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Enzyme properties down the soil profile - A matter of substrate quality in rhizosphere and detritusphere
No full textThe decomposition of soil organic matter depends strongly on its availability to microorganisms and their enzymes. The rhizosphere and detritusphere are microbial hot spots due to additional substrate input, leading to high abundance, specific species diversity and functional diversity of microbial communities. However, rhizosphere and detritusphere differ in substrate quality, localization, and duration of input. We hypothesized that the contrasting substrate availability between rhizosphere and detritusphere affects the activity of microorganisms and associated enzymes. Organic carbon (C) from the rhizosphere and detritusphere decreases with soil depth and, consequently, microbial hot spots become rarer and competition for C and nutrients increases. In deeper soil (>40 cm depth) the amount and quality of substrates is expected to decrease and, therefore, the effect of contrasting substrate input to disappear. Plant N uptake is expected to reduce N availability in the rhizosphere of maize compared to the detritusphere and bare fallow. These hypotheses were tested in a factorial field experiment with 1) maize-planted, 2) maize litter-amended, and 3) bare sites. Enzyme kinetic parameters (V-max, K-m, K-a), extractable organic C and microbial biomass C were compared in soil affected by rhizosphere and detritusphere throughout the profile to 70 cm depth, to assess microbial C and nutrient limitations. A decrease in enzyme activity with depth due to resource scarcity and lower substrate quality appeared in planted and litter -amended soil. N limitation in planted soil increased the activity and substrate affinity of proteolytic enzymes to provide for microbial N demand through SOM decomposition. This was in line with lower Vmax ratios (Vmax for C-cycling enzymes divided by Vmax for N-cycling enzymes) in planted relative to litter -amended topsoil. The catalytic efficiency of enzymes decreased 2- to 20-fold from top (40 cm), irrespective of the substrate input. Substrate quality in the rhizosphere and detritusphere affected enzyme activities only in the topsoil, whereas a sharp decline of C input with depth led to similar activities in the subsoil. Most of the enzyme indexes reflected shifts in allocation of C and nutrients in the rhizosphere and detritusphere. The presented results underline the role of microorganisms as critical links in the C and nutrient transfers in the rhizosphere and detritusphere. (C) 2016 Elsevier Ltd. All rights reserved.German Research Foundation [FOR 918
Substrate quality affects kinetics and catalytic efficiency of exo-enzymes in rhizosphere and detritusphere
No full textMicrobial and enzyme functioning depends on the quality of substrates, which strongly differ in bare soil and in the hotspots of microbial activity such as the rhizosphere and detritusphere. We established a field experiment to determine the effects of contrasting substrate quality, namely, soil organic matter, maize shoot litter (detritusphere) and maize rhizodeposits (rhizosphere) on microorganisms and their extracellular enzymes in an arable soil. Kinetic parameters (V-max and K-m) of four hydrolytic extracellular enzymes: beta-cellobiohydrolase, beta-glucosidase, acid phosphate and beta-xylosidase were analyzed in 0-10 and 10-20 cm to elucidate the effects of substrate content on substrate affinity and catalytic efficiency (V-max/K-m). Living roots increased microbial biomass by 179% and microbial respiration by 100% compared to fallow soil. Lower enzyme affinities to substrates (e.g. 93% for beta-glucosidase) in rooted soil pointed to the domination of r-strategists, which are favored in the decomposition of labile organics common in the rhizosphere. No differences in catalytic properties of cellulolytic enzymes were detected between bulk and litter-treated soil, indicating the recalcitrance of organics in both treatments. The rhizosphere and detritusphere effects on enzyme kinetics were negligible in 10-20 cm, except beta-glucosidase. The reduction of K-m of all enzymes in 10-20 cm versus the upper 10 cm indicated increasing substrate affinity with depth. Nonetheless, the catalytic efficiency increased from 0 to 10 to 10-20 cm (e.g. up to 420% for acid phosphatase), reflecting changes in properties and functioning of enzymatic systems. This pointed to a shift towards a more K-selected microbial community with higher affinity and more efficient substrate utilization. It also indicated the microbial adaptation to decreasing substrate contents with depth by altered enzyme functioning. Overall, the catalytic properties of cellulolytic enzymes were much more strongly affected by plants (substrate quality in the rhizosphere and detritusphere compared to bare fallow) than by depth (substrate content). (C) 2015 Elsevier Ltd. All rights reserved
Substrate quality affects microbial‐ and enzyme activities in rooted soil
No full textThe rhizosphere reflects a sphere of high substrate input by means of rhizodeposits. Active microorganisms and extracellular enzymes are known to be responsible for substrate utilization in soil, especially in rooted soil. We tested for microbial-and enzyme activities in arable soil, in order to investigate the effects of continuous input of easily available organics (e. g., root-exudates) to the microbial community. In a field experiment with maize, rooted and root-free soil were analyzed and rhizosphere processes were linked to microbial activity indicators such as specific microbial growth rates and kinetics of six hydrolytic extracellular enzymes: beta-glucosidase, beta-cellobiohydrolase, beta-xylosidase, acid phosphatase, leucine-and tyrosine-aminopeptidase. Higher potential activities of leucine-aminopeptidase (2-fold) for rooted vs. root-free soil suggested increased costs of enzyme production, which retarded the specific microbial growth rates. Total microbial biomass determined by the substrate-induced respiration technique and dsDNA extraction method was 23% and 42% higher in the rooted surface-layer (0-10 cm) compared to the root-free soil, respectively. For the rooted soil, potential enzyme activities of beta-glucosidase were reduced by 23% and acid phosphatase by 25%, and increased by 300% for beta-cellobiohydrolase at 10-20 cm depth compared to the surface-layer. The actively growing microbial biomass increased by the 17-fold in rooted soil in the 10-20 cm layer compared to the upper 10 cm. Despite the specific microbial growth rates showing no changes in the presence of roots, these rates decreased by 42% at 10-20 cm depth compared to the surface-layer. This suggests the dominance in abundances of highly active but slower growing microbes with depth, reflecting also their slower turnover. Shifts in microbial growth strategy, upregulation of enzyme production and increased microbial respiration indicate strong root effects in maize planted soil.German Research Foundation (DFG) within the Research Unit FOR 91
Rhizosphere priming of barley with and without root hairs
No full textThe influence of plant roots and the associated rhizosphere activities on decomposition of soil organic matter (SOM), the rhizosphere priming effect, has emerged as a crucial mechanism regulating global carbon (C) and nitrogen (N) cycles. However, the role of root morphology in controlling the rhizosphere priming effect remains largely unknown. To investigate the link between root hairs, a critical part of the entire root morphology, and the rhizosphere priming effect, we grew a barley wild type and a barley mutant without root hairs in a greenhouse and continuously labeled them with C-13-depleted CO2. Soil CO2 efflux was measured during tittering and head-emergence stages of plant growth. Based on its delta C-13 signature, total CO2 was partitioned for root-derived and SOM-derived CO2, and the SOM decomposition primed in the rhizosphere was calculated. Soil microbial biomass C and N, and the activities of six extracellular enzymes (beta-cellobiohydrolase, beta-glucosidase, acid phosphatase, beta-xylosidase, leucin-aminopeptidase, and N-acetyl-beta-glucosaminidase) were measured to test the effects of root hairs. During the early stage of development (tillering), when plants were sufficiently supplied with nutrients, the barley mutant without root hairs produced more shoot biomass. In contrast, high C costs for root-hair formation likely reduced the growth of the barley wild type. At this stage, the wild type with regular root hairs produced a positive rhizosphere priming effect (69% increase), but the mutant without root hairs produced a negative priming effect on SOM decomposition (28% decline). At the head emergence stage, when nutrients were scarce, plant biomass production of the mutant was reduced, probably due to inefficient nutrient uptake in the absence of root hairs. At this stage, both barley types produced positive rhizosphere priming effects (72% and 209% increase for the wild type and the mutant, respectively) and the microbial biomass was higher for both planted soils compared to the tillering stage. Extracellular enzymes responsible for the decomposition of stable SOM had higher activities in cases of positive priming effects. Overall, root hairs played an important role in regulating rhizosphere priming. (C) 2016 Elsevier Ltd. All rights reserved
laska
No full textPermafrost-affected soils of the northern circumpolar region represent 50% of the terrestrial soil organic carbon (SOC) reservoir and are most strongly affected by climatic change. There is growing concern that this vast SOC pool could transition from a net C sink to a source. But so far little is known on how the organic matter (OM) in permafrost soils will respond in a warming future, which is governed by OM composition and possible stabilization mechanisms. To investigate if and how SOC in the active layer and adjacent permafrost is protected against degradation, we employed density fractionation to separate differently stabilized SOM fractions. We studied the quantity and quality of OM in different compartments using elemental analysis, C-13 solid-phase nuclear magnetic resonance (C-13-NMR) spectroscopy, and C-14 analyses. The soil samples were derived from 16 cores from drained thaw lake basins, ranging from 0 to 5500years of age, representing a unique series of developing Arctic soils over time. The normalized SOC stocks ranged between 35.5 and 86.2kgSOCm(-3), with the major amount of SOC located in the active layers. The SOC stock is dominated by large amounts of particulate organic matter (POM), whereas mineral-associated OM especially in older soils is of minor importance on a mass basis. We show that tremendous amounts of over 25kgOC per square meter are stored as presumably easily degradable OM rich in carbohydrates. Only about 10kgOC per square meter is present as presumably more stable, mineral-associated OC. Significant amounts of the easily degradable, carbohydrate-rich OM are preserved in the yet permanently frozen soil below the permafrost table. Forced by global warming, this vast labile OM pool could soon become available for microbial degradation due to the continuous deepening of the annually thawing active layer
Microbial Activity ̶ Indicators & Drivers
Full text linkBiota des Kohlenstoffkreislaufs spielen bei der Speicherung und Verteilung des Kohlen-stoffs im Bodennahrungsnetz eine herausragende Rolle. Wobei der Abbau organischer Bodensubstanz stark von deren Verfügbarkeit für Mikroorganismen und Enzyme abhängt. Rhizosphäre und Detritusphäre verfügen über außerordentlich große Mengen an organischem Kohlenstoff. Dies macht diese Biosphären zu Hot-Spots mikrobieller Aktivität.
Während der letzten Jahrzehnte stieg das Interesse an der Forschung zu mikrobieller Aktivität im Boden. Dennoch herrscht noch immer kein umfassendes Verständinis von Indikatoren und Triebkräften mikrobieller Aktivität in der Rhizosphäre und Detritusphäre. Dies ist nicht zuletzt der Tatsache geschuldet, dass es mehr als einer einzigen Methode zur Bestimmung dieser Faktoren bedarf. Aus diesem Grund setzt sich diese Arbeit zum Ziel, die mikrobielle Aktivität, ihre Indikatoren und Treiber zu explorieren.
Folglich wurden diverse Indikatoren mikrobieller Aktivität, wie mikrobielle Respiration, mikrobielle Biomasse und Enzymkinetik, an Proben aus einem Feldexperiment mit diffe-rierendem Substrat-Eintrag (Mais-Rhizodeposite vs. Mais-Streu) ermittelt. Tiefengradienten der Indikatoren mikrobieller Aktivität dienten der Beurteilung der Auswirkungen sinkender Substratqualität und -quantität in Rhizo- und Detritusphäre mit zunehmender Bodentiefe. Besonderer Fokus lag dabei auf den Indizes unterschiedlicher Enzyme und deren Aktivität (z. B. spezifische Aktivität, katalytische Effizienz und Verhältnisse zwischen Enzymen des Kohlenstoff- und Stickstoff-Kreislaufs) im Tiefenprofil des Bodens. Neben dieser Feldstudie wurde das Verhältinis von RNA zu dsDNA als Indikator mikrobieller Aktivität entlang eines klimatischen Grandienten ermittelt, um den metabolischen Status innerhalb unterschiedlicher Bodentypen zu bestimmen. Die Feldstudien wurden um Experimente in Labor und Gewächshaus ergänzt, in denen mittels Isoto-penmarkierungsverfahren die Effekte von Wurzelhaaren und Protisten auf die mikrobielle Aktivität beleuchtet wurden. Diese Methode ermöglichte ein Nachvollziehen des C- und N-Flusses und trug damit zum Verständnis der Verflechtungen der Organismen im terrestrischen Boden-Nahrungsnetz bei. Die räumliche Verteilung der Enzymaktivität in der Rhizosphäre wurde anhand der Boden-Zymographie in situ untersucht.
Durch unterschiedliche Substratverfügbarkeit wurde ein Wandel der funktionellen Eigenschaften der Mikroorganismengemeinschaften und des enzymatischen Systems induziert. Speziell der durchwurzelte Oberbodenhorizont zeigte einen Anstieg der mikro-biellen Aktivität im Vergleich zum Boden mit Streueintrag und der Kontrolle. Rhizodeposite sind eine grundlegende Kohlenstoff- und Energiequelle für Bodenmikroorganismen und stimulieren deren Wachstum und Aktivität. Die Präsenz von Rhizodepositen in Hot-Spots macht diese zu bevorzugten Habitaten für Mikroorganismen. Die Mehrzahl der Indikatoren für mikrobielle Aktivität wurde ausschließlich im Oberboden durch den Substrateintrag beeinflusst. Darunter auch die katalytische Effizienz, die – ungeachtet des Substrateintrags – von Oberboden ( 40 cm) um das 2- bis 20-fache abnahm. Dies ließ auf die Relevanz der mit der Tiefe abnehmenden Menge und Qualität der Substrate im Boden als einflussnehmenden Faktor auf die mikrobielle Aktivität schließen. Das Verhältnis von RNA zu dsDNA spiegelte den metabolischen Status der mikrobiellen Organismengesellschaften in den meisten der beprobten Böden wider. Wohingegen das RNA:dsDNA Verhältnis dieser Indikatoreigenschaft widersprach, lagen erhöhte Tongehalte vor, die nach der Extraktion zu Ungenauigkeiten bei der Bestimmung der RNA-Quantität führten.
Protozoen wird beim Vorgang des Kohlenstoffflusses von Bakterien zu Organismen höherer Trophieebenen eine bedeutende Rolle zugesprochen, was ebenfalls ihren Einfluss auf die mikrobielle Aktivität im Boden unterstreicht. Um diesen Effekten, im Speziellen jenen der Acanthoamoebe auf den Kohlenstoff- und Stickstofffluss, sowie die Indikatoren mikrobieller Aktivität in der Rhizo- und Detritusphäre nachzugehen, wurde ein dreifaches Isotopenmarkierungs-Experiment durchgeführt. Es ergab, dass Kohlenstoffflüsse und Enzymaktivitäten sowohl von Substrateintrag als auch Substratqualität in Rhizo- wie Detritusphäre sowie deren faunistischer Besiedlung abhängen. Daraus erschloss sich, dass die Besiedlung mit Acanthamoeben als potenzielle Triebkraft mikrobieller Aktivität, besonders innerhalb der Rhizosphäre, gedeutet werden kann.
Um den Einfluss von Wurzelhaaren auf die mikrobielle Aktivität und den Priming Effekt in der Rhizosphäre einzuschätzen, wurde ein Experiment im Gewächshaus mit kontinuierlicher Markierung von Boden mit Pflanzenbewuchs und einer Kontrolle ohne Bewuchs mit 13C-Isotopen durchgeführt. Wurzelhaare zeigten sich darin als Initiatoren eines positiven Rhizosphären-Priming Effektes während der Wachstumsphase, wohingegen der Abbau organischer Bodensubstanz in den Kontrollen gehemmt war. Im Falle der positiven Initialwirkung der Wurzelhaare stiegen zudem die Enzymaktivitäten von Chitinase und ß-Xylosidase an, was auf eine Zersetzung stabiler, organischer Bodensubstanz hinwies. Damit konnte ein deutlicher Effekt von Wurzelhaaren auf die mikrobielle Aktivität im Boden während der Phase des Pflanzenwachtums nachgewiesen werden.
Somit vermittelt diese Arbeit ein weiterführendes Verständnis der auf mikrobielle Aktivität im Boden einwirkenden Faktoren und stellt eine Auswahl von Indikatoren zur Charakterisierung dieser Aktivität vor, die sowohl auf der Landschaftsebene als auch in der prozessorientierten Forschung im Wurzelraum Anwendung finden kann.Biota involved in the carbon (C) cycle play a vital role in C sequestration and allocation in the soil food web. Though, the decomposition of soil organics strongly depends on the availability of soil organic matter (SOM) to microorganisms and enzymes. As rhizo-sphere and detritusphere are biospheres with very high availability of C, leading to high abundance, species diversity and contrasting functions of microbial communities, they are worth to be called hot spots of microbial functioning.
During the last decades, the interest on research on microbial activity in soil increased. However, there is a lack of comprehensive understanding of the indicators and drivers of microbial activity in rhizosphere and detritusphere. This is especially due to the objective necessity for more than a single measure to determine these factors. For that reason, this thesis aims to investigate microbial activity, its indicators and its drivers.
An arable field experiment with different substrate input (corn rhizodeposits vs. corn litter) was conducted to determine microbial activity by various activity indicators, such as microbial respiration, microbial biomass and enzyme kinetics. To account for decreasing amount and quality of substrates in rhizosphere and detritusphere with soil depth, we exhibited depth gradients of microbial activity indicators. Special attention was paid to several indices of multiple enzymes and their activity (e.g. specific activity, catalytic efficiency and ratios between C- and N-cycling enzymes) down the soil profile. Not only in the field, but also along a climatic gradient we investigated microbial activity. Therefore, the RNA:dsDNA ratio was determined in order to identify the metabolic status of microbes in contrasting soil types. Alongside with the major field and climatic gradient experiment laboratory and greenhouse studies were performed. These addressed the drivers, such as root hairs and protozoan predation, which were identified by isotopic labelling approaches and several indicators of microbial activity. Isotope technologies facilitate the tracing of e.g. C- and N-fluxes to achieve their central pur-pose of understanding the linkages of biota in terrestrial soil food webs. Soil zymography was used to exhibit the spatial distribution of enzyme activity in the rhizosphere in situ.
Substrates with contrasting availability changed functional properties of the soil microbial community and induced a shift in enzymatic systems. In particular, the rooted surface layer showed increased microbial activity compared to litter-amended and bare fallow soil. Rhizodeposits are an important primary source of C and energy for soil microorganisms, stimulating their growth and activity. Accounted by the availability of rhizodeposits, hot spots in the surface layer provided preferable habitats for microbes.
Most microbial indicators were affected by the substrate input only in the topsoil. Microbial indicators included the catalytic efficiency of enzymes, which decreased by 2- to 20-fold from top- ( 40 cm), irrespective of the substrate input. This suggests that the limited amount and quality of substrates at depth is an important constraint on microbial activity.
The RNA:dsDNA ratios towards the indication of the metabolic status of soil microbial communities was subjected to biased RNA quantity due to high clay contents in Chernozems, whereas at intermediate and low clay contents the RNA reflected reliable results.
Protozoa are assumed to be key-players in the C flux from bacteria to higher trophic levels, thereby affecting soil microbial activity. A triple-labelling experiment was conducted to investigate the effects of grazing by Acanthamoeba on C and N fluxes and microbial activity indicators in the rhizosphere and detritusphere. C fluxes and enzyme activities were driven by substrate input and quality and further stimulated by faunal grazing. This revealed that Acanthamoeba grazing contributes to microbial stimulation, especially in the rhizosphere.
To assess the influence of root hairs on microbial activity and rhizosphere priming, a continuous 13C labelling experiment was conducted in a greenhouse. Root hairs induced positive priming during tillering. Without root hairs SOM decomposition was sup-pressed. Chitinase and ß-xylosidase activities increased during positive priming, indicat-ing decomposition of stable SOM. This clearly showed the strong influence of root hairs on microbial activity during the early stages of plant growth, whereas at later stages the root hairs were a less important driver of microbial activity.
In summary, this thesis extends the understanding of factors affecting microbial activity in soil. It demonstrates that microbial activity can be meaningfully characterized by a careful selection of indicators. The chosen set of indicator is applicable at the landscape scale as well as for process-based investigations at the root scale
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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