Aims The aim of this guide is to provide practical help for ecologists who analyze data from biodiversity–ecosystem functioning experiments. Our approach differs from others in the use of least squares-based linear models (LMs) together with restricted maximum likelihood-based mixed models (MMs) for the analysis of hierarchical data. An original data set containing diameter and height of young trees grown in monocultures, 2- or 4-species mixtures under ambient light or shade is used as an example.
Methods Starting with a simple LM, basic features of model fitting and the subsequent analysis of variance (ANOVA) for significance tests are summarized. From this, more complex models are developed. We use the statistical software R for model fitting and to demonstrate similarities and complementarities between LMs and MMs. The formation of contrasts and the use of error (LMs) or random-effects (MMs) terms to account for hierarchical data structure in ANOVAs are explained.
Important Findings Data from biodiversity experiments can be analyzed at the level of entire plant communities (plots) and plant individuals. The basic explanatory term is species composition, which can be divided into contrasts in many ways depending on specific biological hypotheses. Typically, these contrasts code for aspects of species richness or the presence of particular species. For significance tests in ANOVAs, contrast terms generally are compared with remaining variation of the explanatory terms from which they have been ‘carved out’. Once a final model has been selected, parameters (e.g. means or slopes for fixed-effects terms and variance components for error or random-effects terms) can be estimated to indicate the direction and size of effects.

Aims Soil sample preservation is a challenging aspect in molecular studies on soil microbial communities. The demands for specialized sample storage equipment, chemicals and standardized protocols for nucleic acid extraction often require sample processing in a home laboratory that can be continents apart from sampling sites. Standard sampling procedures, especially when dealing with RNA, comprise immediate snap freezing of soils in liquid nitrogen and storage at ?80°C until further processing. For these instances, organizing a reliable cooling chain to transport hundreds of soil samples between continents is very costly, if possible at all. In this study we tested the effect of soil sample preservation by freeze-drying with subsequent short-term storage at 4°C or ambient temperatures compared to ?80°C freezing by comparative barcoding analyses of soil microbial communities.
Methods Two grassland soil samples were collected in Central Germany in the Biodiversity Exploratory Hainich-Dün. Samples were freeze-dried or stored at ?80°C as controls. Freeze-dried samples were stored at 4°C or ambient temperature. Investigated storage times for both storage temperatures were 1 and 7 days. Total DNA and RNA were extracted and bacterial and arbuscular mycorrhizal (AM) fungal communities were analyzed by amplicon 454 pyrosequencing of the 16S (V4-V5 variable region) and 18S (NS31-AM1 fragment) of ribosomal RNA (rRNA) marker genes, respectively.
Important findings Bacterial communities were sufficiently well preserved at the rDNA and rRNA level although storage effects showed as slightly decreased alpha diversity indices for the prolonged storage of freeze-dried samples for 7 days. AM fungal communities could be studied without significant changes at the rDNA and rRNA level. Our results suggest that proper sampling design followed by immediate freeze-drying of soil samples enables short-term transportation of soil samples across continents.

Aims To quantify the seasonal differences in effects of leaf habit, species identity, initial diameter, neighborhood interaction and stand environment on tree absolute diameter growth rates in a subtropical forest in China.
Methods We used man-made dendrometer bands to record radial increments of all trees with diameter at breast height (DBH) ≥5cm and height ≥3 m within 25 comparative study plots (30×30 m for each) of the 'Biodiversity–Ecosystem Functioning Experiment China' (BEF-China) in the Gutianshan National Nature Reserve, Zhejiang Province, China. We measured stem circumferences twice a year from 2011 to 2014 to calculate absolute diameter growth rate of a warm and wet season (WWS, April to September) and a dry and cold season (DCS, October to the next March) for each individual tree: annual growth (GR year), growth during the WWS (GR WWS) and growth during the DCS (GR DCS). We firstly tested the differences in growth rates between different seasons using paired t -tests with Bonferroni correction. Then we applied linear mixed models to explore the effects of leaf habit, species identity, initial diameter, neighborhood interaction (indicated by richness, density and total basal area of all neighboring trees within a radius of 5 m around target trees), stand age and topography (elevation, slope and aspect) on tree growth rates of the two different seasons in three deciduous and 14 evergreen species.
Important findings GR year, GR WWS and GR DCS varied between 0.04–0.50cm year^-1 (mean = 0.21), 0.03–0.46cm season^-1 (mean = 0.18) and 0.01–0.05cm season^-1 (mean = 0.03) across the 17 species, respectively. GR WWS was significantly higher than GR DCS for all species. Growth rates of faster growing species tended to have larger absolute differences between the WWS and DCS. Tree growth rates of both seasons and of the year (GR year, GR WWS and GR DCS) varied significantly among leaf habit and species, and increased allometrically with initial diameter, decreased with stand age, but were not significantly related to topography and neighborhood richness or density. GR WWS decreased with neighborhood total basal area, while GR DCS did not. In conclusion, species might the temporally complementary, contributing to plot growth at different times of the year.