Species losses, gains, and changes in persistent species are associated with distinct effects on ecosystem functioning in global grasslands

Global change drivers such as anthropogenic nutrient inputs simultaneously alter biodiversity, species composition, and ecosystem functions such as above ground biomass. These changes are interconnected by complex feedbacks among extinction, invasion, and shifting relative abundance. Here, we use a novel temporal application of the Price equation to separate species richness and biomass change through time and quantify the functional contributions of species that are lost, gained, and persist under ambient and experimental nutrient addition in 59 global grasslands. Under ambient conditions, compositional and biomass turnover was high, but species losses (i.e., local extinctions) were balanced by gains (i.e. colonization). Under fertilization, there was biomass loss associated with species loss. Few species were gained in fertilized conditions over time but those that were, and species that persisted, contributed to net biomass gains, outweighing biomass loss. These components of community change are associated with distinct effects on measures of ecosystem functioning.

GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring

GAL08 are bacteria belonging to an uncultivated phylogenetic cluster within the phylum Acidobacteria. We detected a natural population of the GAL08 clade in sediment from a pH-neutral hot spring located in British Columbia, Canada. To shed light on the abundance and genomic potential of this clade, we collected and analyzed hot spring sediment samples over a temperature range of 24.2–79.8°C. Illumina sequencing of 16S rRNA gene amplicons and qPCR using a primer set developed specifically to detect the GAL08 16S rRNA gene revealed that absolute and relative abundances of GAL08 peaked at 65°C along three temperature gradients. Analysis of sediment collected over multiple years and locations revealed that the GAL08 group was consistently a dominant clade, comprising up to 29.2% of the microbial community based on relative read abundance and up to 4.7 × 105 16S rRNA gene copy numbers per gram of sediment based on qPCR. Using a medium quality threshold, 25 single amplified genomes (SAGs) representing these bacteria were generated from samples taken at 65 and 77°C, and seven metagenome-assembled genomes (MAGs) were reconstructed from samples collected at 45–77°C. Based on average nucleotide identity (ANI), these SAGs and MAGs represented three separate species, with an estimated average genome size of 3.17 Mb and GC content of 62.8%. Phylogenetic trees constructed from 16S rRNA gene sequences and a set of 56 concatenated phylogenetic marker genes both placed the three GAL08 bacteria as a distinct subgroup of the phylum Acidobacteria, representing a candidate order (Ca. Frugalibacteriales) within the class Blastocatellia. Metabolic reconstructions from genome data predicted a heterotrophic metabolism, with potential capability for aerobic respiration, as well as incomplete denitrification and fermentation. In laboratory cultivation efforts, GAL08 counts based on qPCR declined rapidly under atmospheric levels of oxygen but increased slightly at 1% (v/v) O2, suggesting a microaerophilic lifestyle.

Revision of the genus Homa Distant (Hemiptera: Cicadellidae: Typhlocybinae)

The leafhopper genus Homa Distant is revised. Four new species, H. osificata Xu, Dietrich & Qin sp. nov., H. oretinia Xu, Dietrich & Qin sp. nov., H. asilata Xu, Dietrich & Qin sp. nov., and H. algulata Xu, Dietrich & Qin sp. nov., are described from Thailand. H. haematoptilus (Kirkaldy) is redescribed based on specimens from the Oriental Region. All included species are illustrated and a key is provided to separate species for which males are known.

Corrections and Additions to Descriptions of Some Species of the Subgenus Orthocladius s. str. (Diptera, Chironomidae, Orthocladiinae)

The larvae of some species of the subgenus Orthocladius s. str. (Diptera, Chironomidae) are here described for the first time with corrections and additions to the descriptions of adult males and pupal exuviae. The identification of larvae is generally not possible without association with pupal exuviae and/or adult males, so the descriptions here are based only on reared material or on pupae with the associated larval exuviae. Usually, Chironomidae larvae can be separated on the basis of morphometric characters, the most discriminant ones are: (1) the ratio between the width of median tooth of mentum (Dm) and the width of the first lateral tooth (Dl) = mental ratio (DmDl), (2) the ratio between the length of the first antennal segment (A1) and the combined length of segments 2–5 (A2–5) = antennal ratio (AR). The shape of mandible, maxilla, and other body parts are almost identical in all the species considered in this study. The larva of Orthocladius (Symposiocladius) lignicola is very characteristic and can be separated by the shape of mentum and the larvae of all the known species of Symposiocladius are characterized by the presence of large Lauterborn organs on antennae and of tufts of setae on abdominal segments. The larvae of Orthocladius (Orthocladius) oblidens and Orthocladius (Orthocladius) rhyacobius can be distinguished from other species basing on their large Dm and to each other by AR. A principal component analysis was carried out using 5 characters: (1) Dm, (2) Dl, (3) length of A1, (4) width of A1 (A1W), (5) combined length of segments 2–5 (A2–5). The most discriminant characters were Dm and A1, confirming that DmDl and AR can be used to separate species at larval stage, but the large superposition of morphometric characters in different species confirms that association with pupal exuviae is in any case needed to identify larvae. In future perspective, the development of reference DNA barcodes from specimens identified by specialists is recommended since possibly the best tool for larvae identification, but association of barcodes with morphotypes is in any case fundamental.

The present status, distribution, demography, and diet of the Dahl’s Jird

Meriones dahli (Shidlovsky, 1962) was previously accepted to be a subspecies of M. meridianus (Pallas, 1773). However, it was later suggested that they are geographically isolated from each other. Although hybridological studies and differences in certain external characteristics support the idea that M. dahli is a separate species, there are still doubts on its species status, and the exact range of its distribution is not known. In this paper, we provide some taxonomic information about the species, and compare these with the information given in previous studies. We argue that some differences exist among Armenian population regarding external measurements. Recent studies indicate that M. dahli is currently only distributed in Turkey, as an endemic mammal species. We provide predictions about the distribution of M. dahli, and report the estimated population size to its maximum value. Food preference studies for this species, conducted under laboratory conditions, are also introduced for the first time. We discuss the ecological data obtained from field studies, and emphasize that the habitat of M. dahli is about to disappear. Consequently, the protection status of this species should urgently be changed to the CR category and conservation studies must be carried out immediately.

A catalogue of 1,167 genomes from the human gut archaeome

The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report the analysis of 1,167 nonredundant archaeal genomes (608 high-quality genomes) recovered from human gastrointestinal tract, sampled across 24 countries and rural and urban populations. We identified previously undescribed taxa including 3 genera, 15 species and 52 strains. Based on distinct genomic features, we justify the split of the Methanobrevibacter smithii clade into two separate species, with one represented by the previously undescribed ‘CandidatusMethanobrevibacter intestini’. Patterns derived from 28,581 protein clusters showed significant associations with sociodemographic characteristics such as age groups and lifestyle. We additionally show that archaea are characterized by specific genomic and functional adaptations to the host and carry a complex virome. Our work expands our current understanding of the human archaeome and provides a large genome catalogue for future analyses to decipher its impact on human physiology.

Singularity Transition in Biosystem with Infinite Number of Conserved Links with Surroundings

Stages of natural evolution such as biogenesis and abiogenesis are the well-recognized terms to characterize the very different phases of life development. Traditionally, an abiogenesis is believed as the early stage of evolution that is mainly the chemistry phase dealing with intercoupling between the complex polymer chains when manifestations of life assumes substantial participation of cooperative effects. It its turn, a biogenesis as the subsequent stage of evolution is the period for prevalence of Darwin’s laws showing, in particular, in battle among separate species in the way of variability-heredity contest. In this article, we discuss possible nature of the transition between above stages as a normal result of progress in an evolutionary system simulated by mathematical model of open system with infinite number of conserved links with system surroundings. It is shown that the biosystem, in transition point experiences the deep reconstruction in existing pattern of energy exchange which leads to emergence of the more complicated and advanced stage of evolution. Our study showed that the found transition point can be considered as a singularity point in system evolution. In its turn, the evolution stages with the dissimilar meaning are the physical placeholders for stage of abiogenesis and biogenesis in natural evolution, correspondingly.

Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus

Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host’s ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.

New records of leeches of the genus Limnatis (Hirudinea, Praobdellidae) from the South Caucasus and Central Asia: phylogenetic relationships of Eurasian and African populations

Leeches of the genus Limnatis Moquin–Tandon, 1827 infest mucous membranes of various mammals, including humans and domestic ungulates. The type species of the genus L. nilotica (Savigny, 1822) was initially thought to occur throughout the Western Palaearctic, from North Africa to the Middle East and Central Asia. It was later found that L. paluda (Tennent, 1859) is a widespread Western Asian species. However, the South Caucasus and vast areas of Central Asia have not been explored sufficiently in terms of leeches of the genus Limnatis. We recorded L. paluda from Azerbaijan and Uzbekistan for the first time. We also carried out the first molecular characterisation of L. nilotica herein. We found a deep genetic differentiation (8 %) between the Western Asian L. paluda and North African (Moroccan) L. nilotica based on their COI sequences. This finding corroborates a previous morphology–based hypothesis on their separate species assignments. The low genetic diversity of L. paluda is explained by the recent colonisation of arid landscapes of Western Asia.