Soil macrofauna communities in Brazilian land-use systems.

Background: Soil animal communities include more than 40 higher-order taxa, representing over 23% of all described species. These animals have a wide range of feeding sources and contribute to several important soil functions and ecosystem services. Although many studies have assessed macroinvertebrate communities in Brazil, few of them have been published in journals and even fewer have made the data openly available for consultation and further use. As part of ongoing efforts to synthesise the global soil macrofauna communities and to increase the amount of openly-accessible data in GBIF and other repositories related to soil biodiversity, the present paper provides links to 29 soil macroinvertebrate datasets covering 42 soil fauna taxa, collected in various land-use systems in Brazil. A total of 83,085 georeferenced occurrences of these taxa are presented, based on quantitative estimates performed using a standardised sampling method commonly adopted worldwide to collect soil macrofauna populations, i.e. the TSBF (Tropical Soil Biology and Fertility Programme) protocol. This consists of digging soil monoliths of 25 x 25 cm area, with handsorting of the macroinvertebrates visible to the naked eye from the surface litter and from within the soil, typically in the upper 0-20 cm layer (but sometimes shallower, i.e. top 0-10 cm or deeper to 0-40 cm, depending on the site). The land-use systems included anthropogenic sites managed with agricultural systems (e.g. pastures, annual and perennial crops, agroforestry), as well as planted forests and native vegetation located mostly in the southern Brazilian State of Paraná (96 sites), with a few additional sites in the neighbouring states of São Paulo (21 sites) and Santa Catarina (five sites). Important metadata on soil properties, particularly soil chemical parameters (mainly pH, C, P, Ca, K, Mg, Al contents, exchangeable acidity, Cation Exchange Capacity, Base Saturation and, infrequently, total N), particle size distribution (mainly % sand, silt and clay) and, infrequently, soil moisture and bulk density, as well as on human management practices (land use and vegetation cover) are provided. These data will be particularly useful for those interested in estimating land-use change impacts on soil biodiversity and its implications for below-ground foodwebs, ecosystem functioning and ecosystem service delivery. New information: Quantitative estimates are provided for 42 soil animal taxa, for two biodiversity hotspots: the Brazilian Atlantic Forest and Cerrado biomes. Data are provided at the individual monolith level, representing sampling events ranging from February 2001 up to September 2016 in 122 sampling sites and over 1800 samples, for a total of 83,085 ocurrences.

Amazonian earthworm biodiversity is heavily impacted by ancient and recent human disturbance.

Despite the importance of earthworms for soil formation, more is needed to know about how Pre-Columbian modifications to soils and the landscape. Gaining a deeper understanding is essential for comprehending the historical drivers of earthworm communities and the development of effective conservation strategies in the Amazon rainforest. Human disturbance can significantly impact earthworm diversity, especially in rainforest soils, and in the particular case of the Amazonian rainforest, both recent and ancient anthropic practices may be important. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by sedentary habits and intensification patterns of pre-Colombian societies primarily developed in the second part of the Holocene period. We have sampled earthworm communities in three Brazilian Amazonian (ADEs) and adjacent reference soils (REF) under old and young forests and monocultures. To better assess taxonomic richness, we used morphology and the barcode region of the COI gene to identify juveniles and cocoons and delimit Molecular Operational Taxonomic Units (MOTUs). Here we suggest using Integrated Operational Taxonomical units (IOTUs) which combine both morphological and molecular data and provide a more comprehensive assessment of diversity, while MOTUs only rely on molecular data. A total of 970 individuals were collected, resulting in 51 taxonomic units (IOTUs, MOTUs, and morphospecies combined). From this total, 24 taxonomic units were unique to REF soils, 17 to ADEs, and ten were shared between both soils. The highest richness was found in old forest sites for ADEs (12 taxonomic units) and REFs (21 taxonomic units). The beta-diversity calculations reveal a high species turnover between ADEs and REF soils, providing evidence that ADEs and REFs possess distinct soil biota. Furthermore, results suggest that ADE sites, formed by Pre-Columbian human activities, conserve a high number of native species in the landscape and maintain a high abundance, despite their long-term nature.

Earthworms from natural and managed ecosystems in Southern Bahia, Brazil.

The earthworms (Crassiclitellata) of the Northern Atlantic Forest region are poorly known, and many new species are expected to be found in the region. Hence, quantitative and qualitative samples were taken in the Atlantic Forest region of southern Bahia State, Brazil, at eight sites to assess species presence and abundance in different land uses (forests, pastures, plantations). Earthworms were also qualitatively collected at an additional eight sites. Only one to two species per site were found in quantitative samples, while qualitative samples generally resulted in higher species recoveries, with highest richness observed at the native Atlantic Forest of Veracel in Porto Seguro. Pontoscolex corethrurus (Müller, 1857) was the dominant species at all sites and in most land use systems, probably favored by human migration and agricultural activities; it was only absent in one primary forest site where native Ocnerodrilidae species predominated. In total at least 14 species were found of which eight were new, belonging to the genus Rhinodrilus and three new genera in the Ocnerodrilidae family (Pauqueba, Parabauba and Diplomoela). Contrary to sites in Southern and Southeastern Brazil, where many native species belong to the Glossoscolecidae family, in southern Bahia, Ocnerodrilidae species tend to be more prevalent, occupying various habitats. More intensive sampling of these habitats, including surface litter, in and under fallen logs and dead tree trunks, under rocks, in bromeliad leaf tanks and deeper soil layers is essential in order to properly characterize earthworm communities in Brazilian Atlantic Forests.

First Patient-to-Patient Intrahospital Transmission of Clade I Candida auris in France Revealed after a Two-Month Incubation Period.

Candida auris is a recently described emerging pathogen in hospital settings. Five genetic clades have been delineated, with each clade being isolated from specific geographic regions. We here describe the first transmission between 2 patients (P0 and P1) of a clade I C. auris strain imported into our burn intensive care unit from the Middle East. The strains have been investigated with whole-genome sequencing, which validated the high similarity of the genomes between isolates from P0 and P1. We repeatedly screened the two patients and contact patients (i.e., other patients present in the same hospital ward at the time of the first positive sample from P0 or P1; n = 49; 268 tests) with fungal culture and a C. auris-specific quantitative PCR assay to assess transmission patterns. We observed that P1 developed C. auris colonization between 41 and 61 days after potential exposure to P0 contamination, despite three negative screening tests as recommended by our national authorities. This study illustrates that transmission of C. auris between patients can lead to long-term incubation times before the detection of colonization. The recommended screening strategy may not be optimal and should be improved in the light of our findings. IMPORTANCE While large outbreaks of C. auris in hospital settings have been described, few clear cases of direct transmission have been documented. We here investigated the transmission of C. auris clade I between two patients with a 41- to 61-day delay between exposure and the development of colonization. This may lead to changes in the recommendations concerning treatment of C. auris cases, as an incubation period of this length is one of the first to be reported.

A "Dirty" Footprint: Macroinvertebrate diversity in Amazonian Anthropic Soils.

Amazonian rainforests, once thought to be pristine wilderness, are increasingly known to have been widely inhabited, modified, and managed prior to European arrival, by human populations with diverse cultural backgrounds. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies with sedentary habits. Much is known about the chemistry of these soils, yet their zoology has been neglected. Hence, we characterized soil fertility, macroinvertebrate communities, and their activity at nine archeological sites in three Amazonian regions in ADEs and adjacent reference soils under native forest (young and old) and agricultural systems. We found 673 morphospecies and, despite similar richness in ADEs (385 spp.) and reference soils (399 spp.), we identified a tenacious pre-Columbian footprint, with 49% of morphospecies found exclusively in ADEs. Termite and total macroinvertebrate abundance were higher in reference soils, while soil fertility and macroinvertebrate activity were higher in the ADEs, and associated with larger earthworm quantities and biomass. We show that ADE habitats have a unique pool of species, but that modern land use of ADEs decreases their populations, diversity, and contributions to soil functioning. These findings support the idea that humans created and sustained high-fertility ecosystems that persist today, altering biodiversity patterns in Amazonia.

Earthworm species in various land use systems in the Campos Gerais region of Lapa, Paraná, Brazil.

The Campos Gerais region of Paraná are on an ancient plateau of sandstone origin and are covered with a diverse vegetation including mainly grasslands and various types of Atlantic Forest (particularly Araucaria forest). The region represents an important natural capital for biodiversity conservation as well as for agricultural and forestry production. However, little is known of the species richness and diversity of soil macroinvertebrates in this region. In the present study we evaluated earthworm species occurrence and richness in five land use systems (LUS) in the southern part of the Campos Gerais in Lapa county. Earthworms were handsorted from up to 18 soil monoliths on five occasions over three years (Feb. 2014, Feb., Mar., Nov. 2015, Jul. 2016) in the following LUS: old native forest, native grassland, young regenerating forest and grass lawn in the Uru Reserve and annual crop fields (soybean) in neighboring private farms (not all systems were sampled on all occasions). Nine earthworm species belonging to four families and five genera were found, of which six were native and three exotic species (Dichogaster gracilis, Amynthas gracilis, A. corticis). Of the native species, Urobenus brasiliensis and Andiorrhinus duseni (a large bodied-worm) are already well known from S and SE Brazil, while the remaining four were new species that require further description (Fimoscolex n.sp.1 and n.sp.2, Glossoscolex n.sp.1 and n.sp.2). In general, more species were found in February (summer) than March and November. The cropping system (soybean) had the lowest abundance and species richness in relation to other sites, although in the young and old forests no earthworms were found on some sample dates. Given the several new species found in this small reserve, and the relatively few sites studied thus far in the Campos Gerais, further efforts are needed to adequately characterize the earthworm fauna of the region, from which many other species are expected.