Metabarcoding data of prokaryotes and eukaryotes inhabiting the phosphogypsum stockpiles on the salt marshes of Huelva (SW Spain)

Around 100 Mt of phosphogypsum (PG) of extreme acidity and with high concentrations of heavy metals and radionuclides have been deposited on the salt marshes of the Tinto River estuary in Huelva (SW Spain) for more than forty years. The microbial community able to thrive in these adverse conditions remains totally unknown, despite the fact that it can highly influence the biogeochemical cycle of the phosphogypsum components and include new species with biotechnological interest. High throughput sequencing of 16S/18S rRNA encoding genes is a potent tool to uncover the microbial diversity of extreme environments. This data article describes for the first time the prokaryotic and eukaryotic diversity of two water samples collected in the Huelva phosphogypsum stacks. The raw amplicons of the 16S/18S rRNA maker genes for the two phosphogypsum samples and two reference samples (seawater and the Tinto River water) obtained after sequencing on MiSeq platform are provided. The operational taxonomic units (OTUs) obtained after the treatment and clustering of the obtained reads with the QIIME2 pipeline and their taxonomic assignation performed by comparison with the SILVA database are also presented to complete the information of the article “Exploring the microbial community inhabiting the phosphogypsum stacks of Huelva (SW, Spain) by a high throughput 16S/18S rDNA Sequencing approach”.

Putative intranuclear coccidium in Mauremys leprosa (Schweigger) from Morocco

Although intranuclear coccidiosis was first identified in chelonians less than 30 years ago, it is now considered an important emerging disease. Symptoms include anorexia, weakness and weight loss, potentially leading to death of the infected animal. The use of molecular tools has led to improved diagnosis and has also led to an increase in known host species. Here we report a putative intranuclear coccidium in Mauremys leprosa (Schweigger), from Morocco, based on 18S rDNA sequence analysis. This is, to the best of our knowledge, the first report of this parasite from a freshwater terrapin species.

Molecular phylogenetic identification and morphological characteristics of Raillietina echinobothrida (Cestoda: Cyclophyllidea: Davaineidae) in commercial chickens in North China

Raillietina echinobothrida (R. echinobothrida) is one of the most pathogenic and prevalent tapeworms threat to the commercial chickens in China. However, there is a lack of research on their molecular identification and morphological characteristics. This study explored the molecular identification markers for R. echinobothrida in North China based on 18s ribosomal RNA (18s rRNA) gene and the ribosomal DNA second internal transcribed spacer (ITS-2) gene. The BLAST results of 18s rRNA (1643 bp) and ITS-2 (564 bp) gene sequences showed that the isolated intestinal tapeworms were R. echinobothrida. Phylogenetic trees obtained by maximum likelihood (ML) or neighbor-joining (NJ) method revealed that the R. echinobothrida in North China had the closest evolutionary relationship with the species found on the Qinghai-Tibet plateau, China. Morphological observations by hematoxylin staining and scanning electron microscope showed four round suckers and a retractable rostellum on the spherical scolex of R. echinobothrida. Two rows of alternately arranged hooks distributed around the rostellum. There were 30-40 testes in each mature segment. A well-developed cirrus pouch lied outside the excretory duct of mature segment. The gravid segment contained 200-400 eggs and there was a well-developed oncosphere in each egg. In addition, abundant ultrastructural features in mature proglottid of R. echinobothrida in North China were identified by transmission electron microscopy. In conclusion, the present study established ways of molecular phylogenetic identification for R. echinobothrida based on 18s rRNA and ITS-2 gene, and identified the morphological and ultrastructural characteristics of R. echinobothrida in North China.

Anthropogenic stressors affect fungal more than bacterial communities in decaying leaf litter: A stream mesocosm experiment

Despite the progress made in environmental microbiology techniques and knowledge, the succession and functional changes of the microbial community under multiple stressors are still poorly understood. This is a substantial knowledge gap as microbial communities regulate the biogeochemistry of stream ecosystems. Our study assessed the structural and temporal changes in stream fungal and bacterial communities associated with decomposing leaf litter under a multiple-stressor scenario. We conducted a fully crossed 4-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 days of colonisation, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S and 18S rRNA genes) to identify changes in microbial community composition. Our results indicate that (1) shifts in relative abundances of the pre-existing terrestrial microbial community, rather than changes in community identity, drove the observed responses to stressors; (2) changes in relative abundances within the microbial community paralleled decomposition rate patterns with time; (3) both fungal and bacterial communities had a certain resistance to stressors, as indicated by relatively minor changes in alpha diversity or multivariate community structure; (4) overall, stressor interactions were more common than stressor main effects when affecting microbial diversity metrics or abundant individual genera; and (5) stressor effects on microbes often changed from 2 weeks to 3 weeks of stressor exposure, with several response patterns being reversed. Our study suggests that future research should focus more on understanding the temporal dynamics of fungal and bacterial communities and how they relate to ecosystem processes to advance our understanding of the mechanisms associated with multiple-stressor interactions.

Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes

Labyrinthulomycetes are heterotrophic stramenopiles that are ubiquitous in a wide range of both marine and freshwater habitats and play important roles in decomposition of organic matter. The diversity and taxonomy of Labyrinthulomycetes has been studied for many years, but we nevertheless lack both a comprehensive reference database and up-to-date phylogeny including all known diversity, which hinders many global insights into their ecological distribution and the relative importance of various subgroups in different environments. Here, we present a curated reference database and a phylogenetic tree of Labyrinthulomycetes small subunit ribosomal RNA (SSU or 18S rRNA) data. Based on this created reference database, we analyzed high-throughput environmental sequencing data, revealing many previously unknown environmental clades and exploring the ecological distribution of various subgroups. Particularly, a number of newly identified environmental clades that are widespread in the open ocean. Comparing the manually curated reference database to existing tools for identification of environmental sequences (e.g. PR2 or SILVA databases) suggests that the curated database provides a higher degree of specificity and a lower frequency of misidentification. The phylogenetic framework and database will be a useful tool for future ecological and evolutionary studies.

Multiple lines of evidence shed light on the occurrence of paramecium (ciliophora, oligohymenophorea) in bromeliad tank water

Phytotelmata are vegetal structures that hold water from the rain, and organic matter from the forest and the soil, resulting in small, compartmentalized bodies of water, which provide an essential environment for the establishment and development of many organisms. These microenvironments generally harbor endemic species, but many organisms that are found in lakes and rivers, are also present. Here, we report, for the first time, the occurrence of the ciliate genus Paramecium in the tank of the bromeliad species Aechmaea distichantha. The identification of the Paramecium species was performed based on live observations, protargol impregnation, scanning electronic microscopy, and sequencing of the 18s rRNA. The absence of Paramecium from bromeliad tank water was highlighted in several earlier investigations, and may be due to the fact that this species is unable to make cysts. The occurrence of Paramecium multimicronucleatum in our samples may be explained by the proximity between the bromeliads and the river, a potential source of the species. Further, we also believe that the counting methodology used in our study provides a more accurate analysis of the species diversity, since we investigated all samples within a maximum period of 6 h after sampling, allowing minimum loss of specimens.