bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of the methanogenic archaeal community in anoxic rice soil upon addition of straw
Authors: Conrad R. , Klose M. 
Published: March 2006

SummaryAddition of rice straw, which is a common practice in rice agriculture, generally results in enhanced production and emission of the greenhouse gas methane (CH4). However, it is unclear whether straw addition affects only the activity or also the composition of the methanogenic microbial community. It is also unclear to what extent methanogenic archaea would be able to proliferate in the soil. Anoxic slurries of Italian rice‐field soil produced CH4 after a lag, during which ferric iron and sulfate were reduced. Addition of rice straw slightly decreased this lag and greatly enhanced the subsequent production of CH4. At the same time, addition of rice straw enhanced the intermediate production of H2 and acetate that served as the methanogenic substrates. Compared with the unamended control, the addition of rice straw resulted in an increased concentration of phospholipid fatty acids in the soil. Quantitative ‘real‐time’ PCR targeting the 16S rRNA gene also showed increased copy numbers of both Bacteria and Archaea in the straw‐amended soil at the end of the experiment. The composition of the archaeal community was followed over time by terminal restriction length polymorphism (T‐RFLP) analysis of the archaeal 16S rRNA genes extracted from straw‐amended soil and the control. Rice Cluster‐I (RC‐I) methanogens and Methanosarcinaceae were the most abundant methanogenic populations, followed by Methanobacteriales, Methanomicrobiales and Methanosaetaceae. Addition of rice straw resulted in a relative increase of Methanosarcinaceae and Methanobacteriales and a relative decrease of RC‐I methanogens and Methanomicrobiales. Our results revealed a dynamic methanogenic community in anoxic rice‐field soil and showed that addition of organic matter selectively enhanced the growth of particular methanogenic populations, which were apparently better adapted to the presence of straw than the others. The extent of archaeal growth was consistent with that expected theoretically from the ambient Gibbs free energies of hydrogenotrophic and acetoclastic methanogenesis.
Influence of available substrates on the decomposition in soil of plant materials with genetic modifications to lignin biosynthesis
Authors: Hopkins D. W. , Webster E. A. , Tilston E. L. , Halpin C. 
Published: March 2006

SummaryThe decomposition in soil of plant material from the stems of uniformly grown tobacco plants with genetic modifications to lignin biosynthesis was investigated by measuring CO2 production over 74 days. The effect on decomposition of readily available C, N and combined C plus N (as glucose, NH4NO3 and alanine, respectively) were determined by adding these compounds to the soil before the addition of plant materials. The genetic modifications to tobacco were the introduction of partial or antisense transgenes for cinnamyl alcohol dehydrogenase (CAD), caffeic acid O‐methyl transferase (COMT) and cinnamoyl CoA reductase (CCR), which are all enzymes that catalyse key steps in the monolignol pathway. In line with previous reports, reduced CCR material decomposed significantly faster than the reduced CAD or reduced COMT materials, which decomposed significantly faster than the unmodified material. All the plant materials had large C‐to‐N ratios (58, 72, 61 and 52 for the unmodified, reduced CAD, reduced COMT and reduced CCR materials, respectively), but the relationships between C‐to‐N ratio and decomposition rate were not consistent across all materials. Addition of glucose slowed the decomposition rate of all the materials. This is consistent with the additional C leading to a surplus of C relative to other nutrients at the sites of plant residue decomposition, but the reduction in decomposition rate was directly related to the combined C‐to‐N ratio of the plant material and soil amendment. In the case of reduced CCR material, addition of N as either NH4NO3 or alanine led to an increase in decomposition rate, indicating that a constraint on decay of this material was alleviated by N addition. However, addition of N did not increase the decomposition of the unmodified, reduced CAD and reduced COMT materials, which indicates that their decomposition was constrained by factors other than N. We have shown significant effects of targeted lignin modification on decomposition in laboratory studies over a relatively short period (< 74 days). However, longer‐term and more detailed field‐based investigations are needed before the wider ecological significance of the differences in decomposition can be properly assessed.
Analysis of variance, inference, multiple comparisons and sampling effects in soil research
Authors: Webster R. 
Published: March 2006

SummaryThe analysis of variance is a crucial step in extracting information from efficiently designed experiments and surveys in soil science. It is only the beginning, however. From it, follow the standard errors (SEs) of means, SEs of differences and other effects provided by experiments, which in turn lead to tests of significance. Use the simple least significant difference (LSD) at some acceptable probability for testing comparisons of individual means. Do not use experiment‐wise multiple comparison tests. In experiments with graded treatments do not make multiple comparisons of any kind; instead fit a response curve and analyse the data by regression. Sampling fluctuation within experimental units and surveys contributes short‐range variation to the residual variance of measured soil properties and increases errors. Diminish this contribution either by replicate sampling and measurement within plots or by bulking before measurement. Sample all replicates in the field; sampling in the laboratory (pseudo‐replication) is no substitute. In almost all investigations the mean values for experimental treatments and survey classes are the most important outcomes. So report them with their SEs; readers will then be able to make of them what they will.L’analyse de variance, inférence, comparaisons multiples et des effets d’échantillonage dans la recherche du solRésuméL’analyse de variance est une étape cruciale pour extraire des informations pertinentes des expériences et prospections conues en science du sol. Neanmoins, elle ne constitue qu’un commencement. D’elle proviennent les écart‐types des moyennes, les écart‐types des différences et d’autres paramètres issus d’expériences, dont la connaissance conduit aux tests de signification. Pour tester les différences entre couples de moyennes, il faut utiliser la plus petite différence significative simple et éviter les tests de comparaisons multiples entre l’ensemble des moyennes d’une expérience. Dans les expériences qui comprennent des traitements progressifs il ne faut pas faire des comparaisons entre les différents niveaux des traitements, mais ajuster une courbe de réponse puis analyser les données par régression. La fluctuation d’échantillonnage dans les unités expérimentales et les prospections contribue aux variations à courte distance au sein de la variance residuelle des propriétés du sol mesurées et augmente les erreurs. Cette contribution est réduite par un échantillonnage avec répétitions des mesures dans les parcelles ou par création d’échantillons composites avant mesure. Les répétitions doivent être effectuées au champ; l’échantillonnage au laboratoire (pseudo‐replication) n’est pas un substitut. Dans presque toutes les investigations les moyennes des traitements expérimentaux et des classes de sols sont les plus importantes. Il faut donc les estimer avec leurs écarts‐types; les lecteurs pourront ensuite effectuer leurs propres inférences.
The diversity and conservation of plant reproductive and dispersal functional traits in human‐dominated tropical landscapes
Authors: MAYFIELD MARGARET M. , ACKERLY DAVID , DAILY GRETCHEN C. 
Published: March 2006

Summary
Human‐altered landscapes dominate the planet, yet little is known about their capacity to sustain plant functional diversity. Most conservation‐orientated studies of such landscapes focus on species diversity, whereas less attention is given to functional traits and their conservation.
We examine the functional diversity of herbaceous and shrubby plant communities in three forest habitats (understorey, tree‐fall gaps and riverbanks) and three deforested habitats (pasture, roadside vegetation and pasture riverbanks), each replicated in three human‐dominated landscapes in southern Costa Rica. We focus on six categorical traits related to forest regeneration, reproduction and dispersal: pollination mechanism, dispersal mechanism, growth form, fruit type, fruit size and seed size.
We compared trait state richness and composition of each trait in forested and deforested habitats and how three pollination states (bat, bird and bee pollination) and three dispersal states (fur, bird and monkey dispersal) of conservation interest were distributed across these landscapes.
Only one trait state was missing from forest, and none was missing from deforested habitats. Understorey and pasture were consistently trait state poor. Forested and deforested plots differed in trait state composition for all traits. Pasture riverbanks and road verges were compositionally similar to forest riverbanks and tree‐fall gaps, for multiple traits. There were more compositional similarities between forested and deforested habitat types when abundance of individuals with a trait state was used as the basis for similarity measures than when the number of species with each trait state was used. Bat‐, bird‐ and bee‐pollinated plants and plants with bird‐ and monkey‐dispersed fruits were most common in forest and pasture riverbanks whereas species with fur‐dispersed seeds were more common in all deforested habitats.
Functional diversity patterns were inconsistent across habitat types and locations but overall functional similarity was high between forested and deforested communities. Patterns of functional diversity were far more variable between habitats and landscapes than the consistent patterns found previously for species diversity.
The effects of neighbouring tree islands on pollinator density and diversity, and on pollination of a wet prairie species, Asclepias lanceolata (Apocynaceae)
Authors: ARTZ DEREK R. , WADDINGTON KEITH D. 
Published: March 2006

Summary
The Everglades (Florida, USA) is a mosaic of different habitats. Tropical and temperate trees grow on patches of high ground (tree islands) surrounded by lower elevation wetland communities (marl prairie).
Tree islands of various sizes provide nesting substrate, larval host plants and floral resources for insect pollinators. Herbaceous plants in the open surrounding wetlands may also depend on these pollinators.
We investigated pollinator diversity and abundances in both tree island and marl prairie habitats using transect sampling methods and estimated pollination success of the milkweed Asclepias lanceolata, an insect‐pollinated marl prairie species, in relation to distance from and size of the closest tree island.
On a total of 11 bayhead tree islands, we found that insect diversity and abundance were greater on the edge of larger tree islands (20–30 m2) than on smaller tree islands (5–10 m2). Pollinator diversity and abundance in the marl prairie decreased with increasing distance from tree islands.
Pairs of potted A. lanceolata plants were placed in the marl prairie at distances up to 1000 m from small and large tree islands. Fruit and seed production were highest for plants placed less than 25 m from tree islands and decreased with increasing distance.
Our results suggest that tree islands are an important source of pollinators for the plants in the tree island and surrounding wetland habitats.
This landscape‐based study illustrates how overall landscape structure affects important biotic interactions, particularly plant–pollinator relationships. Our findings have far‐reaching ecological implications for the reproductive success of plants in small, isolated populations that may depend on insect vectors for pollination.
Metapopulation processes in epiphytes inferred from patterns of regional distribution and local abundance in fragmented forest landscapes
Authors: LÖBEL SWANTJE , SNÄLL TORD , RYDIN HÅKAN 
Published: March 2006

SummaryDeciduous trees within a coniferous forest landscape provide habitat for many organisms. Single trees in deciduous forests form dynamic patches that emerge, grow and fall, but the stands themselves are also dynamic patches established after disturbances and replaced by conifers during succession. Increased dispersal distance, as imposed by landscape fragmentation, may lead to extinctions and reduced biodiversity among species dependent on this dynamic network.We analysed regional frequency distributions, local abundances and spatial occupancy patterns of epiphytic bryophytes in 135 deciduous forest stands in a fragmented landscape in Sweden. We used generalized non‐linear models to test whether these patterns could be assigned to metapopulation dynamics of individual epiphytes by investigating the relative importance of stand size, habitat quality, connectivity and landscape history on species occupancies and local abundances.Most asexually dispersed species were regionally rare, and spatial species occupancy patterns suggest that this is caused by dispersal limitation. In sexually dispersed species, a strong rescue effect was indicated by a bimodal frequency distribution of the species, as well as by increasing local abundance with increasing connectivity to stands present today, or some decades ago. There was a strong positive relationship between regional frequency and local abundance of the species, and between species richness and forest stand size. Vicinity to forest edge negatively affected the local abundance of most species.Our results clearly indicate a metapopulation structure. Sensitivity of epiphytes to habitat fragmentation is caused by decreasing forest sizes, habitat alteration at forest edges and increasing dispersal distances. Even in assumed good dispersers, increasing distances can significantly alter regional dispersal processes. A lower rescue effect leads to smaller stand population sizes with a larger extinction risk. Rapid reduction of the amount of habitat during the last decades and the expected time‐lag in species extinctions suggest that epiphytes will further decline in the future, although there may still be time for restoration programmes to prevent extinction.
Preventing crown collisions increases the crown cover and leaf area of maturing lodgepole pine
Authors: MENG SHAWN X. , RUDNICKI MARK , LIEFFERS VICTOR J. , REID DOUGLAS E. B. , SILINS ULDIS 
Published: March 2006

SummaryCrown collisions induced by tree sway are hypothesized to reduce crown closure and leaf area in maturing cold temperate forests. These declines are thought to lead to the decline in productivity when a stand ages.We tethered groups of lodgepole pine (Pinus contortaDougl. Ex Loud. Var.latifoliaEngelm.) trees in a web pattern at 10 m height, in four 15‐m tall stands in western Alberta, Canada, to determine whether preventing crown collisions would increase crown cover and leaf area.The stands all had less than 65% crown closure at the beginning of study. Photographs of the canopy were taken in each control and webbed plot in 1998 and at the same point in 2004. Six years after webbing, crown cover had increased by 14.4%, compared to a 2.1% increase for the control plots.Webbing also resulted in significant increases in mean branch length, leaf area per branch and foliage density of individual branches from top and middle sections of the crown. Polishing of branches, caused by chronic contact with adjacent trees, was three times as common on control trees compared to webbed trees. The mean leaf area per tree was larger for the webbed trees.Crowns of webbed trees were more symmetrical than those of control trees. Trees from webbed plots, however, had a decline in leaf area density. The branches of control trees were typically curved upward with twigs pointed inward, making the crowns more compact compared to the outwardly expanding crowns of trees from the webbed plots.The fact that crowns expanded laterally after webbing, despite little change in light regime, provides strong evidence against the hypothesis that loss of crown closure in maturing stands is caused by a lack of light.The study indicates that the decline in crown closure and leaf area in maturing and tall stands is at least partly related to wind‐induced sway of trees abrading the edges of crowns.
A stress regulatory network for co‐ordinated activation of proteasome expression mediated by yeast heat shock transcription factor
Authors: Hahn Ji‐Sook , Neef Daniel W. , Thiele Dennis J. 
Published: March 2006

SummaryHeat shock transcription factor (HSF) mediates the transcriptional response of eukaryotic cells to heat, infection and inflammation, pharmacological agents, and other stresses. Although genes encoding heat shock proteins (HSPs) are the best characterized targets of HSF, recent genome‐wide localization of Saccharomyces cerevisiae HSF revealed novel HSF targets involved in a wide range of cellular functions. One such target, the RPN4 gene, encodes a transcription factor that directly activates expression of a number of genes encoding proteasome subunits. Here we demonstrate that HSF co‐ordinates a feed‐forward gene regulatory circuit for RPN4 activation. We show that HSF activates expression of PDR3, encoding a multidrug resistance (MDR) transcription factor that also directly activates RPN4 gene expression. We demonstrate that the HSF binding site (HSE) in the RPN4 promoter is primarily responsible for heat‐ or methyl methanesulphonate induction of RPN4, with a minor contribution of Pdr3 binding sites (PDREs), while a Yap1 binding site (YRE) is responsible for RPN4 induction in response to oxidative stress. Furthermore, heat‐induced expression of Rpn4 protein leads to expression of Rpn4 targets at later stages of heat stress, providing a temporal controlling mechanism for proteasome synthesis upon stress conditions that could result in irreversibly damaged proteins. In addition, the overlapping transcriptional regulatory networks involving HSF, Yap1 and Pdr3 suggest a close linkage between stress responses and pleiotropic drug resistance.
Phosphoenolpyruvate synthetase and pyruvate, phosphate dikinase of Thermoproteus tenax: key pieces in the puzzle of archaeal carbohydrate metabolism
Authors: Tjaden Britta , Plagens André , Dörr Christine , Siebers Bettina , Hensel Reinhard 
Published: March 2006

SummaryThe interconversion of phosphoenolpyruvate and pyruvate represents an important control point of the Embden–Meyerhof–Parnas (EMP) pathway in Bacteria and Eucarya, but little is known about this site of regulation in Archaea. Here we report on the coexistence of phosphoenolpyruvate synthetase (PEPS) and the first described archaeal pyruvate, phosphate dikinase (PPDK), which, besides pyruvate kinase (PK), are involved in the catalysis of this reaction in the hyperthermophilic crenarchaeote Thermoproteus tenax. The genes encoding T. tenax PEPS and PPDK were cloned and expressed in Escherichia coli, and the enzymic and regulatory properties of the recombinant gene products were analysed. Whereas PEPS catalyses the unidirectional conversion of pyruvate to phosphoenolpyruvate, PPDK shows a bidirectional activity with a preference for the catabolic reaction. In contrast to PK of T. tenax, which is regulated on transcript level but exhibits only limited regulatory potential on protein level, PEPS and PPDK activities are modulated by adenosine phosphates and intermediates of the carbohydrate metabolism. Additionally, expression of PEPS is regulated on transcript level in response to the offered carbon source as revealed by Northern blot analyses. The combined action of the differently regulated enzymes PEPS, PPDK and PK represents a novel way of controlling the interconversion of phosphoenolpyruvate and pyruvate in the reversible EMP pathway, allowing short‐term and long‐term adaptation to different trophic conditions. Comparative genomic analyses indicate the coexistence of PEPS, PPDK and PK in other Archaea as well, suggesting a similar regulation of the carbohydrate metabolism in these organisms.
Streptococcus gordonii utilizes several distinct gene functions to recruit Porphyromonas gingivalis into a mixed community
Authors: Kuboniwa Masae , Tribble Gena D. , James Chloe E. , Kilic Ali O. , Tao Lin , Herzberg Mark C. , Shizukuishi Satoshi , Lamont Richard J. 
Published: March 2006

SummaryDental plaque biofilm formation proceeds through a developmental pathway initiated by the attachment of pioneer organisms, such as Streptococcus gordonii, to tooth surfaces. Through a variety of synergistic interactions, pioneer organisms facilitate the colonization of later arrivals including Porphyromonas gingivalis, a potential periodontal pathogen. We have investigated genes of S. gordonii required to support a heterotypic biofilm community with P. gingivalis. By screening a plasmid integration library of S. gordonii, genes were identified that are crucial for the accumulation of planktonic P. gingivalis cells into a multispecies biofilm. These genes were further investigated by specific mutation and complementation analyses. The biofilm‐associated genes can be grouped into broad categories based on putative function as follows: (i) intercellular or intracellular signalling (cbe and spxB), (ii) cell wall integrity and maintenance of adhesive proteins (murE, msrA and atf), (iii) extracellular capsule biosynthesis (pgsA and atf), and (iv) physiology (gdhA, ccmA and ntpB). In addition, a gene for a hypothetical protein was identified. Biofilm visualization and quantification by confocal microscopy confirmed the role of these genes in the maturation of the multispecies community, including biofilm architectural development. The results suggest that S. gordonii governs the development of heterotypic oral biofilms through multiple genetic pathways.
The carboxyl‐terminal linker is important for chemoreceptor function
Authors: Li Mingshan , Hazelbauer Gerald L. 
Published: March 2006

SummarySensory adaptation in bacterial chemotaxis is mediated by chemoreceptor methylation and demethylation. In Escherichia coli, methyltransferase CheR and methylesterase CheB bind both substrate sites and a carboxyl‐terminal pentapeptide sequence carried by certain receptors. Pentapeptide binding enhances enzyme action, an enhancement required for effective adaptation and chemotaxis. Pentapeptides are linked to the conserved body of chemoreceptors through a notably variable sequence of 30–35 residues. We created nested deletions from the distal end of this linker in chemoreceptor Tar. Chemotaxis was eliminated by deletion of 20–40 residues and reduced by shorter deletions. This did not reflect generalized disruption, because all but the most extremely truncated receptors activated kinase, were substrates for adaptational modification and performed transmembrane signalling. In contrast, linker truncations reduced rates of adaptational modification in parallel with chemotaxis. We concluded the linker is important for chemotaxis because of its role in adaptational modification. Effects of linker truncations on CheR binding to receptor‐borne pentapeptide implied linker (i) makes pentapeptide available to modification enzymes by separation from the helical receptor body, and (ii) is a flexible arm allowing dual binding of enzyme to pentapeptide and modification site. The data suggest linker and the helix from which it emerges are structurally dynamic.