three hottest months (June–August 2011) since record keeping began in 1911. The objective of this study was to characterize soil bacterial (16 S rRNA gene) and fungal (internal transcribed spacer 1–4, ITS1-ITS4) species distribution and diversity via pyrosequencing during the peak of the drought/heat wave in July 2011 and when the Drought Index and temperatures were lower in March 2012. Samples were collected from two different soil types (loam and sandy loam) under two different dryland cropping histories (monoculture vs. rotation). Fungal Diversity Indexes were significantly higher after the drought/heat wave while Bacterial Indexes were similar. Bacterial phyla distribution in July 2011 was characterized by lower relative abundance of Acidobacteriaand Verrucomicrobia, and greater relative abundance of Proteobacteria, Chloroflexi, Actinobacteria and Nitrospirae than March 2012 samples. Further grouping of pyrosequencing data revealed approximately equal relative proportions of Gram positive (G+) and Gram negative (G−) bacteria in July 2011, while G− bacteria predominated in March 2012. Fungal class Dothideomycetes was approximately two times greater in July 2011 than in March 2012, while the class Sordariomycetes and a group of unidentified OTUs from Ascomycota increased from July 2011 to March 2012. Microbial community composition was less influenced by management history than by the difference in climatic conditions between the sampling times. Correspondence analysis identified assemblages of fungal and bacterial taxa associated with greater enzyme activities (EAs) of C, N, or P cycling found during the drought/heat wave. Microbial assemblages associated with arylsulfatase activity (key to S cycling), which increased after the drought/heat wave, were identified (Streptomyces parvisporogenes, Terrimonas ferruginea and Syntrophobacter sp.) regardless of the soil and management history. The distinct microbial composition found in July 2011 may represent assemblages essential to maintaining ecosystem function during extreme drought and intense heat waves in semiarid agroecosystems.     

Soil organic matter, microbial biomass and enzyme activities in a tropical agroforestry system

 The effects of growing trees in combination with field crops on soil organic matter, microbial biomass C, basal respiration and dehydrogenase and alkaline phosphatase activities were studied in soils under a 12-year-old Dalbergia sissoo (a N₂-fixing tree) plantation intercropped with a wheat (Triticum aestivum) – cowpea (Vigna sinensis) cropping sequence. The inputs of organic matter through D. sissoo leaf litter increased and crop roots decreased with the increase in tree density. Higher organic C and total N, microbial biomass C, basal soil respiration and activities of dehydrogenase and alkaline phosphatase were observed in treatments with tree-crop combination than in the treatment without trees. Soil organic matter, microbial biomass C and soil enzyme activities increased with the decrease in the spacing of the D. sissoo plantation. The results indicate that adoption of the agroforestry practices led to an improved organic matter status of the soil, which is also reflected in the increased nutrient pool and microbial activities necessary for long-term productivity of the soil. However, tree spacing should be properly maintained to minimize the effects of shading on the intercrops. Received: 21 February 1997     

Response of soil microbial biomass and enzyme activities to the transient elevation of carbon dioxide in a semi-arid grassland

Although elevation of CO₂ has been reported to impact soil microbial functions, little information is available on the spatial and temporal variation of this effect. The objective of this study was to determine the microbial response in a northern Colorado shortgrass steppe to a 5-year elevation of atmospheric CO₂ as well as the reversibility of the microbial response during a period of several months after shutting off the CO₂ amendment. The experiment was comprised of nine experimental plots: three chambered plots maintained at ambient CO₂ levels of 360 μmol mol⁻¹ (ambient treatment), three chambered plots maintained at 720 μmol mol⁻¹ CO₂ (elevated treatment) and three unchambered plots of equal ground area used as controls to monitor the chamber effect.Elevated CO₂ induced mainly an increase of enzyme activities (protease, xylanase, invertase, alkaline phosphatase, arylsulfatase) in the upper 5 cm of the soil and did not change microbial biomass in the soil profile. Since rhizodeposition and newly formed roots enlarged the pool of easily available substrates mainly in the upper soil layers, enzyme regulation (production and activity) rather than shifts in microbial abundance was the driving factor for higher enzyme activities in the upper soil. Repeated soil sampling during the third to fifth year of the experiment revealed an enhancement of enzyme activities which varied in the range of 20-80%. Discriminant analysis including all microbiological properties revealed that the enzyme pattern in 1999 and 2000 was dominated by the CO₂ and chamber effect, while in 2001 the influence of elevated CO₂ increased and the chamber effect decreased.Although microbial biomass did not show any response to elevated CO₂ during the main experiment, a significant increase of soil microbial N was detected as a post-treatment effect probably due to lower nutrient (nitrogen) competition between microorganisms and plants in this N-limited ecosystem. Whereas most enzyme activities showed a significant post-CO₂ effect in spring 2002 (following the conclusion of CO₂ enrichment the previous autumn, 2001), selective depletion of substrates is speculated to be the cause for non-significant treatment effects of most enzyme activities later in summer and autumn, 2002. Therefore, additional belowground carbon input mainly entered the fast cycling carbon pool and contributed little to long-term carbon storage in the semi-arid grassland.     

Soil organic matter dynamics in grassland soils under elevated CO2: Insights from long-term incubations and stable isotopes

Elevated atmospheric carbon dioxide (CO₂) levels generally stimulate carbon (C) uptake by plants, but the fate of this additional C largely remains unknown. This uncertainty is due in part to the difficulty in detecting small changes in soil carbon pools. We conducted a series of long-term (170-330 days) laboratory incubation experiments to examine changes in soil organic matter pool sizes and turnover rates in soil collected from an open-top chamber (OTC) elevated CO₂ study in Colorado shortgrass steppe. We measured concentration and isotopic composition of respired CO₂ and applied a two-pool exponential decay model to estimate pool sizes and turnover rates of active and slow C pools. The active and slow C pools of surface soils (5-10 cm depth) were increased by elevated CO₂, but turnover rates of these pools were not consistently altered. These findings indicate a potential for C accumulation in near-surface soil C pools under elevated CO₂. Stable isotopes provided evidence that elevated CO₂ did not alter the decomposition rate of new C inputs. Temporal variations in measured δ¹³C of respired CO₂ during incubation probably resulted mainly from the decomposition of changing mixtures of fresh residue and older organic matter. Lignin decomposition may have contributed to declining δ¹³C values late in the experiments. Isotopic dynamics during decomposition should be taken into account when interpreting δ¹³C measurements of soil respiration. Our study provides new understanding of soil C dynamics under elevated CO₂ through the use of stable C isotope measurements during microbial organic matter mineralization.     

Soil organic N dynamics and stand quality in Pinus radiata pinewoods of the temperate humid region

Soil organic-N dynamics, its controlling factors and its relationships with stand quality were studied in the 0-15 cm soil layer of 24 pinewoods with contrasting age, productivity and parent material (granite; acid schists), searching for N variables useful to predict stand growth and site quality. No significant differences were found between young and old stands for any of the N variables considered, nor two- or three-order interactions among stand age, site quality and parent material. The soil total-N content, which was correlated positively with the Al oxides content (a soil organic matter (SOM) stabilizing agent), did not vary significantly according to parent material, but it was lower (P≤0.02) in stands with high than with low site index (2.68±1.11 and 3.97±1.13 g N kg⁻¹ soil, respectively). The soil δ¹⁵N ranged from +3.5 to +6.5 δ, without significant differences among stand groups, and it was negatively correlated with water holding capacity, exchangeable bases, Al oxides and N content, suggesting that: (i) N losses by NO₃⁻ leaching are the most important controlling factor of δ¹⁵N in these temperate humid region soils; and (ii) soil N richness is related with limited N losses, which discriminate against ¹⁵N. At any incubation time, no significant differences were found in soil inorganic-N content among stand groups (7.78±4.57, 39.33±16.20 and 67.80±26.50 mg N kg⁻¹ soil at 0, 42 and 84 d, respectively). During the incubation, the relative importance of ammonification decreased and that of the nitrification increased. The net N mineralization rate (NNMR, in percentage of organic N) was significantly higher in granite than in schists soils at both 42 d (1.24±0.34 and 0.75±0.37%, respectively) and 84 d (2.18±0.56 and 1.53±0.66%, respectively). In high quality pinewoods, the NNMR at 42 and 84 d (1.16±0.45 and 2.12±0.79%, respectively) were significantly higher than in low quality stands (0.83±0.35 and 1.59±0.45%, respectively). This result, together with those on soil total-N and inorganic-N supply, suggests that soil N dynamics in low and high quality stands are different: in the former there is a bigger N pool with a slower turnover, whereas in the latter there is a smaller N pool with a faster turnover, both factors being nearly compensated, making the soil available N supply in both types of stand similar. After 42 and 84 d of incubation, the NNMR and the nitrification rates were higher in the coarse textured soils, likely due to the low physical and chemical protection of their SOM; both rates were positively correlated with available P, exchangeable K⁺ and CEC base saturation, suggesting strong relationships among the availabilities of the main plant nutrients, and they increased with SOM quality (low C-to-N ratio). The strong negative correlation of site index with soil total-N (r=−0.707; P≤0.005), and its positive correlations with NNMR after 42 and 84 d of incubation, suggested that site quality and potential productivity are closely related to soil organic-N dynamics. Half of the site index variation in the stands studied could be predicted with a cheap and easy analysis of soil N content, the prediction being slightly improved if soil δ¹⁵N is included and, more significantly, by including N mineralization measurements.     

Local response of bacterial densities and enzyme activities to elevated atmospheric CO2 and different N supply in the rhizosphere of Phaseolus vulgaris L.

Altered flux of labile C from plant roots into soil is thought to influence growth and maintenance of microbial communities under elevated atmospheric CO₂ concentrations. We studied the abundance and function of the soil microbial community at two levels of spatial resolution to assess the response of microorganisms in the rhizosphere of the whole root system and of apical root zones of Phaseolus vulgaris L. to elevated CO₂ and high or low N supply.

At the coarser resolution, microbial biomass C, basal respiration and phospholipid fatty acid (PLFA) patterns in the rhizosphere remained unaffected by elevated CO₂, because the C flux from the whole root system into soil did not change [as shown by Haase, S., Neumann, G., Kania, A., Kuzyakov, Y., Römheld, V., Kandeler, E., 2007. Elevation of atmospheric CO₂ and N-nutritional status modify nodulation, nodule carbon supply, and root exudation of Phaseolus vulgaris L. Soil Biology & Biochemistry 39, 2208–2221]. At a higher spatial resolution, more low-molecular-weight compounds were released from apical root zones under elevated CO₂. Thus, at an early stage of plant growth (12 days after sowing), elevated CO₂ induced an increase of enzyme activities (xylosidase, cellobiosidase and leucine-aminopeptidase) in the rhizosphere soil of apical root zones. At later stages of plant growth (21 days after sowing), however, enzyme activities (those above as well as N-acetyl-β-glucosaminidase and phosphatase) decreased under elevated CO₂. The abundance of total and denitrifying bacteria in the rhizosphere soil of apical root zones was unaffected by CO₂ elevation or N supply. Plant age seemed to be the main factor influencing the density of the bacterial community. In conclusion, the soil microbial community in the apical root zone responded to elevated CO₂ by altered enzyme regulation (production and/or activity) and not by greater bacterial abundance.