Microbial Responses to Long-Term N Deposition in a Semiarid Grassland

Nitrogen (N) enrichment of the biosphere is an expanding problem to which arid ecosystems may be particularly sensitive. In semiarid grasslands, scarce precipitation uncouples plant and microbial activities, and creates within the soil a spatial mosaic of rhizosphere and cyanobacterial crust communities. We investigated the impact of elevated N deposition on these soil microbial communities at a grama-dominated study site located incentral New Mexico (USA). The study plots were established in 1995 and receive 10 kg ha⁻¹ year⁻¹ of supplemental N in the form of NH₄NO₃. Soil samples were collected in July 2004, following 2 years of severe drought, and again in March 2005 following a winter of record high precipitation. Soils were assayed for potential activities of 20 extracellular enzymes and N₂O production. The rhizosphere and crust-associated soils had peptidase and peroxidase potentials that were extreme in relation to those of temperate soils. N addition enhanced glycosidase and phosphatase activities and depressed peptidase. In contrast to temperate forest soils, oxidative enzyme activity did not respond to N treatment. Across sampling dates, extracellular enzyme activity responses correlated with inorganic N concentrations. N₂O generation did not vary significantly with soil cover or N treatment. Microbial responses to N deposition in this semiarid grassland were distinct from those of forest ecosystems and appear to be modulated by inorganic N accumulation, which is linked to precipitation patterns.     

Some Filamentous Fungi on Grassland Vegetation from Kenya

Herbaceous plants endemic to native Kenyan grassland on the Marula Estate were assessed for their phylloplane fungal occurrence using leaf cultures on tap water agar. From 26 sampled plants, 261 fungal isolates representative of 58 genera and 92 taxa were identified. The principal filamentous fungi were of the genera: Alternaria, Bipolaris, Curvularia, Epicoccum, Fusarium, Nigrospora, Periconia, Phoma and Pithomyces. The fungal species that occurred most frequently were: Alternaria alternata aggreate (73%), Pithomyces chartarum (73%) Nigrospora sphaerica (42%), Torula herbarum (30%) and Microsphaeropsis olivacea (27%). Fungi of limited occurrence were: Didymosphaeria oblitescens, Doliomyces mysoriensis, Endophragmiella dimorphospora, Parapericonia angusii, Podospora minicaudata, Spegazzinia tessarthra, Sporormiella minima, Stagonospora vitensis, Stigmella effigurata and Truncatella conorum-piceae. It is postulated that the phylloplane of these endemic plants provides a niche for endemic fungi. This revised version was published online in June 2006 with corrections to the Cover Date.     

Do Grasslands Have a Memory: Modeling Phytomass Production of a Semiarid South African Grassland

We analyzed data sets on phytomass production, basal cover, and monthly precipitation of a semiarid grassland in South Africa for good, medium, and poor rangeland condition (a) to investigate whether phytomass production per unit of basal cover differed among rangeland conditions, (b) to quantify the time scales of a carryover effect from production in previous months, and (c) to construct predictive models for monthly phytomass. Finally, we applied the best models to a 73-year data set of monthly precipitation data to study the long-term variability of grassland production. Our results showed that mean phytomass production per unit of basal cover did not vary significantly among the rangeland conditions—that is, vegetated patches in degraded grassland have approximately the same production as vegetated patches in grassland in good condition. Consequently, the stark decline in production with increasing degradation is a first-order effect of reduced basal area. Current-year precipitation accounted for 64%, 62%, and 36% of the interannual variation in phytomass production for good, medium, and poor condition, respectively. We found that 61%, 68%, and 33%, respectively, of the unexplained variation is related to a memory index that combines mean monthly temperature and a memory of past precipitations. We found a carryover effect in production from the previous 4 years for grassland in good condition and from the previous 1 or 3S month for grassland in medium and poor condition. The memory effect amplified the response of production to changes in precipitation due to alternation of prolonged periods of dry or wet years/months at the time scale of the memory. The interannual variability in phytomass production per unit basal cover (coefficient of variation [CV] = 0.42–0.50 for our 73-year prediction, CV = 0.57–0.71 for the 19-year data) was greater than the corresponding temporal variability in seasonal rainfall (CV = 0.29).     

Solubilization and Mineralization of Lignin by White Rot Fungi

The white rot fungi Lentinula edodes, Phanerochaete chrysosporium, Pleurotus sajor-caju, Flammulina velutipes, and Schizophyllum commune were grown in liquid media containing ¹⁴C-lignin-labelled wood, and the formation of water-soluble ¹⁴C-labelled products and ¹⁴CO₂, the growth of the fungi, and the activities of extracellular lignin peroxidase, manganese peroxidase, and laccase were measured. Conditions that affect the rate of lignin degradation were imposed, and both long-term (0- to 16-day) and short-term (0- to 72-h) effects on the production of the two types of product and on the activities of the enzymes were monitored. The production of ¹⁴CO₂-labelled products from the aqueous ones was also investigated. The short-term studies showed that the different conditions had different effects on the production of the two products and on the activities of the enzymes. Nitrogen sources inhibited the production of both products by all species when differences in growth could be discounted. Medium pH and manganese affected lignin degradation by the different species differently. With P. chrysosporium, the results were consistent, with lignin peroxidase playing a role in lignin solubilization and manganese peroxidase being important in subsequent CO₂ production.     

Calorific Content of Certain Bacteria and Fungi

Calorific contents of dried cells of several representative species of bacteria (gram-negative rods and gram-positive rods and cocci), two species of yeasts, and a filamentous fungus were determined by bomb calorimetry. The grand mean was 5,383 cal per g of ash-free dry weight. This value was then used to determine quantity of energy assimilated (E(a)) during growth. Subsequently, E(a) was employed in the equation: Y(kcal) = Y/(E(a) + E(d)), where Y(kcal) is the yield of cells per kilocalorie of energy taken from a culture medium, Y is the yield per mole of substrate utilized, E(a) is Y times caloric content of the cells, and E(d) is the energy expended by oxidative dissimilation. An estimate of E(d) was obtained for a number of experiments by multiplying the moles of oxygen consumed per mole of substrate utilized during growth by the average quantity of energy utilized to reduce a mole of oxygen with electrons from organic compounds (106 kcal). From previous studies in our laboratories, a value for Y(kcal) of 0.118 g/kcal was predicted. The mean value for data from five studies of aerobic growth of prototrophic heterotrophs was found to be 0.111.     

Controls over Soil Nitrogen Pools in a Semiarid Grassland Under Elevated CO2 and Warming

Long-term responses of terrestrial ecosystems to the combined effects of warming and elevated CO₂ (eCO₂) will likely be regulated by N availability. The stock of soil N determines availability for organisms, but also influences loss to the atmosphere or groundwater. eCO₂ and warming can elicit changes in soil N via direct effects on microbial and plant activity, or indirectly, via soil moisture. Detangling the interplay of direct- and moisture-mediated impacts on soil N and the role of organisms in controlling soil N will improve predictions of ecosystem-level responses. We followed individual soil N pools over two growing seasons in a semiarid temperate grassland, at the Prairie Heating and CO₂ Enrichment experiment. We evaluated relationships of N pools with environmental factors and explored the role of plants by assessing plant biomass, plant N, and plant inputs to soil. We also assessed N forms in plots with and without vegetation to remove plant-mediated effects. Our study demonstrated that the effects of warming and eCO₂ are highly dependent on individual N form and on year. In this water-constrained grassland, eCO₂, warming and their combination appear to impact soil N pools through a complex combination of direct- and moisture-mediated effects. eCO₂ decreased NO₃ ^? but had neutral to positive effects on NH₄ ⁺ and dissolved organic N (DON), particularly in a wet year. Warming increased NO₃ ^? availability due to a combination of indirect drying and direct temperature-driven effects. Warming also increased DON only in vegetated plots, suggesting plant mediation. Our results suggest that impacts of combined eCO₂ and warming are not always equivalent for plant and soil pools; although warming can help offset the decrease in NO₃ ^? availability for plants under eCO₂, the NO₃ ^? pool in soil is mainly driven by the negative effects of eCO₂.     

Hydrocarbon Mineralization in Sediments and Plasmid Incidence in Sediment Bacteria from the Campeche Bank

Rates of degradation of radiolabeled hydrocarbons and incidence of bacterial plasmid DNA were investigated in sediment samples collected from the Campeche Bank, Gulf of Mexico, site of an offshore oil field containing several petroleum platforms. Overall rates of mineralization of [¹⁴C]hexadecane and [¹⁴C]phenanthrene measured for sediments were negligible; <1% of the substrate was converted to CO₂ in all cases. Low mineralization rates are ascribed to nutrient limitations and to lack of adaptation by microbial communities to hydrocarbon contaminants. Plasmid frequency data for sediment bacteria similarly showed no correlation with proximity to the oil field, but, instead, showed correlation with water column depth at each sampling site. Significant differences between sites were observed for proportion of isolates carrying single or multiple plasmids and mean number of plasmids per isolate, each of which increased as a function of depth.     

Factors Affecting Revegetation of Oil Field Access Roads in Semiarid Grassland

We assessed vegetation recovery on access roads removed after well abandonment in an active oil‐producing region of northern Great Plains grasslands. We compared extant vegetation on 58 roads, restored 3–22 years previously, to records of species seeded on each and to adjacent, undisturbed prairie, to evaluate main differences between the restored and adjacent community and to explore patterns in the restored plant community over time. The restored plant community was dominated by low richness of seeded non‐native and native grasses and forbs, whereas adjacent prairie had numerous, abundant native graminoids and shrubs and higher richness of native forbs. Cover of seeded species on roads was double that of colonizing species. Disparity in cover of dominant native grasses between the adjacent community and relatively narrow restored roadway suggests that conditions for germination and survival in roadbeds are poor. This is at least partly due to persistence of seeded species. Differences in restored plant composition over time were best explained by changes in species seeded, from non‐natives to natives, and secondarily by successional shifts from ruderal to perennial non‐seeded species. Of the 30 species seeded at least once on these roads, only 10 were commonly used. The long‐term influence of seeding choices in grassland road restorations implies that improvements in these practices will be critical to reversing ecological impacts of roads.     

Antibiosis between Ruminal Bacteria and Ruminal Fungi

Cellulose digestion, bacterial numbers, and fungal numbers were monitored over time in vitro by using a purified cellulose medium with and without antibiotics (penicillin and streptomycin). All fermentations were inoculated with a 1:10 dilution of whole rumen contents (WRC). Without antibiotics, cellulose digestion was higher (P < 0.01) at 24, 30, 48, and 72 h; fungi had almost disappeared by 24 h, while bacterial concentrations increased over 100-fold in 24 h and then decreased gradually up to 72 h. In those fermentations with added antibiotics, fungal concentrations increased 4-fold by 30 h and up to 42-fold at 72 h; bacterial concentrations were markedly reduced by 24 h and remained low through 72 h. Similar results were obtained with ground alfalfa as a substrate. In further studies, the in vitro fermentation of purified cellulose without antibiotics was stopped after 18 to 20 h, and the microbial population was killed by autoclaving. Antibiotics were added to half of the tubes, and all tubes were reinoculated with WRC. After 72 h, extensive cellulose digestion had occurred in those tubes without antibiotics, as compared to very low cellulose digestion with added antibiotics. The extent of this inhibition was found to increase in proportion to the length of the initial fermentation period, suggesting the production of a heat-stable inhibitory factor or factors. The inhibitory activity was present in rumen fluid, could be extracted from lyophilized rumen fluid (LRF) with water, and was stable in response to proteolytic enzymes. In addition, the water-extracted residue of LRF was found to contain growth factor activity for rumen fungi in vitro.     

Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi

Background

Polyketides are natural products with a wide range of biological functions and pharmaceutical applications. Discovery and utilization of polyketides can be facilitated by understanding the evolutionary processes that gave rise to the biosynthetic machinery and the natural product potential of extant organisms. Gene duplication and subfunctionalization, as well as horizontal gene transfer are proposed mechanisms in the evolution of biosynthetic gene clusters. To explain the amount of homology in some polyketide synthases in unrelated organisms such as bacteria and fungi, interkingdom horizontal gene transfer has been evoked as the most likely evolutionary scenario. However, the origin of the genes and the direction of the transfer remained elusive.

Methodology/Principal Findings

We used comparative phylogenetics to infer the ancestor of a group of polyketide synthase genes involved in antibiotic and mycotoxin production. We aligned keto synthase domain sequences of all available fungal 6-methylsalicylic acid (6-MSA)-type PKSs and their closest bacterial relatives. To assess the role of symbiotic fungi in the evolution of this gene we generated 24 6-MSA synthase sequence tags from lichen-forming fungi. Our results support an ancient horizontal gene transfer event from an actinobacterial source into ascomycete fungi, followed by gene duplication.

Conclusions/Significance

Given that actinobacteria are unrivaled producers of biologically active compounds, such as antibiotics, it appears particularly promising to study biosynthetic genes of actinobacterial origin in fungi. The large number of 6-MSA-type PKS sequences found in lichen-forming fungi leads us hypothesize that the evolution of typical lichen compounds, such as orsellinic acid derivatives, was facilitated by the gain of this bacterial polyketide synthase.     

油茶根际溶磷菌的分离、鉴定及溶磷能力研究

采用传统的微生物分离培养法,对油茶根际溶磷细菌进行了分离,共筛选得到17株溶磷细菌。利用透明圈法对油茶根际土壤中具有溶磷能力的细菌进行初筛;采用钼锑抗比色法测定发酵液的可溶性磷含量,对解磷菌株进行复筛,得出菌株6-Y-09溶磷活性最强。根据进行菌落形态特征、生理生化特征、16S r DNA序列和系统发育分析等研究,初步鉴定菌株6-Y-09为洋葱伯克霍尔德菌。该菌株在后续微生物菌肥研制中具有较大潜力,为通过生物途径改善油茶磷素供应,促进油茶生长提供了优良的菌株资源。     

Juniper Shade Enables Terricolous Lichens and Mosses to Maintain High Photochemical Efficiency in a Semiarid Temperate Sand Grassland

On a semiarid sand grassland (Festucetum vaginatae) colonised by juniper (Juniperus communis L.) shrubs terricolous lichens and mosses segregate strongly between microhabitats: certain species grow in the open grassland, others almost exclusively in the shade of junipers. The contrasting irradiances of these microhabitats influence much the metabolism of these organisms, and thus affect their small-scale distribution. This was confirmed by determining the efficiency of photochemical energy conversion by measuring chlorophyll a fluorescence parameters. In the open grassland maximum photochemical efficiency of photosystem 2 (PS2, F_v/F_m) declined from the humid spring to the hot and dry summer in all species, and this was caused by an increase in base fluorescence (F₀), but not by the decrease in fluorescence maximum (F_m). In summer, mosses and lichens growing in the open grassland generally possessed lower F_v/F_m than cryptogams growing in the shade cast by juniper shrubs. Thus mosses and lichens in the open grassland suffer lasting reduction in photochemical efficiency in summer, which is avoided in the shade of junipers. Juniper shrubs indeed influence the composition and small-scale spatial pattern of sympatric terricolous lichen and moss communities by—among others—providing a shelter against high light in summer.