Soil bacterial diversity in a loblolly pine plantation: influence of ectomycorrhizas and fertilization

We studied the effect of ectomycorrhizas and fertilization on soil microbial communities associated with roots of 10-year-old loblolly pine. Ectomycorrhizas were identified using a combination of community terminal restriction fragment profiling and matching of individual terminal restriction fragments to those produced from ectomycorrhizal clones and sequences recovered from roots and sporocarps. Differences between bacterial communities were initially determined using cluster analysis on community terminal restriction fragment profiles and through subsequent recovery of 16S rDNA clones. Analysis of bacterial clones revealed that terminal restriction fragment length was often shared between taxonomically dissimilar bacterial types. Consequently, we could not reliably infer the identity of peaks in the bacterial community profile with some exceptions, notably chloroplast rDNA that generated an approximate peak size of 80.2 bp. Fertilization increased the frequency of a Piloderma-like ectomycorrhiza. However, we did not detect clear effects of fertilization or the presence of viable ectomycorrhizas on bacterial communities. Bacterial communities seemed to be determined largely by the carbon and nitrogen content of soil. These results suggest that important soil microbial groups respond differently to soil conditions and management practices, with ectomycorrhizal communities reflecting past nutrient conditions and bacterial communities reflecting current environmental conditions of soil microsites.     

Vegetation characteristics influence fine-scale intensity of habitat use by wild turkey and white-tailed deer in a loblolly pine plantation

Habitat quality is often evaluated based on food availability. However, ecological theory suggests cover should be a more important decision rule when food is not a proximate threat to fitness, as cover mediates predation risk as well as other important factors of fitness. In reality, vegetation characteristics related to food availability and cover are rarely coupled with animal use in the same space and time to determine their relative influences on habitat use. Using an array of 81 camera traps in a matrix of forest management strategies used to deliberately cause a wide disparity in vegetation characteristics, we monitored intensity of use by white-tailed deer (Odocoileus virginianus) and wild turkey (Meleagris gallopavo). We measured vegetation characteristics related to food and cover at each camera trap location then used a generalized additive model to determine how vegetation characteristics specific to the location affected intensity of habitat use by animals at the location. Consistent among both species, cover best explained intensity of habitat use. Contrastingly, food did not explain intensity of habitat use well for either species. Some vegetation simultaneously provides cover and food, and our data indicate that areas with vegetation characteristics providing both resources had the greatest influence on intensity of habitat use by both species. Our results suggest deer and turkey may perceive cover as a more important habitat component when food is not a proximate fitness threat.     

Magnesium uptake kinetics in loblolly pine seedlings

Recent studies have suggested that the growth of loblolly pine (Pinus taeda L.) has declined in the southern United States and it has been hypothesized that foliar Mg deficiency may play an important role in the perceived decline. Quantitative nutrient uptake models such as the Barber-Cushman model have been used successfully to investigate nutrient uptake by crop species under a variety of field and experimental conditions and may provide one approach to evaluating this question. However, in order to use this approach it is necessary to develop, for the plant species and nutrient of interest, values for maximal nutrient influx rate at high solution concentrations (I_max), the solution concentration where net influx is 0.5 I_max (K_m), and the nutrient concentration below which influx ceases (C_min). As a first step in evaluating the potential of such an approach, two sets of experiments using established solution nutrient depletion techniques were used to define these values for loblolly pine seedlings 180, 240, 365, and 425 days in age. Observed I_max values for Mg range from 7.90E-8 to 1.29E-7 mol cm^–2 s^–1 with younger seedlings having higher values. Values of K_m for all seedling ages were quite similar ranging from 8.69 to 8.58E-3 mol cm^–3. Most importantly, the results of both experiments indicate that during a growth flush, seedlings will withdraw Mg from solution until the concentration is essentially zero (C_min=0). During non-flush periods uptake rates appear to be greatly reduced. Therefore, efforts to model Mg uptake will need to take these differences as well as seedling age influences into consideration.     

Inheritance of RFLP loci in a loblolly pine three-generation pedigree

Summary A high-density restriction fragment length polymorphism (RFLP) linkage map is being constructed for loblolly pine (Pinus taeda L.). Loblolly pine cDNA and genomic DNA clones were used as probes in hybridizations to genomic DNAs prepared from grandparents, parents, and progeny of a three-generation outbred pedigree. Approximately 200 probes were evaluated for their ability to detect polymorphic loci between DNAs prepared from the two parent trees, 20–1010 and 11–1060, and cut with four different restriction enzymes: BamHI, DraI, EcoRI, and HindIII. More than half of the probes detecting single- or low-copy number sequences (56%) revealed polymorphisms between the two parents with at least one restriction enzyme. If necessary, an additional hybridization to DNAs prepared from the four grandparent trees was conducted to determine the zygosity of parent trees. Ten of these probes were hybridized to progeny DNAs from this cross and, as expected, the markers were inherited as simple codominant Mendelian alleles. Four of the ten probes detected segregation of three alleles at one locus, and four probes detected more than one independently segregating locus. RFLPs can be used immediately to assess genetic diversity in conifer populations and to efingerprint genotypes in tree improvement programs.     

Average effect of a mutation in lignin biosynthesis in loblolly pine

Cinnamyl alcohol dehydrogenase (CAD, E.C. 1.1.1.195) is a monolignol biosynthetic enzyme that catalyzes the final step of lignin subunit biosynthesis in higher plants. Recently, a mutant allele of the cad gene, cad-n1, encoding for the CAD enzyme, was discovered in loblolly pine. By reducing the expression of the cad gene, this mutant has a decreased lignin content and major changes in the lignin composition in wood. In this study, we found that the substitution of a wild-type allele by cad-n1 was associated with a significant effect on 2nd-year shoot elongation in a half-sib family of loblolly pine (designated family 7–1037). The average effect of cad-n1 appeared to increase with tree growth and was greater for stem radial growth than height growth. An increase of 14.1% in de-barked volume in year 4 was associated with cad-n1. Co-segregation analysis indicated that the cad locus itself might represent a gene that governs stem growth in pine. The significance of the mutation cad-n1 for tree growth and wood processing is discussed. Received: 31 December 1998 / Accepted: 30 January 1999     

Nutrient proportions in foliage of semi-mature loblolly pine

Summary Nitrogen and phosphorus limitations to growth are common in many loblolly pine (Pinus taeda) stands. Interactions of these nutrients may complicate interpretation of foliar nutrient analysis for predicting response to forest fertilization. Proportions of foliar nutrient concentrations (and the changes in these proportions following fertilization) were examined in 36 semi-mature loblolly pine plantations in the southeastern United States. Mean proportions of nutrient concentrations (NPKCaMg) for non-fertilized stands were 1009.336.517.29.2. Potassium and phosphorus were higher. Nitrogen fertilization generally decreased the PN ratio and enhanced growth, indicating a nitrogen deficiency in most stands under study. Additions of nitrogen and phosphorus together yielded a significant increase in the PN ratio. Effects of fertilization effects on other nutrient concentration ratios were also examined.Paper No. 9401 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695.     

Patterns of saproxylic beetle succession in loblolly pine

• 1 Patterns of insect succession in dead wood remain unclear, particularly beyond the first several years of decay. In the present study, saproxylic beetles were sampled from loblolly pine (Pinus taeda L.) logs aged between 1 month and 9 years old using both emergence traps attached to logs in the field and rearing bags in the laboratory.
• 2 Species richness peaked within the first year as a result of a diverse assemblage of bark beetles, wood‐borers and predators associated with young logs. After the phloem phase, there were no significant differences in species richness among decay classes.
• 3 Beetle communities differed significantly among decay classes, with 25 and seven species being significantly associated with young and old logs, respectively.

     

Characterization of EST-SSRs in loblolly pine and spruce

In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia) and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce, respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for in-silico approaches for marker development.     

Gas exchange and canopy structure of 9-year-old loblolly pine,pitch pine and pitch x loblolly hybrids

Summary Seasonal gas exchange and canopy structure were compared among 9-year-old loblolly pine (Pinus taeda L.), pitch pine (Pinus rigida Mill.), and pitch x loblolly hybrids (Pinus rigida x taeda) growing in an F2 plantation located in Critz, Va., USA. Leaf net photosynthesis, conductance, internal CO₂ concentration (c_i), water use efficiency (WUE; photosynthesis/conductance), dark respiration and the ratio of net photosynthesis/respiration did not vary among or within the three taxa. Significant differences in volume production, crown length, total crown leaf surface area and the silhouette area of shade shoots among the taxa were observed. The loblolly-South Carolina source had greater volume and crown surface area than the pitch pine, and the hybrid taxa were intermediate between the two. Although the silhouette area ratio of shade foliage varied among taxa, it was not related to volume. A strong relationship between total leaf surface area and volume was observed. Leaf conductance, c_i, WUE and leaf water potential were the physiological parameters significantly and positively correlated with volume. This study suggests that the amount of needle surface in the canopy is more important in early stand volume growth than the leaf carbon exchange rate and the degree of needle self-shading in the lower canopy.     

Winter nitrogen fertilization of loblolly pine seedlings

Loblolly pine (Pinus taeda L.) seedlings were nitrogen fertilized during winter in a bare root forest tree nursery located in the coastal plain of the southeastern United States. Total application rates were 0, 50, 100, and 200 kg/N/ha applied in split applications 4 weeks apart in January and February. Seedlings were lifted and outplanted in March, 4 weeks after the second fertilization and measured at 3 and 6 months after outplanting. No seedling morphological differences were encountered at the time of lifting and outplanting although seedling shoot nitrogen content was 28% greater in the highest fertilization treatment compared to the check. Shoot nitrogen concentrations fell after outplanting regardless of treatment, decreasing from an average of 1.51% across all treatments at the time of planting to 0.64% at 6 months after planting. When measured at 6 months after outplanting, seedling dry weight and height growth after planting was shown to increase by 12% and 24%, respectively, for the high nitrogen treatment. This and other studies across a variety of sites have found positive post-outplanting seedling growth response after nutrient loading in the nursery.     

Timber! Felling the loblolly pine genome

Conventional short read sequences derived from haploid DNA were extended into long super-reads enabling assembly of the massive 22 Gbp loblolly pine, Pinus taeda, genome.See related research http://genomebiology.com/2014/15/3/R59     

An empirical analysis of the factors contributing to 20-year decrease in soil pH in an old-field plantation of loblolly pine

The pH of weak-acid solutions is controlled by acid concentration (HA + A^–), the degree of acid dissociation (A^–/HA), and the strength of the acids present (pK_a). We developed an empirical approach that allows the relative importance of each of these factors to be estimated for soils. This empirical model was applied to soils collected from an old-field plantation of loblolly pine (Pinus taeda L.) at 5 and 25 years of age. During this period, soil pH dropped by 0.3 to 0.8 units, and extractable calcium, magnesium and potassium declined by 20 to 80%. The empirical model indicates that the decline in pH resulted largely from the reduction in base saturation of the exchange complex. However, the average acid strength of the exchange complex decreased during the 20 years, preventing a greater decline of perhaps 0.1 to 0.2 units in the observed pH. The rate of decrease in the acid neutralizing capacity to pH 3.5 was about 1.3 kmol_c/ha annually, while the increase in base neutralizing capacity was about 2.7 and 1.6 kmol_c/ha annually to pH 5.5 and 8.2, respectively. Extractable alkali and alkaline earth cations declined by about 2.2 kmol_c/ha annually, matched by the rate of increase in aluminium. These changes demonstrated the dynamic nature of poorly buffered soils, and indicated that changes in soil acidity may be expected over a period of decades (especially following changes in land-use).     

Throughfall chemistry in a loblolly pine plantationunder elevated atmospheric CO2 concentrations

Accelerated tree growth under elevatedatmospheric CO₂ concentrations may influencenutrient cycling in forests by (i) increasingthe total leaf area, (ii) increasing the supplyof soluble carbohydrate in leaf tissue, and (iii) increasing nutrient-use efficiency. Here wereport the results of intensive sampling andlaboratory analyses of NH ₄ ⁺ , NO ₃ ^– , PO ₄ ^3– , H⁺, K⁺, Na⁺,Ca²⁺, Mg²⁺, Cl^–, SO ₄ ^2– , and dissolved organic carbon (DOC) in throughfallprecipitation during the first 2.5+ years of the DukeUniversity Free-Air CO₂ Enrichment (FACE)experiment. After two growing seasons, a largeincrease (i.e., 48%) in throughfall deposition of DOCand significant trends in throughfall volume and inthe deposition of NH ₄ ⁺ , NO ₃ ^– , H⁺, and K⁺ can be attributed to the elevatedCO₂ treatment. The substantial increase indeposition of DOC is most likely associated withincreased availability of soluble C in plant foliage,whereas accelerated canopy growth may account forsignificant trends toward decreasing throughfallvolume, decreasing deposition of NH ₄ ⁺ ,NO ₃ ^– , and H⁺, and increasing deposition of K⁺ under elevated CO₂. Despiteconsiderable year-to-year variability, there wereseasonal trends in net deposition of NO ₃ ^– ,H⁺, cations, and DOC associated with plant growthand leaf senescence. The altered chemical fluxes inthroughfall suggest that soil solution chemistry mayalso be substantially altered with continued increasesin atmospheric CO₂ concentrations in the future.     

Functional genomics and cell wall biosynthesis in loblolly pine

Loblolly pine (Pinus taeda L.) is the most widely planted tree species in the USA and an important tree in commercial forestry world-wide. The large genome size and long generation time of this species present obstacles to both breeding and molecular genetic analysis. Gene discovery by partial DNA sequence determination of cDNA clones is an effective means of building a knowledge base for molecular investigations of mechanisms governing aspects of pine growth and development, including the commercially relevant properties of secondary cell walls in wood. Microarray experiments utilizing pine cDNA clones can be used to gain additional information about the potential roles of expressed genes in wood formation. Different methods have been used to analyze data from first-generation pine microarrays, with differing degrees of success. Disparities in predictions of differential gene expression between cDNA sequencing experiments and microarray experiments arise from differences in the nature of the respective analyses, but both approaches provide lists of candidate genes which should be further investigated for potential roles in cell wall formation in differentiating pine secondary xylem. Some of these genes seem to be specific to pine, while others also occur in model plants such as Arabidopsis, where they could be more efficiently investigated.     

Growth of loblolly pine callus on a variety of carbohydrate sources

Callus derived from stem segments of loblolly pine (Pinus taeda L.) was subcultured to media containing 0.5% of various mono-, di-, tri- or polysaccharides. None of the carbohydrate sources tested were superior to sucrose. Growth on twelve of the 20 carbohydrates tested was more than 75% of that obtained for sucrose; growth on two other carbohydrates became >75% of the value for sucrose by the second interval on the new carbon source. Ribose and galactose-containing sugars are among those which support pine callus growth. Dramatic differences in ribose utilization are noted on media supplemented with glutamine vs. NH₄/NO₃ nitrogen sources.Abbreviations NAA -naphthaleneacetic acid - BAP benzylaminopurine - BL Brown and Lawrence's medium Paper No. 10377 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695-7601, USA     

湿地松和马尾松人工林土壤甲烷代谢微生物群落的结构特征

土壤甲烷代谢微生物影响甲烷的产生和氧化,然而关于林型对土壤中甲烷代谢微生物群落结构影响的研究较少。采用基因芯片GeoChip 3.0研究了湿地松人工林和马尾松人工林土壤甲烷代谢微生物群落结构特征。结果如下,(1)两种林型的甲烷代谢微生物群落结构存在极显著差异(P=0.008),林型能解释其34.9%的变异;(2)产甲烷菌(包含甲基辅酶M还原α亚基基因mcrA的微生物)的优势菌群发生了变化,湿地松人工林的的优势菌为Methanocorpusculum labreanum Z,马尾松人工林的优势菌群除Methanocorpusculum labreanum Z外,还包括产甲烷古菌和Methanosarcina mazei Gol;(3)甲烷营养菌(包含甲烷单加氧酶基因pmoA基因的微生物)的优势菌为Ⅱ型,有3种不可培养细菌只在湿地松人工林检测到,在马尾松人工林中未检测到;(4)mcrA基因丰度或同源基因数量与土壤容重正相关,与土壤粘粒含量呈显著负相关;pmoA基因信号强度或多样性指数与土壤全碳含量、全磷含量和速效氮含量显著正相关。总之,相比本地种马尾松人工林,引进种湿地松人工林的土壤甲烷代谢微生物群落结构发生了显著变化。     

Peroxidase activity of desiccation-tolerant loblolly pine somatic embryos

Summary Desiccation tolerance can be induced by culturing somatic embryos of loblolly pine (Pinus taeda L.) on medium supplemented with 50 μM abscisic acid (ABA) and/or 8.5% polyethylene glycol (PEG₆₀₀₀). Scanning electron microscopy of desiccated somatic embryos showed that the size and external morphology of the desiccation-tolerant somatic embryos recovered to the pre-desiccation state within 24–36 h, whereas the non-desiccation-tolerant somatic embryos did not recover and remained shriveled, after rehydration. Peroxidase activity of desiccated somatic embryos increased sharply after 1 d of desiccation treatment at 87% relative humidity (RH), and desiccation-tolerant somatic embryos had higher peroxidase activity compared to sensitive somatic embryos. Higher peroxidase activity of desiccation-tolerant somatic embryos may have allowed them to catalyze the reduction of H₂O₂ produced by drought stress, and protected them from oxidative damage.