Aging exo-enzymes can create temporally shifting,temperature-dependent resource landscapes for microbes

The rate at which catalytic capacity of microbial exo-enzymes degrades post-exudation will influence the time during which return on microbes’ investment in exo-enzyme production can be realized. Further, if exo-enzyme degradation rates vary across exo-enzymes, microbial investment returns may vary by element across time. We quantify how aging of two soil organic matter (SOM)-decaying enzymes (β-D-cellobioside, BGase; and N-acetyl-β-D-glucosaminide, NAGase) influences enzyme-substrate V _max at multiple temperatures (5, 15, 25 °C), and compute how enzyme age influences relative availabilities of C and N. Both BGase and NAGase exhibited similar, exponential declines in catalytic rate with age at 25 °C (0.22 ± 0.02 and 0.36 ± 0.14 d^?1, respectively). At 15 °C, NAGase exhibited exponential declines in catalytic rates with age (0.79 ± 0.31 d^?1), but BGase exhibited no decline. Neither enzyme exhibited a decline in catalytic rate over 72 h at 5 °C. At 15 °C, the amount of C liberated from cellulose and chitin analogues relative to N increased, on average, by more than one order of magnitude. The ratio of C:N liberated from the two substrates remained constant across enzyme age at 25 and 5 °C, but for different reasons: no differences in decay rate across enzymes at 25 °C, and no observed decay at 5 °C. Thus, temperature-dependent decreases of catalytic activity over time may influence microbial resource allocation strategies and rates of SOM decomposition. Because the enzyme decay rates we observed differ considerably from values assumed in most models, such assumptions should be revisited when parameterizing microbial process models.     

Future challenges in coupled C–N–P cycle models for terrestrial ecosystems under global change: a review

Climate change has consequences for terrestrial functioning, but predictions of plant responses remain uncertain because of the gaps in the representation of nutrient cycles and C–N–P interactions in ecosystem models. Here, we review the processes that are included in ecosystem models, but focus on coupled C–N–P cycle models. We highlight important plant adjustments to climate change, elevated atmospheric CO₂, and/or nutrient limitations that are currently not—or only partially—incorporated in ecosystem models by reviewing experimental studies and compiling data. Plant adjustments concern C:N:P stoichiometry, photosynthetic capacity, nutrient resorption rates, allocation patterns, symbiotic N₂ fixation and root exudation (phosphatases, carboxylates) and the effect of root exudation on nutrient mobilization in the soil rhizosphere (P solubilization, biochemical mineralization of organic P and priming effect). We showed that several plant adjustments could be formulated and calibrated using existing experimental data in the literature. Finally, we proposed a roadmap for future research because improving ecosystem models necessitate specific data and collaborations between modelers and empiricists.     

Omgaan met somberheid op oudere leeftijd: een kwalitatieve studie

Background

To gain new insights for support for older people with low mood, we explored the perceptions of ‘screenpositive’ older people on underlying causes and possible solutions.

Design and method

We conducted two in-depth interviews with 38 participants (≥77 years) who screened positive for depressive symptoms in general practice. To investigate the influence of the presence of complex health problems, we included 19 persons with and 19 without complex problems. Complex problems were defined as a combination of functional, somatic, psychological or social problems.

Results

All participants used several cognitive, social or practical coping strategies. Four patterns emerged: mastery, acceptance, ambivalence, and need for support. Some participants, especially those with complex problems, were ambivalent about possible interventions.

Conclusion

Most older participants perceived their coping strategies as sufficient. General practitioners can support self-management by exploring the (effectiveness of) personal coping strategies, providing information, elaborating on perceptions of risks and discussing alternative options with older persons.

     

Carbon,nitrogen and phosphorus net mineralization in organic horizons of temperate forests: stoichiometry and relations to organic matter quality

The rates of mineralization processes influence C sequestration and soil fertility, but despite their importance for ecosystem functioning, C, N and P net mineralization rates are seldom investigated together. Hence, we studied the relationships between net mineralization rates and organic matter stoichiometry in an 8-week incubation experiment with Oi, Oe and Oa horizon material of six beech, one spruce and one pine site. We determined C, N and P net mineralization rates, organic C quality and C:N:P stoichiometry. Net N mineralization only occurred below molar organic matter C:N ratios of 40 (Oi) or 28 (Oa) and N:P ratios of 42 (Oi) or 60 (Oa), and increased with decreasing C:N and N:P ratios. Net P mineralization only occurred below C:P ratios of 1400 (Oi) and N:P ratios of 40 (Oi), and increased with decreasing C:P and N:P ratios. Net N and P mineralization were strongly positively correlated with each other (r = 0.64, p < 0.001), whereas correlations of both net N and net P mineralization with C mineralization were weak. The average C:N:P stoichiometry of net mineralization was 620:4:1 (beech, Oi), 15,350:5:1 (coniferous, Oi), 1520:8:1 (Oe) and 2160:36:1 (Oa). On average, ratios of C:N net mineralization were higher, and ratios of N:P net mineralization lower than organic matter C:N and N:P ratios. This difference contributed to the decrease of C:N ratios and increase of N:P ratios from the Oi to the Oa horizons. In conclusion, the study shows that C, N and P net mineralization rates were closely correlated with the organic matter stoichiometry and that these correlations were modified by the degree of decomposition of the organic matter.     

Human thinking,shared intentionality,and egocentric biases

The paper briefly summarises and critiques Tomasello’s (2014) A Natural History of Human Thinking. After offering an overview of the book, the paper focusses on one particular part of Tomasello’s proposal on the evolution of uniquely human thinking and raises two points of criticism against it. One of them concerns his notion of thinking. The other pertains to empirical findings on egocentric biases in communication.     

Site-directed mutagenesis of α-<Emphasis Type="SmallCaps">l</Emphasis>-rhamnosidase from <Emphasis Type="Italic">Alternaria</Emphasis> sp. L1 to enhance synthesis yield of reverse hydrolysis based on rational design

The α-l-rhamnosidase catalyzes the hydrolytic release of rhamnose from polysaccharides and glycosides and is widely used due to its applications in a variety of industrial processes. Our previous work reported that a wild-type α-l-rhamnosidase (RhaL1) from Alternaria sp. L1 could synthesize rhamnose-containing chemicals (RCCs) though reverse hydrolysis reaction with inexpensive rhamnose as glycosyl donor. To enhance the yield of reverse hydrolysis reaction and to determine the amino acid residues essential for the catalytic activity of RhaL1, site-directed mutagenesis of 11 residues was performed in this study. Through rationally designed mutations, the critical amino acid residues which may form direct or solvent-mediated hydrogen bonds with donor rhamnose (Asp²⁵², Asp²⁵⁷, Asp²⁶⁴, Glu⁵³⁰, Arg⁵⁴⁸, His⁵⁵³, and Trp⁵⁵⁵) and may form the hydrophobic pocket in stabilizing donor (Trp²⁶¹, Tyr³⁰², Tyr³¹⁶, and Trp³⁶⁹) in active-site of RhaL1 were analyzed, and three positive mutants (W261Y, Y302F, and Y316F) with improved product yield stood out. From the three positive variants, mutant W261Y accelerated the reverse hydrolysis with a prominent increase (43.7 %) in relative yield compared to the wild-type enzyme. Based on the 3D structural modeling, we supposed that the improved yield of mutant W261Y is due to the adjustment of the spatial position of the putative catalytic acid residue Asp²⁵⁷. Mutant W261Y also exhibited a shift in the pH-activity profile in hydrolysis reaction, indicating that introducing of a polar residue in the active site cavity may affect the catalysis behavior of the enzyme.     

The relativity of Darwinian populations and the ecology of endosymbiosis

If there is a single discipline of science calling the basic concepts of biology into question, it is without doubt microbiology. Indeed, developments in microbiology have recently forced us to rethink such fundamental concepts as the organism, individual, and genome. In this paper I show how microorganisms are changing our understanding of natural aggregations and develop the concept of a Darwinian population to embrace these discoveries. I start by showing that it is hard to set the boundaries of a Darwinian population, and I suggest thinking of a Darwinian population as a relative property of a Darwinian individual. Then I argue, in contrast to the commonly held view, that Darwinian populations are multispecies units, and that in order to accept the multispecies account of Darwinian populations we have to separate fitness from natural selection. Finally, I show how all these ideas provide a theoretical framework leading to a more precise understanding of the ecology of endosymbiosis than is afforded by poetic metaphors such as ‘slavery’.     

A levels-of-selection approach to evolutionary individuality

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken in Clarke (J Philos 110(8):413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided.