Estimating the age–diameter relationship of oak species in Switzerland using nonlinear mixed-effects models

Tree growth plays a key role in forest dynamics, yet little attention has been paid to quantifying tree age–diameter relationships. Predicting diameter growth of oaks is especially important due to their role in nature conservation and adaptive forest management under climate change. Thus, we (1) identified environmental variables that shape age–diameter relationships of oaks and (2) quantified the accuracy of predictions based on these variables. We determined the age–diameter relationship of 243 oaks (Quercus spp.) growing in Switzerland by using tree-ring samples. Nonlinear mixed-effects models based on a modified Chapman-Richards equation were fitted with environmental variables included as covariates. The fixed effects elevation, slope and water-holding capacity were most important in shaping the age–diameter relationships. Lower elevations, steeper slopes, north-facing aspects, higher water-holding capacities and moister summers resulted in larger maximum diameters. For 75 % of the oaks, age–diameter relationships predicted by the fixed effects matched fairly well the observations (root mean square error between predictions and observations <6 cm); the inclusion of random effects reduced root mean square errors for 86 % of the trees. These results suggest that water runoff plays a key role for the age–diameter relationships, accompanied by limiting temperature effects at higher elevations. The fixed effects covered variability in site quality, whereas the random effects included tree-specific deviations from expected age–diameter relationships, potentially due to neighbourhood effects such as stand density and competition.     

Impacts of changing climate and land use on vegetation dynamics in a Mediterranean ecosystem: insights from paleoecology and dynamic modeling

Forests near the Mediterranean coast have been shaped by millennia of human disturbance. Consequently, ecological studies relying on modern observations or historical records may have difficulty assessing natural vegetation dynamics under current and future climate. We combined a sedimentary pollen record from Lago di Massacciucoli, Tuscany, Italy with simulations from the LandClim dynamic vegetation model to determine what vegetation preceded intense human disturbance, how past changes in vegetation relate to fire and browsing, and the potential of an extinct vegetation type under present climate. We simulated vegetation dynamics near Lago di Massaciucoli for the last 7,000 years using a local chironomid-inferred temperature reconstruction with combinations of three fire regimes (small infrequent, large infrequent, small frequent) and three browsing intensities (no browsing, light browsing, and moderate browsing), and compared model output to pollen data. Simulations with low disturbance support pollen-inferred evidence for a mixed forest dominated by Quercus ilex (a Mediterranean species) and Abies alba (a montane species). Whereas pollen data record the collapse of A. alba after 6000 cal yr bp, simulated populations expanded with declining summer temperatures during the late Holocene. Simulations with increased fire and browsing are consistent with evidence for expansion by deciduous species after A. alba collapsed. According to our combined paleo-environmental and modeling evidence, mixed Q. ilex and A. alba forests remain possible with current climate and limited disturbance, and provide a viable management objective for ecosystems near the Mediterranean coast and in regions that are expected to experience a mediterranean-type climate in the future.     

Soil organic carbon in the rocky desert of northern Negev (Israel)

Purpose

So far, the soil organic carbon (SOC) literature is dominated by studies in the humid environments with huge stocks of vulnerable carbon. Limited attention has been given to dryland ecosystems despite being often considered to be highly sensitive to environmental change. Thus, there is insufficient research about the spatial patterns of SOC stocks and the interaction between soil depth, ecohydrology, geomorphic processes, and SOC stocks. This study aimed at identifying the relationship between surface characteristics, vegetation coverage, SOC, and SOC stocks in the arid northern Negev in Israel.

Materials and methods

The study site Sede Boker is ideally suited because of well-researched but variable ecohydrology. For this purpose, we sampled five slope sections with different ecohydrologic characteristics (e.g., soil and vegetation) and calculate SOC stocks. To identify controlling factors of SOC stocks on rocky desert slopes, we compared soil properties, vegetation coverage, SOC concentration, and stocks between the five ecohydrologic units.

Results and discussion

The results show that in Sede Boker, rocky desert slopes represent a significant SOC pool with a mean SOC stock of 0.58?kg?C?m^?2 averaged over the entire study area. The spatial variability of the soil coverage represents a strong control on SOC stocks, which varies between zero in uncovered areas and 1.54?kg?C?m^?2 on average in the soil-covered areas. Aspect-driven changes of solar radiation and thus of water availability are the dominant control of vegetation coverage and SOC stock in the study area.

Conclusions

The data indicate that dryland soils contain a significant amount of SOC. The SOC varies between the ecohydrologic units, which reflect (1) aspect-driven differences, (2) microscale topography, (3) soil formation, and (4) vegetation coverage, which are of greatest importance for estimating SOC stocks in drylands.     

Detection of expressed fungal Type I polyketide synthase genes in a forest soil

Secondary metabolites synthesized via the polyketide pathway are thought to mediate interference competition between soil microorganisms as well as cell-to-cell signaling. Although their synthesis has been documented in laboratory culture, it remains uncertain whether these compounds are actually produced under field conditions. Here, we report the presence and expression of fungal Type I polyketide synthase (PKS) genes in the organic horizon of a forest soil. If these expressed PKS genes produce compounds that elicit antagonistic interactions among soil microorganisms, then it could be a factor structuring microbial communities in soil.     

GOAnnotator: linking protein GO annotations to evidence text

Background

Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators.

Results

In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins.

Conclusion

The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

     

Soil organic C as affected by silvicultural and exploitative interventions in Nothofagus pumilio forests of the Chilean Patagonia

This study evaluates the effect of silvicultural and exploitative interventions on soil organic carbon (SOC) in Chilean Lenga (Nothofagus pumilio (Poepp et Endl.) Krasser) forests in south Patagonia. We analyzed SOC and the organic soil horizons in five stands at different stages of development: intact native forest (NI); a 3-year-old shelterwood stand (S3); an 8-year-old shelterwood stand (S8); a 14-year-old stand that was initially treated with shelterwood and subsequently final cut (10 years after the first intervention) (S14), and a 25-year-old stand subject to a exploitative intervention (E25). The SOC under the forest stands, down to a depth of 50 cm (including the Oi horizon), was 60, 55, 71, 85, and 67 Mg ha⁻¹ for the NI, S3, S8, S14, and E25 forest stands, respectively. A significant decrease in SOC occurred 3 years after an intensive shelterwood cut (S3), particularly in the first 5 cm of the mineral soil. Slightly higher carbon contents were observed in the upper horizons of the mineral soil in both the S8 and S14 stands. Consequently, the applied shelterwood system appears to generate only short-term losses of SOC in the Lenga forest. Soil organic carbon increased over the medium term but decreased to the level observed in intact native forests over the long term. Regeneration, which influences stand microclimate (a factor in SOC storage) and provides an important source of organic soil material, was identified as one of the most important factors influencing SOC.     

Ecological and economical sustainability assessment of community forest management in Nepal: A reality check

This study analyzes the sustainability of community forest management, representing four forest types of two physiographic region Hills and Terai of Nepal. We assess the sustainability based on species composition, stand density, growing stock volume, and growth-to-removal ratio using inventory data of 109 permanent forest plots from four consecutive intervals of three to five years. In addition, forest users, forest committee members, and forest officials were consulted. We observed increment on the representation of economically valuable tree species in all forest types of both regions. The pole-size tree dominates in all forest types with declining number of trees and regeneration. In case of Hills forests, they were over-harvested until 2013 but were under-harvested in the recent period. In contrary, forests were under-harvested in the Terai. We found that ecological objectives of sustainable management are fully achieved while economic benefits remained unharnessed where harvesting is far below the growth. We conclude that maintaining a large number of trees may contribute to ecological but not on economical sustainability. We argue to rationalize annual harvest in all categories of the forest to enhance resource conditions together with regular benefits to the local communities.     

Considerations on the future biomass production potential of Iceland,and what role that could have in future fuel supply and carbon balances

This study suggests that Iceland may be able to produce sufficient liquid hydrocarbon fuels from biological sources in the future to substitute the Icelandic 2016 consumption of fossil fuels, by using forest products. The authors evaluate a strategy to put forest on up to 35,000 km² in Iceland to 2050. The preliminary study shows that Iceland could reach climate neutrality around 2050 and be a significant net carbon sequester for the next 250 years. Approximate estimates suggest that the total forest biomass production could reach about 10 million m³yr^?1, comprising 3.1 million m³yr^?1 of roundwood, 3.1 million m³yr^?1 for generic biomass, and about 4.2 million m³yr^?1 woody material for biofuel use. This could result in a net annual carbon dioxide sequestration of 2–2.5 mill ton CO₂ yr^?1 by 2100. The calculations suggest that such an afforestation and land restoration undertaking would be long term profitable in economic terms and that the payback time would be about 2050. The method applied in this study is that of a static mass balance calculations at different time points into the future. Parallel to this work, a full integrated regional forest production model is being developed and will be applied to this issue.