Detection and Identification of Aster Yellows Phytoplasma Associated with Lipstick Yellow Frond Disease in Malaysia

Yellowing symptoms similar to coconut yellow decline phytoplasma disease were observed on lipstick palms (Cyrtostachys renda) in Selangor state, Malaysia. Typical symptoms were yellowing, light green fronds, gradual collapse of older fronds and decline in growth. Polymerase chain reaction assay was employed to detect phytoplasma in symptomatic lipstick palms. Extracted DNA was amplified from symptomatic lipstick palms by PCR using phytoplasma‐universal primer pair P1/P7 followed by R16F2n/R16R2. Phytoplasma presence was confirmed, and the 1250 bp products were cloned and sequenced. Sequence analysis indicated that the phytoplasmas associated with lipstick yellow frond disease were isolates of ‘Candidatus Phytoplasma asteris’ belonging to the 16SrI group. Virtual RFLP analysis of the resulting profiles revealed that these palm‐infecting phytoplasmas belong to subgroup 16SrI‐B and a possibly new 16SrI‐subgroup. This is the first report of lipstick palm as a new host of aster yellows phytoplasma (16SrI) in Malaysia and worldwide.     

The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon Basin

Aim Edaphic heterogeneity may be an important driver of population differentiation in the Amazon but remains to be investigated in trees. We compared the phylogeographic structure across the geographic distribution of two Protium (Burseraceae) species with different degrees of edaphic specialization: Protium alvarezianum, an edaphic specialist of white‐sand habitat islands; and Protium subserratum, an edaphic generalist found in white sand as well as in more widespread soil types. We predicted that in the edaphic specialist, geographic distance would structure populations more strongly than in the edaphic generalist, and that soil type would not structure populations in the edaphic generalist unless habitat acts as a barrier promoting population differentiation. Location Tropical rain forests of the Peruvian and Brazilian Amazon, Guyana and French Guiana. Methods We sequenced 1209–1211 bp of non‐coding nuclear ribosomal DNA (internal transcribed spacer and external transcribed spacer) and a neutral low‐copy nuclear gene (phytochrome C) from P. subserratum (n = 65, 10 populations) and P. alvarezianum (n = 19, three populations). We conducted a Bayesian phylogenetic analysis, constructed maximum parsimony haplotype networks and assessed population differentiation among groups (soil type or geographic locality) using analysis of molecular variance and spatial analysis of molecular variance. Results The edaphic specialist exhibited considerable genetic differentiation among geographically distant populations. The edaphic generalist showed significant genetic differentiation between the Guianan and Amazon Basin populations. Within Peru, soil type and not geographic distance explained most of the variation among populations. Non‐white‐sand populations in Peru exhibited lower haplotype/nucleotide diversity than white‐sand populations, were each other’s close relatives, and formed an unresolved clade derived from within the white‐sand populations. Main conclusions Geographic distance is a stronger driver of population differentiation in the edaphic specialist than in the generalist. However, this difference did not appear to be related to edaphic generalism per se as adjacent populations from both soil types in the edaphic generalist did not share many haplotypes. Populations of the edaphic generalist in white‐sand habitats exhibited high haplotype diversity and shared haplotypes with distant white‐sand habitat islands, indicating that they have either efficient long‐distance dispersal and/or larger ancestral effective population sizes and thus retain ancestral polymorphisms. These results highlight the importance of edaphic heterogeneity in promoting population differentiation in tropical trees.     

Soil phosphorus and disturbance influence liana communities in a subtropical montane forest

Questions: What are the effects of soil, topography, treefall gaps, tree species composition, and tree density on liana species composition and total liana abundance? Location: A 6‐ha permanent plot in a subtropical montane forest in northwest Argentina. Methods: Multiple regressions were used to quantify associations of liana species composition and total liana abundance with edaphic, disturbance and tree community variables. Gradients in liana and tree species composition were quantified using principal components analysis (PCA). Results: Liana species composition was correlated most strongly with soil phosphorus concentration (R²=0.55). Total liana aanased with phosphorus and the density of recent treefall gaps (R²=0.60). Conclusions: In our study area, liana composition and abundance are most strongly correlated with features of the physical environment, rather than host tree characteristics. Our results support the hypothesis that recent increases in liana abundance in mature tropical forests may be related to increased rates of gap formation.     

THE CONTRIBUTION OF EDAPHIC HETEROGENEIYT TO THE EVOLUTION AND DIVERSITY OF BURSERACEAR TREES IN THE WESTERN AMAZON

Abstract —Environmental heterogeneity in the tropics is thought to lead to specialization in plants and thereby contribute to the diversity of the tropical flora. We examine this idea with data on the habitat specificity of 35 western Amazonian species from the genera Protium, Crepidospermum, and Tetragastris in the monophyletic tribe Protieae (Burseraceae) mapped on a molecular‐based phylogeny. We surveyed three edaphic habitats that occur throughout terra firme Amazonia: white‐sand, clay, and terrace soils in eight forests across more than 2000 km in the western Amazon. Twenty‐six of the 35 species were found to be associated with only one of three soil types, and no species was associated with all three habitats; this pattern of edaphic specialization was consistent across the entire region. Habitat association mapped onto the phylogenetic tree shows association with terrace soils to be the probable ancestral state in the group, with subsequent speciation events onto clay and white‐sand soils. The repeated gain of clay association within the clade likely coincides with the emergence of large areas of clay soils in the Miocene deposited during the Andean uplift. Character optimizations revealed that soil association was not phylogenetically clustered for white‐sand and clay specialists, suggesting repeated independent evolution of soil specificity is common within the Protieae. This phylogenetic analysis also showed that multiple cases of putative sister taxa with parapatric distributions differ in their edaphic associations, suggesting that edaphic heterogeneity was an important driver of speciation in the Protieae in the Amazon basin.     

Effects of nutrient additions on ecosystem carbon cycle in a Puerto Rican tropical wet forest

Wet tropical forests play a critical role in global ecosystem carbon (C) cycle, but C allocation and the response of different C pools to nutrient addition in these forests remain poorly understood. We measured soil organic carbon (SOC), litterfall, root biomass, microbial biomass and soil physical and chemical properties in a wet tropical forest from May 1996 to July 1997 following a 7‐year continuous fertilization. We found that although there was no significant difference in total SOC in the top 0–10 cm of the soils between the fertilization plots (5.42±0.18 kg m^?2) and the control plots (5.27±0.22 kg m^?2), the proportion of the heavy‐fraction organic C in the total SOC was significantly higher in the fertilized plots (59%) than in the control plots (46%) (P<0.05). The annual decomposition rate of fertilized leaf litter was 13% higher than that of the control leaf litter. We also found that fertilization significantly increased microbial biomass (fungi+bacteria) with 952±48 mg kg^?1soil in the fertilized plots and 755±37 mg kg^?1soil in the control plots. Our results suggest that fertilization in tropical forests may enhance long‐term C sequestration in the soils of tropical wet forests.     

Long‐term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil

Nitrogen (N) deposition is a component of global change that has considerable impact on belowground carbon (C) dynamics. Plant growth stimulation and alterations of fungal community composition and functions are the main mechanisms driving soil C gains following N deposition in N‐limited temperate forests. In N‐rich tropical forests, however, N deposition generally has minor effects on plant growth; consequently, C storage in soil may strongly depend on the microbial processes that drive litter and soil organic matter decomposition. Here, we investigated how microbial functions in old‐growth tropical forest soil responded to 13 years of N addition at four rates: 0 (Control), 50 (Low‐N), 100 (Medium‐N), and 150 (High‐N) kg N ha^?1 year^?1. Soil organic carbon (SOC) content increased under High‐N, corresponding to a 33% decrease in CO₂ efflux, and reductions in relative abundances of bacteria as well as genes responsible for cellulose and chitin degradation. A 113% increase in N₂O emission was positively correlated with soil acidification and an increase in the relative abundances of denitrification genes (narG and norB). Soil acidification induced by N addition decreased available P concentrations, and was associated with reductions in the relative abundance of phytase. The decreased relative abundance of bacteria and key functional gene groups for C degradation were related to slower SOC decomposition, indicating the key mechanisms driving SOC accumulation in the tropical forest soil subjected to High‐N addition. However, changes in microbial functional groups associated with N and P cycling led to coincidentally large increases in N₂O emissions, and exacerbated soil P deficiency. These two factors partially offset the perceived beneficial effects of N addition on SOC storage in tropical forest soils. These findings suggest a potential to incorporate microbial community and functions into Earth system models considering their effects on greenhouse gas emission, biogeochemical processes, and biodiversity of tropical ecosystems.     

Tree growth and soil acidification in response to 30 years of experimental nitrogen loading on boreal forest

Relations among nitrogen load, soil acidification and forest growth have been evaluated based on short‐term (<15 years) experiments, or on surveys across gradients of N deposition that may also include variations in edaphic conditions and other pollutants, which confound the interpretation of effects of N per se. We report effects on trees and soils in a uniquely long‐term (30 years) experiment with annual N loading on an un‐polluted boreal forest. Ammonium nitrate was added to replicated (N=3) 0.09 ha plots at two doses, N1 and N2, 34 and 68 kg N ha^?1 yr^?1, respectively. A third treatment, N3, 108 kg N ha^?1 yr^?1, was terminated after 20 years, allowing assessment of recovery during 10 years. Tree growth initially responded positively to all N treatments, but the longer term response was highly rate dependent with no gain in N3, a gain of 50 m³ ha^?1 stemwood in N2 and a gain of 100 m³ ha^?1 stemwood in excess of the control (N0) in N1. High N treatments caused losses of up to 70% of exchangeable base cations (Ca²⁺, Mg²⁺, K⁺) in the mineral soil, along with decreases in pH and increases in exchangeable Al³⁺. In contrast, the organic mor‐layer (forest floor) in the N‐treated plots had similar amounts per hectare of exchangeable base cations as in the N0 treatment. Magnesium was even higher in the mor of N‐treated plots, providing evidence of up‐lift by the trees from the mineral soil. Tree growth did not correlate with the soil Ca/Al ratio (a suggested predictor of effects of soil acidity on tree growth). A boron deficiency occurred on N‐treated plots, but was corrected at an early stage. Extractable NH₄⁺ and NO₃^?were high in mor and mineral soils of on‐going N treatments, while NH₄+ was elevated in the mor only in N3 plots. Ten years after termination of N addition in the N3 treatment, the pH had increased significantly in the mineral soil; there were also tendencies of higher soil base status and concentrations of base cations in the foliage. Our data suggest the recovery of soil chemical properties, notably pH, may be quicker after removal of the N‐load than predicted. Our long‐term experiment demonstrated the fundamental importance of the rate of N application relative to the total amount of N applied, in particular with regard to tree growth and C sequestration. Hence, experiments adding high doses of N over short periods do not mimic the long‐term effects of N deposition at lower rates.     

A major role for nitrification in the weathering of minerals of brown acid forest soils

Experiments employing lysimeters and a comparison of soil leachates at >‐0.03 MPa and soil solutions extracted at ‐2.5 MPa showed the importance of nitrification in the weathering of minerals of brown acid forest soils (dys‐trochrept) which are formed over large areas in temperate climates.

Mineralization of litter from plants characteristic of such soils (in particular Festuca silvatica and Abies pectinata) produces large amounts of nitric acid. This bacterial nitrification is responsible for the solubilization of Ca²⁺, Mg²⁺, and K⁺ and must be involved in the slow weathering of minerals by acidolysis and in the biogeochemical cycling of Ca²⁺, Mg²⁺, and K⁺ in these soils. Soil solutions extracted at ‐2.5 MPa reflect much more the microbial activity than the leachates from soil and provide interesting information.     

Role of Zinc in Rhizobacteria-Mediated Suppression of Root-Infecting Fungi and Root-Knot Nematode

Understanding the environmental factors that influence the rhizosphere and inner root colonization of the disease‐suppressive strains of fluorescent pseudomonads is an essential step towards improving the level and reliability of their biocontrol activity. Soil amendment with Zn at 0.8 or 1.6 mg/kg of soil alone or in combination with Pseudomonas aeruginosa IE‐6S⁺significantly reduced nematode penetration in tomato roots. Zn applied alone did not reduce root infection caused by Macrophomina phaseolina or Fusarium solani but did reduce when used in combination with IE‐6S⁺. Soil amendment with Zn at 0.8 or 1.6 mg/kg of soil alone or in conjunction with IE‐6S⁺ markedly suppressed Rhizoctonia solani infection. Plant height, fresh weight of shoot and protein contents of the leaves substantially improved when used with Zn, however, plants growing in the soil treated with 1.6 mg/kg of Zn in the absence of IE‐6S⁺ not only reduced plant growth but also showed necrotic symptoms on the leaves. Zn application in the soil decreased populations of IE‐6S⁺ both in the rhizosphere and root. A positive correlation between bacterial rhizosphere and inner root colonization was also observed. With an increase in nematode densities in the soil, nematode penetration and subsequent galling due to Meloidogyne javanica increased. Regardless of the nematode densities, Zn applied alone or in combination with IE‐6S⁺ caused marked suppression of M. javanica. At all the population densities of M. javanica, Zn enhanced the efficacy of IE‐6S⁺ to reduce nematode invasion and subsequent gall development. IE‐6S⁺ caused significant suppression of soil‐borne root‐infecting fungi both in Zn‐sufficient and Zn‐deficient soil although this suppressive effect accentuated in Zn‐sufficient soils. In the absence of IE‐6S⁺ and/or Zn, increased nematode densities in the soil significantly reduced plant height, fresh weight of shoot and protein contents of the shoots. With an increase in nematode densities, populations of IE‐6S⁺ in the rhizosphere and root increased regardless of the Zn application. However, Zn‐deficient soils supported larger populations of IE‐6S⁺ compared with those of Zn‐sufficient soils.     

A California grasslands alkali specialist,Hemizonia pungens ssp. pungens,prefers non‐alkali soil

Question: Edaphically severe habitats commonly support edaphic endemics, specialized plant species that do not occur elsewhere. The endemism of native plant species in edaphically specialized habitats suggests either (a) that these native endemic species are uniquely specialized to survive and grow better under the conditions prevalent in these harsh areas, or (b) that these areas represent refuges from competition with other (often exotic) species. Location: Central Valley, California, USA. Methods: We surveyed the vegetation distribution in alkali sinks and carried out a reciprocal transplant greenhouse experiment crossed with a competition treatment to examine the interplay between interspecific competition and edaphic factors in determining relative performance of an alkali endemic forb (Hemizonia pungens ssp. pungens) and its exotic grass competitor (Lolium multiflorum). Results: Lolium consistently performed better in non‐alkali soil. In contrast, Hemizonia, in the absence of competition, performed significantly better on the non‐alkali soils, but in competition with Lolium, performed equally well on alkali and non‐alkali soils. Conclusions: These results suggest that Hemizonia does not inherently prefer harsh alkali soil, but is better able to tolerate alkali soil and may be excluded from more moderate soils by competition. Therefore, edaphic and biotic effects may interact to determine the spatial distribution of this edaphic endemic. Our data suggest a mechanism by which competition between native and exotic species on impoverished soils leads to dominance of native species and creation of refugia for native species where exotic species are unable to thrive.     

Soil carbon balance following conversion of grassland to oil palm

Oil palm (Elaeis guineensis Jacq.) crops are expanding rapidly in the tropics, with implications for the global carbon cycle. Little is currently known about soil organic carbon (SOC) dynamics following conversion to oil palm and virtually nothing for conversion of grassland. We measured changes in SOC stocks following conversion of tropical grassland to oil palm plantations in Papua New Guinea using a chronosequence of plantations planted over a 25‐year period. We further used carbon isotopes to quantify the loss of grassland‐derived and gain in oil palm‐derived SOC over this period. The grassland and oil palm soils had average SOC stocks of 10.7 and 12.0 kg m^?2, respectively, across all the study sites, to a depth of 1.5 m. In the 0–0.05 m depth interval, 0.79 kg m^?2 of SOC was gained from oil palm inputs over 25 years and approximately the same amount of the original grass‐derived SOC was lost. For the whole soil profile (0–1.5 m), 3.4 kg m^?2 of SOC was gained from oil palm inputs with no significant losses of grass‐derived SOC. The grass‐derived SOC stocks were more resistant to decrease than SOC reported in other studies. Black carbon produced in grassfires could partially but not fully account for the persistence of the original SOC stocks. Oil palm‐derived SOC accumulated more slowly where soil nitrogen contents where high. Forest soils in the same region had smaller carbon stocks than the grasslands. In the majority of cases, conversion of grassland to oil palm plantations in this region resulted in net sequestration of soil organic carbon.     

Large seasonal variation of soil respiration in a secondary tropical moist forest in Puerto Rico

Tropical forests are the largest contributors to global emissions of carbon dioxide (CO₂) to the atmosphere via soil respiration (R_s). As such, identifying the main controls on R_s in tropical forests is essential for accurately projecting the consequences of ongoing and future global environmental changes to the global C cycle. We measured hourly R_s in a secondary tropical moist forest in Puerto Rico over a 3‐year period to (a) quantify the magnitude of R_s and (b) identify the role of climatic, substrate, and nutrient controls on the seasonality of R_s. Across 3 years of measurements, mean R_s was 7.16 ± 0.02 μmol CO₂ m^‐2 s^‐1 (or 2,710 g C m^‐2 year^‐1) and showed significant seasonal variation. Despite small month‐to‐month variation in temperature (~4°C), we found significant positive relationships between daily and monthly R_s with both air and soil temperature, highlighting the importance of temperature as a driver of R_s even in warm ecosystems, such as tropical forests. We also found a significant parabolic relationship between mean daily volumetric soil moisture and mean daily R_s, with an optimal moisture value of 0.34 m³ m^‐3. Given the relatively consistent climate at this site, the large range in mean monthly R_s (~7 μmol CO₂ m^‐2 s^‐1) was surprising and suggests that even small changes in climate can have large implications for ecosystem respiration. The strong positive relationship of R_s with temperature at monthly timescales particularly stands out, as moisture is usually considered a stronger control of R_s in tropical forests that already experience warm temperatures year‐round. Moreover, our results revealed the strong seasonality of R_s in tropical moist forests, which given its high magnitude, can represent a significant contribution to the seasonal patterns of atmospheric (CO₂) globally.     

Elevated CO2 increases microbial carbon substrate use and nitrogen cycling in Mojave Desert soils

Identifying soil microbial responses to anthropogenically driven environmental changes is critically important as concerns intensify over the potential degradation of ecosystem function. We assessed the effects of elevated atmospheric CO₂ on microbial carbon (C) and nitrogen (N) cycling in Mojave Desert soils using extracellular enzyme activities (EEAs), community‐level physiological profiles (CLPPs), and gross N transformation rates. Soils were collected from unvegetated interspaces between plants and under the dominant shrub (Larrea tridentata) during the 2004–2005 growing season, an above‐average rainfall year. Because most measured variables responded strongly to soil water availability, all significant effects of soil water content were used as covariates to remove potential confounding effects of water availability on microbial responses to experimental treatment effects of cover type, CO₂, and sampling date. Microbial C and N activities were lower in interspace soils compared with soils under Larrea, and responses to date and CO₂ treatments were cover specific. Over the growing season, EEAs involved in cellulose (cellobiohydrolase) and orthophosphate (alkaline phosphatase) degradation decreased under ambient CO₂, but increased under elevated CO₂. Microbial C use and substrate use diversity in CLPPs decreased over time, and elevated CO₂ positively affected both. Elevated CO₂ also altered microbial C use patterns, suggesting changes in the quantity and/or quality of soil C inputs. In contrast, microbial biomass N was higher in interspace soils than soils under Larrea, and was lower in soils exposed to elevated CO₂. Gross rates of NH₄⁺ transformations increased over the growing season, and late‐season NH₄⁺ fluxes were negatively affected by elevated CO₂. Gross NO₃⁻ fluxes decreased over time, with early season interspace soils positively affected by elevated CO₂. General increases in microbial activities under elevated CO₂ are likely attributable to greater microbial biomass in interspace soils, and to increased microbial turnover rates and/or metabolic levels rather than pool size in soils under Larrea. Because soil water content and plant cover type dominates microbial C and N responses to CO₂, the ability of desert landscapes to mitigate or intensify the impacts of global change will ultimately depend on how changes in precipitation and increasing atmospheric CO₂ shift the spatial distribution of Mojave Desert plant communities.     

Carbon accumulation of tropical peatlands over millennia: a modeling approach

Tropical peatlands cover an estimated 440 000 km² (~10% of global peatland area) and are significant in the global carbon cycle by storing about 40–90 Gt C in peat. Over the past several decades, tropical peatlands have experienced high rates of deforestation and conversion, which is often associated with lowering the water table and peat burning, releasing large amounts of carbon stored in peat to the atmosphere. We present the first model of long‐term carbon accumulation in tropical peatlands by modifying the Holocene Peat Model (HPM), which has been successfully applied to northern temperate peatlands. Tropical HPM (HPMTrop) is a one‐dimensional, nonlinear, dynamic model with a monthly time step that simulates peat mass remaining in annual peat cohorts over millennia as a balance between monthly vegetation inputs (litter) and monthly decomposition. Key model parameters were based on published data on vegetation characteristics, including net primary production partitioned into leaves, wood, and roots; and initial litter decomposition rates. HPMTrop outputs are generally consistent with field observations from Indonesia. Simulated long‐term carbon accumulation rates for 11 000‐year‐old inland, and 5 000‐year‐old coastal peatlands were about 0.3 and 0.59 Mg C ha^?1 yr^?1, and the resulting peat carbon stocks at the end of the 11 000‐year and 5 000‐year simulations were 3300 and 2900 Mg C ha^?1, respectively. The simulated carbon loss caused by coastal peat swamp forest conversion into oil palm plantation with periodic burning was 1400 Mg C ha^?1 over 100 years, which is equivalent to ~2900 years of C accumulation in a hectare of coastal peatlands.     

Influence of mound construction by red and hybrid imported fire ants on soil chemical properties and turfgrass in a sod production agroecosystem

Mound construction by imported fire ants (Solenopsis spp.) actively modify the biogeochemical and physical properties of soil; however, their influence on nutrient levels in surrounding vegetation is poorly understood. Aside from the reported persistence of elevated available P and K levels in clay-rich soils one year after mound abandonment, the relative stability of nutrient concentrations from one season to the next is largely unknown. Nutrient concentrations were concurrently analysed from ant mounds and undisturbed soils as well as plant samples collected from warm-season turfgrass in a commercial sod production agroecosystem. Initial collection of soil and turfgrass samples coincided with peak annual biomass (September 2006); the second soil sample collection occurred over twelve weeks later during turfgrass dormancy and ant brood minimum (December 2006). Total C, C/N ratios, organic matter (OM), and Zn²⁺ concentrations as well as pH of ant mound soils were significantly higher than control plot soils; these trends persisted across seasons. Turfgrass harvested from ant mound perimeters in September exhibited elevated N, P, Ca²⁺, S, Cu²⁺, Fe²⁺, and Na⁺ concentrations. Evaluation of the relative stability of soil parameters across seasons revealed a significant drop in ant nest pH from September to December 2006. Total N of mound soils was distinctively greater than control soil counterparts during September only. Soil P, K⁺, Ca²⁺, Mg²⁺ and S (all macronutrients), as well as Na⁺ concentrations from ant mound soils were substantially elevated during the late Autumn to Winter transition compared to control soil locations, whereas Fe²⁺ and Mn²⁺ levels (both micronutrients) were significantly lower in ant mound soils versus control soil environments. Continuous pedoturbation by imported fire ants as well as seasonal shifts in mound soil chemistry resulting from changes in assimilation/dissimilation among mound biota may influence the site-specific effectiveness of microfaunal pathogens (e.g., Thelohania solenopsae) or parasites (e.g., Orasema spp.) identified as classical biological control agents of non-native Solenopsis spp. Therefore, further study of the intrinsic complexities of soil ecosystem dynamics of imported fire ant mounds across several seasons is warranted. Received 10 September 2007; revised 23 April 2008; accepted 1 May 2008.     

Chemistry and Microbial Functional Diversity Differences in Biofuel Crop and Grassland Soils in Multiple Geographies

We obtained soil samples from geographically diverse switchgrass (Panicum virgatum L.) and sorghum (Sorghum bicolor L.) crop sites and from nearby reference grasslands and compared their edaphic properties, microbial gene diversity and abundance, and active microbial biomass content. We hypothesized that soils under switchgrass, a perennial, would be more similar to reference grassland soils than sorghum, an annual crop. Sorghum crop soils had significantly higher NO₃ ^? -N, NH₄ ⁺ -N, SO₄ ^2? -S, and Cu levels than grassland soils. In contrast, few significant differences in soil chemistry were observed between switchgrass crop and grassland soils. Active bacterial biomass was significantly lower in sorghum soils than switchgrass soils. Using GeoChip 4.0 functional gene arrays, we observed that microbial gene diversity was significantly lower in sorghum soils than grassland soils. Gene diversity at sorghum locations was negatively correlated with NO₃ ^? -N, NH₄ ⁺ -N, and SO₄ ^2? -S in C and N cycling microbial gene categories. Microbial gene diversity at switchgrass sites varied among geographic locations, but crop and grassland sites tended to be similar. Microbial gene abundance did not differ between sorghum crop and grassland soils, but was generally lower in switchgrass crop soils compared to grassland soils. Our results suggest that switchgrass has fewer adverse impacts on microbial soil ecosystem services than cultivation of an annual biofuel crop such as sorghum. Multi-year, multi-disciplinary regional studies comparing these and additional annual and perennial biofuel crop and grassland soils are recommended to help define sustainable crop production and soil ecosystem service practices.     

不同恢复阶段热带森林土壤nirS型反硝化微生物群落结构及多样性特征

探明热带森林土壤反硝化微生物群落结构及多样性,对于理解反硝化引起的N₂O排放及缓解全球变暖具有重要意义。本研究以西双版纳3个不同恢复阶段热带森林类型[即白背桐（Mallotus paniculatus,MP）、崖豆藤（Millttia leptobotrya,ML）群落、群落及高檐蒲桃（Syzygium oblatum,SO）群落]为研究对象,揭示土壤nirS型反硝化微生物群落组成及多样性的干湿季变化,分析热带森林恢复过程中土壤理化环境变化对nirS型反硝化细菌群落的影响。结果表明,变形菌门（Proteobacteria）和酸杆菌门（Acidobacteria）相对丰度表现为恢复前期高于恢复后期,而脱氯单胞菌属（Dechloromonas）、嗜盐单胞菌属（Halomonas）和罗思河小杆菌属（Rhodanobacter）表现为恢复后期高于恢复前期;绿弯菌门（Chloroflexi）和放线菌门（Actinobacteria）均随恢复年限增加而增加,而贪铜菌属（Cupriavidus）和假单胞菌属（Pseudomonas）的相对丰度表现为随恢复年限增加而降低。9月份各样地新检测出的属数量表现为：SO （19种） > MP （13种） > ML （7种）。土壤nirS型反硝化微生物群落的Shannon多样性指数表现为：高檐蒲桃群落 > 崖豆藤群落 > 白背桐群落,且9月（湿季） > 3月（干季）。相关分析表明,热带森林恢复引起土壤N库（全氮、NH₄⁺、NO₃^-）、C有效性（微生物量碳、易氧化碳）及微气候（土壤含水率与温度）的改变,能够显著影响nirS型反硝化细菌群落的结构及多样性。主成分分析结果表明,土壤硝态氮、微生物量碳、全氮及易氧化碳是调控不同恢复阶段热带森林土壤nirS型反硝化细菌群落结构及多样性变化的主控因子,其次为土壤水分、温度、水解氮、pH、铵态氮、有机碳、容重及C/N。     

Amino acid abundance and proteolytic potential in North American soils

Studies of nitrogen (N) cycling have traditionally focused on N mineralization as the primary process limiting plant assimilation of N. Recent evidence has shown that plants may assimilate amino acids (AAs) directly, circumventing the mineralization pathway. However, the general abundance of soil AAs and their relative importance in plant N uptake remains unclear in most ecosystems. We compared the concentrations and potential production rates of AAs and NH₄ ⁺, as well as the edaphic factors that influence AA dynamics, in 84 soils across the United States. Across all sites, NH₄ ⁺ and AA-N comprised similar proportions of the total bioavailable N pool (~20%), with NO₃ ⁻ being the dominant form of extractable N everywhere but in tundra and boreal forest soils. Potential rates of AA production were at least comparable to those of NH₄ ⁺ production in all ecosystems, particularly in semi-arid grasslands, where AA production rates were six times greater than for NH₄ ⁺ (P < 0.01). Potential rates of proteolytic enzyme activity were greatest in bacteria-dominated soils with low NH₄ ⁺ concentrations, including many grassland soils. Based on research performed under standardized laboratory conditions, our continental-scale analyses suggest that soil AA and NH₄ ⁺ concentrations are similar in most soils and that AAs may contribute to plant and microbial N demand in most ecosystems, particularly in ecosystems with N-poor soils.     

Dissolved organic carbon affects soil microbial activity and nitrogen dynamics in a Mexican tropical deciduous forest

Seasonal variation of dissolved organic C (DOC) and its effects on microbial activity and N dynamics were studied during two consecutive years in soils with different organic C concentrations (hilltop and hillslope) in a tropical deciduous forest of Mexico. We found that DOC concentrations were higher at the hilltop than at the hillslope soils, and in both soils generally decreased from the dry to the rainy season during the two study years. Microbial biomass and potential C mineralization rates, as well as dissolved organic N (DON) and NH₄⁺ concentrations and net N immobilization were higher in soils with higher DOC than in soils with lower DOC. In contrast, net N immobilization and NH₄⁺ concentration were depleted in the soil with lowest DOC, whereas NO₃⁻ concentrations and net nitrification increased. Negative correlations between net nitrification and DOC concentration suggested that NH₄⁺ was transformed to NO₃⁻ by nitrifiers when the C availability was depleted. Taken together, our results suggest that available C appears to control soil microbial activity and N dynamics, and that microbial N immobilization is facilitated by active heterotrophic microorganisms stimulated by high C availability. Soil autotrophic nitrification is magnified by decreases in C availability for heterotrophic microbial activity. This study provides an experimental data set that supports the conceptual model to show and highlight that microbial dynamics and N transformations could be functionally coupled with DOC availability in the tropical deciduous forest soils. Responsible Editor: Chris Neill