A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

Diversity and abundance of soil macroinvertebrates along a contamination gradient in the Central Urals, Russia

Since the late 1980s, long-term monitoring of terrestrial ecosystems in metal-contaminated areas near the Middle Ural Copper Smelter has been carried out in the Central Urals. As a part of these monitoring programmes, the data on species diversity, community composition and abundance of soil macroinvertebrates continue to be gathered.The dataset (available from the GBIF network at https://www.gbif.org/dataset/61e92984-382b-4158-be6b-e391c7ed5a64) includes a 2004 census for soil macroinvertebrates of spruce-fir forests along a pollution gradient in the Central Urals. The dataset describes soil macrofauna’s abundance (the number of individuals per sample, i.e. the density) and community structure (list of supraspecific taxa, list of species for most abundant taxa and supraspecific taxa or species abundance). Seventeen sampling plots differed in the levels of toxic metal (Cu, Zn, Pb, Cd and Fe) soil contamination from air emissions of the Middle Ural Copper Smelter (heavily polluted, moderately polluted and unpolluted areas). The dataset consists of 340 sampling events (= samples corresponding to upper and lower layers of the 170 soil monoliths) and 64658 rows (2907 and 61751 for non-zero and zero density of taxa, respectively). Arachnida (Araneae and Opiliones), Carabidae (imagoes), Elateridae (larvae), Chilopoda, Diplopoda, Gastropoda, Staphylinidae (imagoes) and Lumbricidae were identified to species level. In contrast, Mermithida, Enchytraeidae, Lepidoptera larvae, Diptera larvae, Hemiptera, Hymenoptera and some other insects were identified to family or order levels. In total, 8430 individuals of soil macroinvertebrates were collected in two soil layers (organic and organic-mineral horizons), including 1046 Arachnida (spiders and harvestmen), 45 Carabidae, 300 Elateridae, 529 Myriapoda, 741 Gastropoda, 437 Staphylinidae, 623 Lumbricidae and 4709 other invertebrates. The presence-absence data on each taxon are provided for each sampling event. An overwhelming majority of such absences can be interpreted as “pseudo-absences” at the scale of sampling plots or study sites. The dataset contains information helpful for long-term ecotoxicological monitoring of forest ecosystems and contributes to studying soil macrofauna diversity in the Urals

Arachnids (Araneae, Opiliones) from grass stand and forest litter in the Urals, Russia

Since the late 1980s, long-term monitoring of various components of natural ecosystems under conditions of industrial pollution has been carried out in the Central Urals. In the mid-2000s, similar programmes were started in the Southern Urals. As a part of these monitoring programmes, the data on invertebrates in different types of biotopes, collected with different methods and in a different time intervals, continue to be gathered. Amongst the most well-studied groups of invertebrates are spiders and harvestmen whose communities are a convenient indicator of the environment. The data collected through these monitoring programmes can also be used to study natural local biodiversity.The dataset, presented here, includes information from a long-term monitoring programme for Araneae and Opiliones that inhabit grass stands of secondary dry meadows and litter of spruce-fir, aspen-birch and pine-birch forests in the Central and Southern Urals. The dataset (available from the GBIF network at https://www.gbif.org/dataset/e170dbd1-a67f-4514-841c-5296b290ca90) describes the assemblage structure of spiders and harvestmen (list of species and their abundance), age-sex composition and seasonal and inter-annual dynamics for two large areas in the southern taiga zone of the Ural Mountains. The dataset includes 1,351 samples, which correspond to 5,462 occurrences identified during 2004–2009, 2013 and 2018. In total, we collected 10,433 specimens, representing 178 species (36% of arachnofauna of the Urals), 115 genera (54%) and 23 families (100%). Most of the data (4,939 of 5,462 occurrences, 90%) were collected in the western macro-slope of the Ural Mountains (European part of Russia), the rest in the eastern macro-slope (Asian part). All represented data were sampled in industrially undisturbed areas and are used as a local reference for ecotoxicological monitoring. The dataset provides new useful information for recording the state of biodiversity for the Central and Southern Urals and contributes to the study of biodiversity conservation

Diversity and abundance of soil macroinvertebrates along a contamination gradient in the Central Urals, Russia

Since the late 1980s, long-term monitoring of terrestrial ecosystems in metal-contaminated areas near the Middle Ural Copper Smelter has been carried out in the Central Urals. As a part of these monitoring programmes, the data on species diversity, community composition and abundance of soil macroinvertebrates continue to be gathered.The dataset (available from the GBIF network at https://www.gbif.org/dataset/61e92984-382b-4158-be6b-e391c7ed5a64) includes a 2004 census for soil macroinvertebrates of spruce-fir forests along a pollution gradient in the Central Urals. The dataset describes soil macrofauna’s abundance (the number of individuals per sample, i.e. the density) and community structure (list of supraspecific taxa, list of species for most abundant taxa and supraspecific taxa or species abundance). Seventeen sampling plots differed in the levels of toxic metal (Cu, Zn, Pb, Cd and Fe) soil contamination from air emissions of the Middle Ural Copper Smelter (heavily polluted, moderately polluted and unpolluted areas). The dataset consists of 340 sampling events (= samples corresponding to upper and lower layers of the 170 soil monoliths) and 64658 rows (2907 and 61751 for non-zero and zero density of taxa, respectively). Arachnida (Araneae and Opiliones), Carabidae (imagoes), Elateridae (larvae), Chilopoda, Diplopoda, Gastropoda, Staphylinidae (imagoes) and Lumbricidae were identified to species level. In contrast, Mermithida, Enchytraeidae, Lepidoptera larvae, Diptera larvae, Hemiptera, Hymenoptera and some other insects were identified to family or order levels. In total, 8430 individuals of soil macroinvertebrates were collected in two soil layers (organic and organic-mineral horizons), including 1046 Arachnida (spiders and harvestmen), 45 Carabidae, 300 Elateridae, 529 Myriapoda, 741 Gastropoda, 437 Staphylinidae, 623 Lumbricidae and 4709 other invertebrates. The presence-absence data on each taxon are provided for each sampling event. An overwhelming majority of such absences can be interpreted as “pseudo-absences” at the scale of sampling plots or study sites. The dataset contains information helpful for long-term ecotoxicological monitoring of forest ecosystems and contributes to studying soil macrofauna diversity in the Urals

Discovery of terrestrial allabogdanite (Fe,Ni)2P(Fe,Ni)_{2}P, and the effect of Ni and Mo substitution on the barringerite-allabogdanite high-pressure transition

Minerals formed at high pressures are sensitive indicators of extreme pressure-temperature conditions that occur in nature. The discovery of the high-pressure polymorph of (Fe,Ni)$_2$P, allabogdanite in the surficial pyrometamorphic rocks of the Hatrurim Formation (the Mottled Zone) surrounding the Dead Sea basin in Israel is the first terrestrial occurrence of a mineral previously only found in iron meteorites. Stepwise annealing experiments demonstrate that allabogdanite is metastable at ambient pressure and that it irreversibly transforms into its low-pressure polymorph, barringerite, upon heating to 850±50°C. High-pressure high-temperature diamond-anvil cell (DAC) experiments confirm the results of annealing experiments. The DAC data indicate that Hatrurim allabogdanite is metastable below 7.4 GPa, and the low- to high-pressure phase transition (barringerite→allabogdanite) occurs at 25±3 GPa and 1400±100°C. The observed transition pressure of Hatrurim allabogdanite is significantly higher than that of pure synthetic Fe$_2$P (8 GPa), due to partial substitution of Fe for Ni (4 wt.%) and Mo (2.5 wt.%). Because the influence of substituting impurities on the conditions of phase transitions can be unexpectedly strong, our findings confirm that caution should be exercised when extrapolating data from experiments on synthetic compounds to natural systems. Based on the discovery of terrestrial allabogdanite (Fe,Ni)$_2$P coupled with experiments probing the phase transitions in this natural composition, we contend that terrestrial allabogdanite formed via transformation from barringerite and posit potential scenarios of its formation

1,3-Dipolar Cycloaddition of Nitrones to Gold(III)-Bound Isocyanides

Treatment of gold­(III)-isocyanides [AuCl₃(CNR¹)] (R¹ = Xyl <b>1</b>, Cy <b>2</b>, Bu^<i>t</i> <b>3</b>) with an equimolar amount of 5,5-dimethyl-1-pyrroline-<i>N</i>-oxide (<b>4</b>) in CH₂Cl₂ at −74 °C leads to the generation of the heterocyclic aminocarbene species [AuCl₃{C­(ON^<i>a</i>CMe₂CH₂CH₂C^<i>b</i>H)N^<i>e</i>R¹}­(N^<i>a</i>–C^<i>b</i>)­(C^<i>b</i>–N^<i>e</i>)] <b>8</b> (for R¹ = Bu^<i>t</i>) or gold­(III) complexes <i>cis</i>-[AuCl₂{N^<i>a</i>(CMe₂CH₂CH₂C^<i>b</i>N^<i>e</i>R¹)­C^<i>d</i>O}­(N^<i>a</i>C^<i>b</i>)­(N^<i>e</i>–C^<i>d</i>)] <b>9</b> and <b>10</b> (for R¹ = Xyl and Cy) in good isolated yields (75–87%). DFT calculations show that deprotonation of the endocyclic CH group in the carbene ligand leads to spontaneous N–O bond cleavage, and acidity of this group is a factor controlling the different chemical behavior of <b>1</b>–<b>3</b> depending on the nature of substituent R¹. The reaction of equimolar amounts of the aldonitrone <i>p</i>-TolCHN⁺(Me)­O^– (<b>5</b>) or the ketonitrones Ph₂CN⁺(R²)­O^– (R² = Ph <b>6</b>, CH₂Ph <b>7</b>) with <b>1</b>–<b>3</b> in CD₂Cl₂ at −70 °C in air (or under N₂) revealed the formation of the carbene complexes [AuCl₃{C­(ONMeC^<i>a</i>H-<i>p</i>-Tol)N^<i>b</i>R¹}­(C^<i>a</i>–N^<i>b</i>)] (R¹ = Cy <b>11</b>, Xyl <b>12</b>, Bu^<i>t</i> <b>13</b>), [AuCl₃{C­(ONPhC^<i>a</i>Ph₂)N^<i>b</i>R¹}­(C^<i>a</i>–N^<i>b</i>)] (R¹ = Cy <b>14</b>, Bu^<i>t</i> <b>15</b>), or [AuCl₃{C­(ON­(CH₂Ph)­C^<i>a</i>Ph₂)N^<i>b</i>R¹}­(C^<i>a</i>–N^<i>b</i>)] (R¹ = Cy <b>16</b>, Xyl <b>17</b>), as studied by ¹H NMR. The reaction of <b>6</b> with <b>1</b> and of <b>7</b> with <b>3</b> did not furnish carbene products. Compounds <b>8</b>–<b>10</b> were characterized by ESI-MS, IR, 1D (¹H, ¹³C­{H}) and 2D (¹H,¹H–COSY, ¹H,¹³C-HSQC, ¹H,¹³C-HMBC) NMR spectroscopic techniques, and, only for <b>8</b>, elemental analyses (C, H, N), while compounds <b>11</b>–<b>17</b> were characterized by 1D (¹H, ¹³C­{H}) and 2D (¹H,¹³C-HSQC) NMR. Structures of compounds <b>8</b>, <b>9</b>, and <b>13</b> were additionally established by single-crystal X-ray diffraction

CESTES - A global database for metaCommunity Ecology: Species, Traits, Environment and Space

CESTES is a global database for metaCommunity Ecology: Species, Traits, Environment and Space. It compiles 80 datasets from trait-based studies. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. CESTES presents a harmonized structure and covers a diversity of ecosystem types (marine, terrestrial, freshwater), taxonomic groups (plants, vertebrates, invertebrates...), geographical regions, and spatial scales. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available (https://icestes.github.io/sharedata). A zipped folder called “CESTES.zip” includes two alternative formats for the CESTES database: - a “xCESTES” folder that includes 80 Excel files (one file per dataset), each named according to the following structure: “AuthorPublicationYear.xlsx” - a “rCESTES” folder that includes the CESTES core processed database (comm, traits, envir, coord matrices) as an R list object “CESTES.RData” plus two R scripts, and two metadata tables for data processing and exploration. This “CESTES.zip” folder also includes: - an extended metadata table, “CESTES_metadata.xlsx”, that provides the general metadata information of all the datasets, - a tutorial document, “HOW_TO_SHARE_MY_DATA_FOR_CESTES.pdf”, that explains how to share data for integrating future datasets in the database. A second zipped folder, called "ceste.zip", corresponds to the non-spatial ancillary to CESTES. We provide access to 10 additional datasets that were not completely suitable for the CESTES database, due to the absence of spatial information or insufficient metadata but that were potentially valuable for their three other data matrices (comm, traits, envir). They follow the same structure as CESTES, except that they do not present the “coord” sheet and sometimes include only partial metadata. The “ceste.zip” zipped folder includes the 10 data files + 1 metadata file called "ceste_metadata.xlsx"

Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space

An amendment to this paper has been published and can be accessed via a link at the top of the paper

A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES". Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology