Ecological data in Darwin Core: the case of earthworm surveys

This sampling-event dataset provides primary data about species diversity, age structure, abundance (in terms of biomass and density) and seasonal activity of earthworms (Lumbricidae). The study was carried out in old-growth broad-leaved and young forests of two protected areas ("Kaluzhskiye Zaseki" Nature Reserve and Ugra National Park) of Kaluga Oblast (Russia). The published dataset provides new data about earthworm communities in European Russia. We propose a new schema according to Darwin Core for the standardisation of the soil invertebrates survey data.

Long-term dynamics of the abundance of earthworms and enchytraeids (Annelida, Clitellata: Lumbricidae, Enchytraeidae) in forests of the Central Urals, Russia

Since the late 1980s, long-term monitoring of terrestrial ecosystems in metal-contaminated areas has been carried out in the Central Urals. As a part of these monitoring programmes, the data on soil macroinvertebrates in undisturbed areas as reference sites continues to be gathered. These data help study the local biodiversity and long-term dynamics of soil macroinvertebrate abundance in non-polluted areas. The dataset (available from the GBIF network at https://www.gbif.org/dataset/bf5bc7f6-71a3-4abd-8abc-861ee3cbf84a) includes information from a long-term monitoring programme for two taxa of Annelids, Lumbricidae and Enchytraeidae, which dwell in the topsoil of spruce-fir, birch, pine and floodplain forests in the Central Urals. The dataset includes information on the earthworm community structure (list of species, species abundance, number of egg cocoons, cocoon exuvia, juveniles and adults) and enchytraeid abundance. The dataset consists of 553 sampling events (= samples, corresponding to upper and lower layers of the soil monoliths) and 12739 occurrences (earthworms, mainly identified to species and earthworm cocoons and enchytraeids, identified to family) collected during 1990–1991, 2004, 2014–2016 and 2018–2020. In total, 3305 individuals of earthworms were collected, representing ten (out of twelve) species and all eight genera recorded for the fauna of the Central Urals. In addition, 7292 earthworm egg cocoons and cocoon exuvia and 6926 individuals of enchytraeids were accumulated. The presence-absence data on each of the ten earthworm species, egg cocoons, cocoon exuvia and enchytraeids are provided for each sampling event. All data were collected in undisturbed non-polluted areas and are used as a local reference for ecotoxicological monitoring. The dataset provides valuable information for estimating the composition and abundance of earthworm communities in different habitats over a long time and contributes to the study of soil fauna biodiversity in the Urals.

The ground beetles (Caraboidea) of the southern Sikhote-Alin Mountains

This paper presents the results of 30 years of field studies on the Caraboidea fauna of the southern Sikhote-Alin Mountain, Russian Far East. Material was collected at 300+ geographical localities within 18 administrative and seven urban districts of the Primorsky Krai, Russia. A total of 55,953 adult ground beetles belonging to 426 subspecies, 411 species, 86 genera and three families were studied. The families Rhysodidae and Trachypachidae are represented by one species each, while the family Carabidae the remaining 409 species. The resulting sampling-event dataset includes 12,852 occurrences. This is the first dataset underlying an accurate and referenced taxonomic composition, as well as the geographic distribution of the Caraboidea in the southern Sikhote-Alin Mountains, Primorsky Krai, Russian Far East.

7Be/210Pbxs Ratio-Derived Age and Residence Time of Suspended Sediments in Galveston Bay

The winds associated with the passage of meteorological fronts cause waves that induce sediment remobilization/resuspension, especially within shallow estuaries such as Galveston Bay. The passage of cold fronts, collectively, on an annual to decadal basis, generate more sediment resuspension than most hurricanes and tropical storms. With a warming climate, the intensity of all meteorological events is shifting toward having greater impacts on these biologically productive environments. To better understand sediment resuspension within the bay, water samples were collected during frontal passages at two locations in Galveston Bay, including one location in the middle portion of the bay and another closer to the mouth of the bay. By collecting precipitation, water samples in both the middle and lower bay, and measuring the ratio of 7Be/210Pbxs in these samples; we quantified the residence times of total suspended sediment (TSS) in middle and lower Galveston Bay. Our results showed that suspended sediment age increased and percent of new suspended sediment decreased along the axis from the middle bay to the lower bay. This results from the initial introduction of newly labeled isotopes and suspended load coming from fluvial discharges which enter at the top of the bay and travel through the bay. The age of suspended sediment from the first sampling event was 70 ± 10 days, whereas the age in the second event was 16 ± 3 days greater. In the last sampling event, the age of suspended sediment event was 35 ± 7.4 days younger than the second, suggesting that the majority of suspended sediments was likely transported entirely out of the bay by the second cold front, prior to the final sampling event. This indicates that there are longer suspended sediment residence times when the water is trapped within the bay. Our estimated residence time of suspended sediments (51–105 days) suggest the particle-bound contaminants adsorb to suspended sediment may spend months suspended in the bay before exiting the bay or being accreted into the bay sediment column, increasing the exposure time of living organisms to various particle-bound contaminants.

Communities of ground beetles (Carabidae, Coleoptera) in broad-leaved forests of protected and urban areas of the Kaluga Oblast (European Russia)

This sampling-event dataset provides primary data about species diversity, population and seasonal activity of ground beetles (Carabidae, Coleoptera). The study was carried out in broad-leaved forests of protected ("Kaluzhskiye Zaseki" Nature Reserve and Ugra National Park) and urban areas (the Kaluga City) of the Kaluga Oblast. Carabids were collected from April to October during 1995-1998 by pitfall traps. In total, 108,000 adult individuals of the Carabidae family were sampled; 105 species from 38 genera were counted. This dataset is the first sampling-event dataset about the Carabidae family for the European part of Russia. It provides biodiversity data for new territory (Kaluga Oblast) and contributes to filling gaps in the global biodiversity distribution of the Carabidae family. Part of the data was collected from unique old-growth broad-leaved forests.

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms as well as macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes that currently only use the kick-net technique to sample macroinvertebrates.

Carabid beetles of the environs of Lake Elton: fauna, population dynamics, demography

The present paper includes the results of a year-round pitfall trapping survey of ground beetles in the region of Lake Elton, Volgograd Area, Russia. The main objectives of the project lie in studying the local fauna of Carabidae in the Lake Elton region, as well as their demographic structure and dispersal potential of the local populations of particular carabid species. A total of ten model habitats: six zonal (characteristic of that particular biogeographic area) and four azonal (present in a variety of biogeographical areas) were studied. In each model habitat, ten pitfall traps were set from 10 May 2006 until 10 May 2007 and were checked at 10-day intervals except for the period with negative temperatures (from 1 November 2006 until 31 March 2007). During the period of observation, 51,314 specimens of Carabidae, belonging to 149 species, were trapped. The resulting sampling-event dataset includes 24,291 plot-based observations (= sampling events), some of them containing zero records of particular species in a certain habitat and time. This is the first sampling-event dataset of a year-round pitfall trapping survey (from May 2006 until May 2007) of ground-beetle communities and the demographic structure of local populations of particular species in the Lake Elton region, Volgograd Area, Russia.

Modeling cow somatic cell count using sensor data as input to generalized additive models

This research paper presents a study investigating if sensor data from an automatic milking rotary could be used to model cow somatic cell count (composite milk SCC: CMSCC). CMSCC is valuable for udder health monitoring and individual cow udder health surveillance could be improved by predicting CMSCC between routine samplings. Data regularly recorded in the automatic milking rotary, in one German dairy herd, were collected for analysis. The cows (Holstein-Friesian, n = 372) were milked twice daily and sampled once weekly in afternoon milkings for 8 weeks for CMSCC. From the potential independent variables, including quarter conductivity, milk flow, blood in milk, kick-offs, not milked quarters and incomplete milkings, new variables that combined quarter data were created. Past period records, i.e. lags, of up to seven days before the actual CMSCC sampling event were added in the dataset to investigate if they were of use in modeling the cell count. Univariable generalized additive models (GAM) were used to screen the data to select potential independent variables. Furthermore, several multivariable GAM were fitted in order to compare the importance of the potential independent variables and to explore how the model performance would be affected by using data from various number of days before the CMSCC sampling event. The result of the model selection showed that the best explanation of CMSCC was provided by the model incorporating all significant variables from the variable screening for the seven preceding days, including the day of the CMSCC sampling event. However, using data from only three days before the CMSCC sampling event is suggested to be sufficient to model CMSCC. Variables combining conductivity quarter data, together with quarter conductivity, are suggested to be important in describing CMSCC. We conclude that CMSCC can be modeled with a high degree of explanation using the information routinely recorded by the milking robot.