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Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses - many without known hosts but which have been found in association with eukaryotes. Similar advances in cellular genomics have revealed that many eukaryotes have endogenous sequences homologous to viral Reps, which not only provide 'fossil records' to reconstruct the evolutionary history of CRESS DNA viruses but also reveal potential host species for viruses known by their sequences alone. The Rep protein is a conserved protein that all CRESS DNA viruses use to assist rolling-circle replication that is known to be endogenized in a few eukaryotic species (notably tobacco and water yam). A systematic search for endogenous Rep-like sequences in GenBank's non-redundant eukaryotic database was performed using tBLASTn. We utilized relaxed search criteria for the capture of integrated Rep sequence within eukaryotic genomes, identifying 93 unique species with an endogenized fragment of Rep in their nuclear, plasmid (one species), mitochondrial (six species) or chloroplast (eight species) genomes. These species come from 19 different phyla, scattered across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA viral Rep tree topology suggested potential hosts for one family of uncharacterized viruses and supports a primarily fungal host range for genomoviruses.

Bacterial secondary metabolites are rich sources of novel drug leads. The diversity of secondary metabolite biosynthetic gene clusters (BGCs) in genome-sequenced bacteria, which will provide crucial information for the efficient discovery of novel natural products, has not been systematically investigated. Here, the distribution and genetic diversity of BGCs in 10 121 prokaryotic genomes (across 68 phyla) were obtained from their PRISM4 outputs using a custom python script. A total of 18 043 BGCs are detected from 5743 genomes with non-ribosomal peptide synthetases (25.4%) and polyketides (15.9%) as the dominant classes of BGCs. Bacterial strains harbouring the largest number of BGCs are revealed and BGC count in strains of some genera vary greatly, suggesting the necessity of individually evaluating the secondary metabolism potential. Additional analysis against 102 strains of discovered bacterial genera with abundant amounts of BGCs confirms that Kutzneria, Kibdelosporangium, Moorea, Saccharothrix, Cystobacter, Archangium, Actinosynnema, Kitasatospora, and Nocardia, may also be important sources of natural products and worthy of priority investigation. Comparative analysis of BGCs within these genera indicates the great diversity and novelty of the BGCs. This study presents an atlas of bacterial secondary metabolite BGCs that provides a lot of key information for the targeted discovery of novel natural products.

International audience; The family Smacoviridae (order Cremevirales, class Arfiviricetes, phylum Cressdnaviricota) is comprised of viruses with small circular single-stranded DNA genomes of ~2.3-3 kb in length that have primarily been identified in fecal sample of various animals. Smacovirus genomes carry two genes in ambisense orientation encoding a capsid protein and a rollingcircle replication initiation protein, respectively. We have revised the taxonomy of the family by assigning 138 new genomic sequences deposited in GenBank to already established taxa as well as 41 new species and six new genera. Furthermore, we have adopted binomial species nomenclature, conforming to the "Genus + freeform epithet" format for all 84 species from 12 genera. The updated Smacoviridae taxonomy presented in this article has been ratified by the International Committee on Taxonomy of Viruses (ICTV).

The composition of microbial communities in rock samples, reservoir water, and enrichment cultures from subsurface horizons of an uranium deposit (Russia) was determined. The studied horizons were located in the zone of hindered water exchange at a depth of 513–544 m, characterized by moderate salinity (up to 15 g/L) of reservoir water and the presence of charry plant organic matter. The biodiversity of autochthonous subsurface prokaryotes was determined by high-throughput sequencing of the V4 region of the 16S rRNA gene. Bacterial phyla predominant in the rock samples were Firmicutes (24.2%), Fusobacteriota (23.0%), Proteobacteria (18.7%), Actinobacteriota (15.5%) and Bacteroidota (9.0%). The predominant bacterial phylum in the reservoir water was Proteobacteria (90.7%), including representatives of the genera Methylophaga, Porphyrobacter, Roseovarius, Pseudomonas, and Methylococcus. Sequencing of the internal transcribed spacer (ITS) revealed occurrence of lower fungi of the genera Mucor and Thamnidium (phylum Mucoromycota) and of the genus Penicillium (phylum Ascomycota) in the rock samples; members of these genera are known for their resistance to heavy metals and the ability to use complex organic substrates. The functional characteristics of bacterial communities of the rock and reservoir water samples, predicted by the iVicodak program and the KEGG database, showed that reservoir water bacteria had a higher potential ability to carry out the pathways of carbohydrate, nitrogen, and sulfur metabolism, degradation of xenobiotics, benzoate, polycyclic aromatic hydrocarbons and chlorinated organic compounds than the rock microbiota. Enrichment cultures of iron-reducing and sulfate-reducing bacteria and pure cultures of denitrifying bacteria of the genera Bacillus, Paenibacillus, and Acinetobacter were obtained. These results indicate the presence of a small but viable microbial community that can participate in the processes of transformations of carbon, nitrogen, sulfur, and metals in the subsurface horizon when water exchange is activated.

The gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.

The Gangwon-do Province in Korea features abundant limestone areas and numerous limestone caves; however, few studies have conducted systematic research on the limestone caves in this area. In this study, we observed and explored the biota of three undisclosed caves located in Pyeongchang-gun, Gangwon-do Province (Jangamgul Cave, Baramgul Cave, and Ssanggul Cave) to further understand their ecology. As a result, a total of four phyla, 12 classes, 30 orders, 77 families, and 125 species of cave organisms were discovered, including three phyla, 11 classes, 23 orders, 51 families, and 77 species in Jangamgul Cave; four phyla, 10 classes, 23 orders, 43 families, and 52 species in Baramgul Cave; and three phyla, nine classes, 20 orders, 41 families, and 54 species in Ssanggul Cave. Several threatened species such as Plecotus auritus (Linnaeus, 1758), designated as Class 2 endangered wildlife in Korea, Onychodactylus fischeri (Boulenger, 1886), designated as a least concern (LC) species by the IUCN, and Galloisiana sp., described as an extant species of the relict insect were found in this study. Our results are significant in providing information on the distribution of cave organisms living by adapting to the cave environment.

Microorganisms are widely distributed throughout the built environment and even those found in concealed environments such as sink P‐traps can have an impact on our health. To date, most studies on sink bacterial communities focused on those present in hospitals with no to little information regarding sinks in residential or communal settings. Here, we conducted a characterization using 16S rRNA sequencing of the bacterial communities of communal restroom sinks located on a university campus to investigate the diversity, prevalence, and abundances of the bacteria that reside in this understudied environment. The study found that community composition and structure were highly variable across individual sinks, and there were marginal differences between buildings and the two different parts of sink examined. Proteobacteria were the most abundant phylum in the sink communities, and the families Burkholderiaceae, Moraxellaceae, and Sphingomonadaceae were found to be ubiquitous across all sinks. Notably, human skin was identified as a primary contributor to the below‐strainer sink bacterial community. These data provide novel insight into the sink bacterial communities' constituents and serve as the foundation for subsequent studies that might explore community stability and resilience of in situ sinks.

Ciliophora is a phylum of unicellular eukaryotes that are common and have pivotal roles in aquatic environments. Sea ice is a marine habitat, which is composed of a matrix of solid ice and pockets of saline water in which Ciliophora thrive. Here, we used phylogenetic placement to identify Ciliophora 18S ribosomal RNA reads obtained from wintertime water and sea ice, and assigned functions to the reads based on this taxonomic information. Based on our results, sea-ice Ciliophora assemblages are poorer in taxonomic and functional richness than under-ice water and water-column assemblages. Ciliophora diversity stayed stable throughout the ice-covered season both in sea ice and in water, although the assemblages changed during the course of our sampling. Under-ice water and the water column were distinctly predominated by planktonic orders Choreotrichida and Oligotrichida, which led to signifcantly lower taxonomic and functional evenness in water than in sea ice. In addition to planktonic Ciliophora, assemblages in sea ice included a set of moderately abundant surface-oriented species. Omnivory (feeding on bacteria and unicellular eukaryotes) was the most common feeding type but was not as predominant in sea ice as in water. Sea ice included cytotrophic (feeding on unicellular eukaryotes), bacterivorous and parasitic Ciliophora in addition to the predominant omnivorous Ciliophora. Potentially mixotrophic Ciliophora predominated the water column and heterotrophic Ciliophora sea ice. Our results highlight sea ice as an environment that creates a set of variable habitats, which may be threatened by the diminishing extent of sea ice due to changing climate. DNA metabarcoding · Phylogenetic placement · Mixotrophy · Predator–prey interactions · Winter ecology

The flaviviruses (family Flaviviridae) are a group of positive-strand RNA viruses, many of which pose serious risks to human health on a global scale. Here, we calibrate the timeline of flavivirus evolution using flavivirus-derived DNA sequences identified in animal genomes. We demonstrate that the family is at least 100 million years old and show that this timing can be integrated with dates inferred from co-phylogenetic analysis and paleontological records to produce a cohesive overview of flavivirus evolution in which the main subgroups originate early in animal evolution and broadly co-diverge with animal phyla. In addition, we show that the arthropod-borne ‘classical’ flaviviruses first evolved from tick-specific viruses, and only later adapted to become insect-borne. Our findings demonstrate that the biological properties of flaviviruses have been acquired over many millions of years of evolution, implying that broad-scale comparative analysis can reveal fundamental insights into flavivirus biology. We implement a novel approach to computational genomic studies of viruses that can support these efforts by enabling more efficient utilization of evolution-related domain knowledge in virus research. Significance Understanding how pathogenic viruses evolved can provide vital insights into their biology. In this study we use genomic data to show that flaviviruses – a group of viruses that includes important pathogens such as Dengue virus and hepatitis C virus - arose through an extended history of evolutionary interaction with host and vector species. Our findings show that comparative studies can productively utilise genomic data to reveal insights into flavivirus biology, which will help to facilitate the development of more effective antiviral treatments and strategies.

Molluscs are remarkably diverse and are found across nearly all ecosystems, meaning that members of this ancient animal phylum provide a powerful means to study genomic-phenotype connections in a climate change framework. Recent advances in genomic sequencing technologies and genome assembly approaches finally allow the relatively cheap and tractable assembly of high-quality mollusc genome resources. After a brief review of these issues and advances, we use a case-study approach to provide some concrete examples of phenotypic plasticity and genomic adaptation in molluscs in response to environmental factors expected to be influenced by climate change. Our goal is to use molluscs as a “common currency” to demonstrate how organismal and evolutionary biologists can use natural systems to make phenotype-genotype connections in the context of changing environments. In parallel, we emphasize the critical need to collaborate and integrate findings across taxa and disciplines in order to use new data and information to advance our understanding of mollusc biology in the context of global environmental change. We end with a brief synthetic summary of the papers inspired by the 2021 SICB Symposium “Genomic Perspectives in Comparative Physiology of Molluscs: Integration across Disciplines”.

Fungi have evolved diverse strategies to acquire nutrients as endophytes, saprobes, symbionts, or pathogens. Appressoria have been intensively studied due to their importance in attaching and breaching the host surface. These specialized infection structures have evolved into various morpho-types: proto-appressoria, hyaline appressoria, melanized (dark) appressoria, and compound appressoria. In this review, we discuss the differences in the formation, differentiation, and function of appressoria among fungi with diverse life strategies. Using DNA sequence information, LSU, 5.8S, SSU and rpb2 gene fragments, we reconstructed the ancestral states for appressorial types in the main phyla of fungi and fungus-like organisms and found that the hyaline appressoria was the most ancestral form. Our analysis estimated proto-appressoria diversification during the Mesozoic period (92–239 million years ago), however, its origin remains inconclusive. Our data suggest that these hyaline appressoria diversified into melanized or compound appressoria, with evidence of adaptive radiation.

We studied the microbial communities associated with the Baikal ostracods, Candona sp. (Candonidae). Bacterial biofilms were identified on the shell valves of the ostracods localized near epibiotic ciliates of the genus Lagenophrys (Ciliophora: Lagenoprydae). In situ hybridization confirmed the presence of eubacterial cells in different parts of the ostracod’s body. Bacteria of two morphotypes were detected in bacterial biofilms, including filamentous bacteria. Next-generation sequencing of 16S rRNA bacterial gene fragment allowed us to identify representatives of five bacterial phyla. Members of the phyla Proteobacteria and Bacteroidetes typical of non-marine epibiotic associations of ostracods were dominant taxa in the ostracod microbiomes. Members of other taxa (Actinobacteria, Gracilibacteria and Cyanobacteria) are likely facultative and consumed by ostracods together with detritus. In the ostracod microbiome, a significant proportion (20% of all reads) belonged to the sequences of the genus Rickettsia related to intracellular parasites.

Sufu is a common solid-state traditional fermented food made from soybean. Huase sufu is a typical type found in several provinces of China, especially in Hubei. However, little is known about the bacterial community. High-throughput sequencing technology revealed that the dominant taxa at phylum level were: Firmicutes, Proteobacteria and Bacteroides, and at the genus level were: Pseudomonas, Lactococcus, Acinetobacter, etc. Additionally, LEfSe revealed that compared with the bacterial community of red sufu and white sufu, the biomarker genera for both huase sufu were Enterococcus, and Myroides. Moreover, there were twenty-eight hubs for the huase sufu samples, and four of them were dominant genera: Citrobacter, Myroides, Vagococcus, and Enterococcus. These results provide a new insight into our understanding of the bacterial diversity of huase sufu, and will facilitate the isolation, screening, and development potential bacterial strains for production of huase sufu. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-021-00963-3.

Archaea, one of the three domains of life along with Bacteria and Eukarya, contains ancient life forms such as methanogen that are observed today on Earth, and one lineage Asgard archaea is also considered the closest ancestor of Eukarya. Recently, with the development of interdisciplinary studies from Earth and Life sciences, archaeal organisms are considered to play pivotal roles in geochemical cycling in nature. However, our understanding of the attributes, origin and evolution, geochemical and ecological functions of Archaea is hampered by the scarcity of archaeal isolates, which has represented a challenge to researchers for the last 40 years. Cultivation-independent sequencing and phylogenomic analyses have demonstrated a considerable diversity of Archaea with more than 20 novel phyla. However, only four archaeal phyla have cultured representatives, leaving large gaps in our knowledge of the metabolic capabilities and ecological functions of the majority of archaeal strains identified exclusively by DNA sequencing. In this review, we summarize the discovery and development of archaeal research, highlight the knowledge gap between uncultured and cultured archaeal microbes, and call on the importance of devoting greater research efforts to archaeal cultivation. Finally, we outlined new ideas and strategic approaches, namely, (1) genome-based methods, (2) microbial network information-based methods, (3) genome-scale model-guided methods, and (4) machine learning methods, to enable the cultivation of uncultivated archaeal microbes using accumulated high-throughput sequencing data.

There is growing interest in the study of avian endoparasite communities, and metabarcoding is a promising approach to complement more conventional or targeted methods. In the case of eukaryotic endoparasites, phylogenetic diversity is extreme, with parasites from 4 kingdoms and 11 phyla documented in birds. We addressed this challenge by comparing different primer sets across 16 samples from 5 bird species. Samples consisted of blood, feces, and controlled mixes with known proportions of bird and nematode DNA. Illumina sequencing revealed that a 28S primer set used in combination with a custom blocking primer allowed detection of various plasmodiid parasites and filarioid nematodes in the blood, coccidia in the feces, as well as two potentially pathogenic fungal groups. When tested on the controlled DNA mixes, these primers also increased the proportion of nematode DNA by over an order of magnitude. An 18S primer set, originally designed to exclude metazoan sequences, was the most effective at reducing the relative number of avian DNA sequences and was the only one to detect Trypanosoma in the blood. Expectedly, however, it did not allow nematode detection and also failed to detect avian malaria parasites. This study shows that a 28S set including a blocking primer allows detection of several major and very diverse bird parasite clades, while reliable amplification of all major parasite groups may require a combination of markers. It helps clarify options for bird parasite metabarcoding, according to priorities in terms of the endoparasite clades and the ecological questions researchers wish to focus on., Parasites of birds are extremely diverse, spanning no less than four different kingdoms (Chromista, Protozoa, Metazoa and Fungi). Our understanding of these communities and their fascinating interactions could benefit from metabarcoding approaches. This report provides a side‐by‐side comparison of different metabarcoding options for a broad description of avian eukaryotic endoparasite communities.

Background/purpose The estimated prevalence of xerostomia (lack of saliva) ranges from 10% to 50% of the general population. The oral cavity provides a multivariant environmental habitat to over 700 species of bacteria and fungi. We hypothesized that xerostomia will alter the composition of oral microbiota. Material and methods Nineteen xerostomia patients and 10 healthy normal volunteers were studied for the oral microbiota. Gingival plaques were collected and microbiota were detected using bacterial 16S ribosomal RNA and analyzed based on the levels of phylum and class. Results In all cases, phyla of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria make up to 100% of oral microbiota at phylum level. Analyzing individual phylum, presence of Bacteroidetes in xerostomia patients and normal subjects were 23.12 ± 2.56% and 23.23 ± 2.58%, respectively. Mean percentage presence of Firmicutes phylum in xerostomia patients and normal subjects were 18.94 ± 1.83% and 14.06 ± 0.98%, respectively. Statistically significant difference was not observed between xerostomia patients and normal subjects in this study. Conclusion These observations revealed obvious but not statistically significant changes in oral major microorganism phylum between xerostomia patients and normal subjects in this study. More samples are needed to verify the current results and to use oral microbiota as a tool in the diagnosis of xerostomia.

Penelope-like elements (PLEs) are an enigmatic clade of retroelements whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical EN+ PLEs encodes RT and a C-terminal GIY-YIG endonuclease (EN) that enables intrachromosomal integration, while EN–PLEs lack endonuclease and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, while EN–PLEs occur in several kingdoms. Here we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY-YIG endonuclease is linked to a C-terminal RT by a short domain with a characteristic Zn-finger-like motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune and Nematis clades, and show insertion bias for microsatellites, but lack hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiad clade is found in numerous invertebrate phyla, where they can reach tens of thousands of copies per genome. Naiads in spiders and clams independently evolved to encode selenoproteins. Chlamys, which lack the CCHH motif universal to PLE endonucleases, occur in green algae, spike mosses (targeting ribosomal DNA) and the slime mold Physarum. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain, strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, distribution and abundance is comparable to non-LTR and LTR-retrotransposons.

The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI "barcoding" primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata (Ctenophora; Tentaculata; Lobata). The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar undescribed lobates (Lampocteis sp. "V" stratified by depth, and "A" differentiated by colour). The newly designed primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyse environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.

The gram-negative Pseudomonas aeruginosa is an opportunistic human pathogen that contains two different types of strains: the "classical" and the "outlier". In the "classical" strain, its bacterial subfamily I.1 lipases, such as LipA and LipC in P. aeruginosa PAO1, play critical roles in its pathogenicity. However, less is known about the subfamily I.1 lipases in the "outlier" strain, nor the evolution paths of those lipases in both types of P. aeruginosa strains. Our genome-scale investigation on I.1 lipases across different bacterial strains demonstrates the presence of one LipA-like and one new type of I.1 lipase (LipC2) in those "outlier" strains. The related genomic islands analyses further suggest that the LipC counterpart gene in the "outlier" strain was lost by gene truncation. In addition, the evolutionary analyses also indicates the horizontal LipC2 gene transfer from other gammaproteobacterial species, as well as the horizontal LipA gene transfer between two different phyla, both suggesting that the gene transfer of bacterial I.1 lipases might occur in different taxonomical levels. Our results not only provide an evidence to understand the pathogenicity among different P. aeruginosa strains, but add to the knowledge of I.1 lipase evolution in bacteria.

Parasites are important components of biodiversity and contributors to ecosystem functioning, but are often neglected in ecological studies. Most studies examine model parasite systems or single taxa, thus our understanding of community composition is lacking. Here, the seasonal and annual dynamics of parasites was quantified using a 5-year metabarcoding time-series of freshwater plankton, collected weekly. We first identified parasites in the dataset using literature searches of the taxonomic match and using sequence metadata from the National Center for Biotechnology Information (NCBI) nucleotide database. In total, 441 amplicon sequence variants (belonging to 18 phyla/clades) were classified as parasites. The four phyla/clades with the highest relative read abundance and richness were Chytridiomycota, Dinoflagellata, Oomycota and Perkinsozoa. Relative read abundance of total parasite taxa, Dinoflagellata and Perkinsozoa significantly varied with season and was highest in summer. Parasite richness varied significantly with season and year, and was generally lowest in spring. Each season had distinct parasite communities, and the difference between summer and winter communities was most pronounced. Combining DNA metabarcoding with searches of the literature and NCBI metadata allowed us to characterize parasite diversity and community dynamics and revealed the extent to which parasites contribute to the diversity of freshwater plankton communities.

The Cambrian Explosion by nature is a three-phased explosion of animal body plans alongside episodic biomineralization, pulsed change of generic diversity, body size variation, and progressive increase of ecosystem complexity. The Cambrian was a time of crown groups nested by numbers of stem groups with a high-rank taxonomy of Linnaean system (classes and above). Some stem groups temporarily succeeded while others were ephemeral and underrepresented by few taxa. The high number of stem groups in the early history of animals is a major reason for morphological gaps across phyla that we see today. Most phylum-level clades achieved their maximal disparity (or morphological breadth) during the time interval close to their first appearance in the fossil record during the early Cambrian, whereas others, principally arthropods and chordates, exhibit a progressive exploration of morphospace in subsequent Phanerozoic. The overall envelope of metazoan morphospace occupation was already broad in the early Cambrian though it did not reach maximal disparity nor has diminished significantly as a consequence of extinction since the Cambrian. Intrinsic and extrinsic causes were extensively discussed but they are merely prerequisites for the Cambrian Explosion. Without the molecular evolution, there could be no Cambrian Explosion. However, the developmental system is alone insufficient to explain Cambrian Explosion. Time-equivalent environmental changes were often considered as extrinsic causes, but the time coincidence is also insufficient to establish causality. Like any other evolutionary event, it is the ecology that make the Cambrian Explosion possible though ecological processes failed to cause a burst of new body plans in the subsequent evolutionary radiations. The Cambrian Explosion is a polythetic event in natural history and manifested in many aspects. No simple, single cause can explain the entire phenomenon.

The work was aimed at detection of potential degraders of polyethylene terephthalate (PET), polystyrene (PS), and steel 20 based on comparison of the taxonomic composition of the biofilm communities formed on these materials immersed in aqueous environments of diverse origin (marine, natural freshwater, and industrial) in different climatic regions. The libraries obtained by high-throughput sequencing of the 16S rRNA gene V3–V4 region were mainly grouped according to the media types. The composition and relative abundance of the taxa (both at the phylum/class and the genus levels) differed significantly between the groups of libraries; within the groups, these parameters varied depending mainly on the incubation time and on antimicrobial treatment (for industrial samples), while the material of the samples had less effect. Our results indicated that industrial recirculated water was more aggressive against polymer materials, with potential degraders of the polymers (PET and PS) belonging to the genera Pseudomonas, Acidovorax, and Arenimonas. Iron- and sulfur-oxidizing bacteria of the genera Sulfurimonas and Mariprofundus are probably involved in steel biocorrosion in seawater.

Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing rate. The high number of species that have yet to be described have generated extreme crisis to the taxonomist. Therefore, more than in any other era, effective ways to discover and delimitate species are needed. This paper reviews the historically foremost approaches used to delimit species in Ascomycota, the most speciose phylum of Fungi. These include morphological, biological, and phylogenetic species concepts. We argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and disadvantages. Recently the rate of species discovery has increased because of the advancement of phylogenetic approaches. However, traditional phylogenetic methods with few gene regions lack species-level resolution, and do not allow unambiguous conclusions. We detail the processes that affect gene tree heterogeneity, which acts as barriers to delimiting species boundaries in classical low-rank phylogenies. So far, limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal species. In addition to reviewing concepts and methodologies used to delimit species, we present a case study. We applied different species delimitation methods to understand species boundaries in the plant pathogenic and cryptic genus Phyllosticta (Dothideomycetes, Botryosphaeriales). Several DNA-based methods over-split the taxa while in some methods several taxa fall into a single species. These problems can be resolved by using multiple loci and coalescence-based methods. Further, we discuss integrative approaches that are crucial for understanding species boundaries within Ascomycota and provide several examples for ideal and pragmatic approaches of species delimitation.

Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidiomycota, the second largest phylum of Fungi that contains some of the best known species of mushrooms, rusts, smuts, and jelly fungi. In general, best practice is to delimitate species, publish new taxa, and conduct taxonomic revisions based on as many independent lines of evidence as possible, that is, by applying a so-called unifying (or integrative) conceptual framework. However, the types of data used vary considerably from group to group. For this reason we discuss the different classes of Basidiomycota, and for each provide: (i) a general introduction with difficulties faced in species recognition, (ii) species concepts and methods for species delimitation, and (iii) community recommendations and conclusions.

The fossil record, including the record of Burgess Shale-type deposits, is biased towards late ontogenetic stages. Larval stages, juvenile and subadult specimens exist but are very rare and often preserved as phosphatic fossils, resulting in biased population structures. Here, we report a new Burgess Shale-type Lagerstatte from Haiyan, China. The Haiyan palaeocommunity is extraordinary in that it is rich in fossils of early and middle ontogenetic stages of various phyla, with eggs also commonly found in the studied interval. This Lagerstatte also hosts a considerable number of new taxa—many related to later biotas of Gondwana and Laurentia. We propose that the deposit may either preserve one of the earliest nurseries in the fossil record or, alternatively, records several attempted invasions. Our study highlights the complexity of biotas and their interactions in the lower Cambrian ocean and calls for a better understanding of the mechanisms responsible for the observed spatial variation of fossil community composition in the Cambrian. The authors report a new lower Cambrian Burgess Shale-type Lagerstatte from Haiyan, southwest China which preserves an unusually high number of juvenile and larval forms.

The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.

Fly ash dumps of thermal power stations have been increasing in area worldwide due to the growing demand for power. One of the cost-effective approaches for restoring such sites is spontaneous revegetation in those areas where adjacent indigenous ecosystems can supply seeds and living organisms. We assessed microbiome taxonomic diversity in a Technosol developed during nine years of spontaneous revegetation of the terminated fly ash pond of a thermal power station in Novosibirsk, Russia, in comparison with microbiome diversity in undisturbed Phaeozem under adjacent birch forest by using 16S (V3–V4) and ITS2 (ITS3–ITS4) amplicon sequencing with Illumina MiSeq. We identified 577 fungal and 5542 bacterial operational taxonomic units (OTUs); 95–99% of them were minor or rare species. The dominant OTUs were completely different in the studied soils. At the phylum level, the ultimate dominants were Ascomycota (84%) in the Technosol and Basidiomycota (89%) in the Phaeozem. Three phyla (Proteobacteria, Acidobacteria and Actinobacteria), together comprising more than a half of the bacteriobiome, prevailed in both soils; however, at the OTU level, soil-related differences were found for 31% of the OTUs. The Technosol bacteriobiome was less structured and more diverse compared to the mycobiome, displaying the same phylum-level structure and OTU-based α-biodiversity as in the adjacent mature soil. Our finding that few fungal and bacterial OTUs dominated in the soil microbiome, the majority being minor or rare members, implies that key ecosystem processes performed by soil microorganisms rely on a very limited taxonomic diversity, both in young and mature soils.

Zoosporic fungi play an important role in aquatic environments, but their diversity, especially that of parasitic fungi of phytoplankton, has still not been fully revealed. We conducted monthly analyses of the community structure of zoosporic fungi at a pelagic site in Lake Biwa, Japan, from May to December 2016. Metabarcoding analysis, targeted to a large subunit region of ribosomal DNA in the nano-size fraction of particles (2-20 µm), was carried out on the samples. We also counted large phytoplankton and chytrid sporangia attached to the hosts. We detected 3 zoosporic fungal phyla (Blastocladiomycota, Chytridiomycota and Cryptomycota) within 107 operational taxonomic units (OTUs), in which Chytridiomycota was the most diverse and abundant phylum. Few fungal OTUs overlapped between months, and specific communities were detected in each month. These results showed that diverse zoosporic fungi with high temporal variability inhabited the lake. Five large phytoplankton species were found to be infected by chytrids: Staurastrum dorsidentiferum, S. rotula, Closterium aciculare, Asterionella formosa and Aulacoseira granulata. Some chytrids were detected by metabarcoding analysis: Zygophlyctis asterionellae infecting A. formosa, Staurastromyces oculus infecting S. dorsidentiferum and Pendulichytrium sphaericum infecting A. granulata. One OTU detected in association with infected C. aciculare by microscopic counting might have been an obligate parasitic chytrid of C. aciculare. The results indicated that a combination of metabarcoding and microscopic analysis revealed more information on zoosporic fungi, including those that are parasitic.

The first results of a study into the microbiomes of benthic invertebrates found in sites with seeps (containing methane, oil, or a combination of methane and mud) and an underwater low-temperature vent of Lake Baikal are presented. Microorganisms were detected in the intestine of an oligochaete from the cold methane seep using microscopy. Analysis of 16S rRNA gene libraries revealed that the highest diversity of microorganisms was found in the nematode microbiomes where the members of 11 phyla were identified. Some of the detected prokaryotes are methanogens, nitrifiers, and nitrogen fixators, while some are involved in the sulfur cycle. Methanotrophs were detected in the microbiomes of oligochaetes and chironomids. The microbiomes of nematodes, chironomids, and bathynellids are composed of members of the Bacteroidetes and Firmicutes phyla, which are related to the symbiotic bacteria found in insects and animals from other ecotopes. Microorganisms typically found in the water and sediments of Lake Baikal were also detected in the invertebrates microbiomes.

An overwhelming majority of bacterial life remains uncharacterized. Recent efforts to assemble genomes from metagenomes have provided invaluable insights into these yet-uncultured bacterial lineages. We report on the characterization of 30 genomes belonging to three novel classes within the phylum Desulfobacterota. One class (proposed name Candidatus “Anaeroferrophillalia”) was characterized by the capacity for heterotrophic growth, either fermentatively or utilizing polysulfide, tetrathionate and thiosulfate as electron acceptors. Autotrophic growth using the Wood Ljungdahl pathway and hydrogen or Fe(II) as an electron donor could also occur in absence of organic carbon sources. The second class (proposed name Candidatus “Anaeropigmentia”) was characterized by its capacity for fermentative or aerobic growth at low oxygen thresholds using a broad range of sugars and amino acids, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoids (lycopene) production, as well as the occurrence of the majority of genes involved in bacteriochlorophyll a biosynthesis. The third class (proposed name Candidatus “Zymogenia”) was characterized by the capacity for heterotrophic growth fermentatively using broad sugars and amino acids as carbon sources, and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial (e.g. hydrocarbon contaminated environments, wetlands, bioreactors), freshwater (e.g. ground water and gas-saturated temperate lakes), and marine (e.g. hydrothermal vents, marine sediments, and coastal sediments) environments, over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus “Zymogenia” to hypersaline environments, e.g. hypersaline microbial mats and lagoons was observed.ImportanceCulture-independent diversity surveys conducted in the last three decades have clearly demonstrated that the scope of microbial diversity is much broader than that inferred from isolation efforts. Multiple reasons have been put forth to explain the refractiveness of a wide range of the earth’s microbiome to isolation efforts. Documenting the scope of high-rank phylogenetic diversity on earth, as well as deciphering and documenting the metabolic capacities, physiological preferences, and putative ecological roles of these yet-uncultured lineages represents one of the central goals in current microbial ecology research. Recent efforts to assemble genomes from metagenomes have provided invaluable insights into these yet-uncultured lineages. This study expands our knowledge of the phylum Desulfobacterota through the characterization of 30 genomes belonging to three novel classes. The analyzed genomes were either recovered from Zodletone Spring in southwestern Oklahoma in this study, or recently binned from public metagenomes as part of the Global Earth Microbiome initiative. Our results expand the high-rank diversity within the bacterial tree of life by describing three novel classes within the phylum Desulfobacterota, document the utilization of multiple metabolic processes, e.g. iron-oxidation, aromatic hydrocarbon degradation, reduction of sulfur-cycling intermediates, and features, e.g. coenzyme M biosynthesis, and pigmentation, as salient characteristics in these novel Desulfobacterota classes.

Strain RF1110005T, which was isolated from brackish lake water sampled at Lake Sanaru in Japan as a “filterable” bacterial strain, was characterized as a novel species in the genus Fluviispira, family Silvanigrellaceae, order Silvanigrellales, the class Oligoflexia and the phylum Bdellovibrionota. Cells of RF1110005T were aerobic, Gram stain negative, and show a pleomorphic morphology of spiral, filamentous and rod shapes. Catalase reaction was positive. Strain RF1110005T grew optimally at 30 °C, pH 7.0–8.0 and 0.5% NaCl (w/v). The major polar lipids in RF1110005T were phosphatidylethanolamine and phosphatidylglycerol. The predominant cellular fatty acids were iso-C15:0 and anteiso-C15:0. Phylogenetic analysis based on 16S rRNA gene sequences and concatenates of core gene sequence showed that the nearest neighbor of strain RF1110005T was Fluviispira multicolorata strain 33A1-SZDPT with 98.4% 16S rRNA gene sequence similarity. The genome size of strain RF1110005T was 3.5 Mbp with two plasmids (80 kb and 69 kb), and the G + C content was 33.7 mol%. Comparisons with genome-wide analyses and chemotaxonomic characters clearly showed that strain RF1110005T differed from F. multicolorata. Therefore, a novel species in Fluviispira sanaruensis, sp. nov., is proposed for strain RF1110005T (= JCM 31447 T = LMG 30360 T).

Fungi produce a wide variety of volatile organic compounds (VOCs), which play central roles in the initiation and regulation of fungal interactions. Here we introduce a global overview of fungal VOC patterns and chemical diversity across phylogenetic clades and trophic modes. The analysis is based on measurements of comprehensive VOC profiles of forty-three fungal species. Our data show that the VOC patterns can describe the phyla and the trophic mode of fungi. We show different levels of phenotypic integration (PI) for different chemical classes of VOCs within distinct functional guilds. Further computational analyses reveal that distinct VOC patterns can predict trophic modes, (non)symbiotic lifestyle, substrate-use and host-type of fungi. Thus, depending on trophic mode, either individual VOCs or more complex VOC patterns (i.e., chemical communication displays) may be ecologically important. Present results stress the ecological importance of VOCs and serve as prerequisite for more comprehensive VOCs-involving ecological studies., Guo et al. characterize the volatilomes of 43 fungal species using an automated cuvette system and mass spectrometry. Their results show that VOC patterns can predict trophic modes, symbiotic lifestyle, substrate-use and host-type of fungi.

Coral reefs are cornerstone of global marine ecosystems, providing shelter for over one third of marine organisms. Currently, along with global warming and increased human activities, large-scale decline of coral reefs has become a severe ecosystem problem, and now quantitative detection of heat shock protein (HSP) gene by nanotechnology has become a research hotspot in this field. However, Acropora muricata is one of the most important dominant reef-building corals in Indo- Pacific region, encounter an urgent obstacle on the HSP detection research by nanoscience and nanotechnology for lack of sequence background. Here, we combined PacBio single molecular real-time (SMRT) and HiSeq X Ten sequencing technologies to perform full-length transcriptome sequencing of heat shock proteins in Acropora muricata, a reef-building coral dominant in many Indo-Pacific reefs, to annotate them. Thirteen functional heat shock proteins (HSPs) were identified using phylogenetic analysis, classified into three subgroups as HSP60, HSP70 and HSP90. HSPs are widely distributed in all animal phyla, having evolved from the last prokaryotic common ancestor. Additionally, phylogenetic and tertiary nanostructure analyses suggested that HSP70 is the most diverse HSP in A. muricata, with extensive sequence and structure differences indicating adaptations to warming water and suggesting its utility in studies of El Niño and other warming events. A greater understanding of the HSP gene family is likely to also be of value in studies of coral nanotechnological detection that can be used to protect reef ecosystems.

Gap analysis of the available genomic data (i.e. identifying taxonomic groups with no representative genome assemblies) is a fundamental first step to design effective sampling strategies for whole genome sequencing (WGS) initiatives. We identified the significant holes that remain in genomic resources of the Ascomycota – the largest fungal phylum including many species of medicinal, ecological and/or economic significance – in order to prioritise WGS efforts towards reconstructing the Ascomycota tree of life. In doing so, we additionally looked at the existing genome size data for ascomycetes, given the importance of knowing the size of the genome to ensure sufficient sequencing coverage and assess the completeness and quality of genome assemblies. We found that 50 % of the ascomycete orders have no representative genome assembly and over 75 % have no reliably measured genome size data. We propose that integrating routine cytometric genome size measurements into WGS and genome assembly pipelines will provide both a valuable assembly quality metric and contribute data for addressing fundamental evolutionary questions.

Polypodium hydriforme is an enigmatic parasite that belongs to the phylum Cnidaria. Its taxonomic position has been debated: whereas it was previously suggested to be part of Medusozoa, recent phylogenomic analyses based on nuclear genes support the view that P. hydriforme and Myxozoa form a clade called Endocnidozoa. Medusozoans have linear mitochondrial (mt) chromosomes, whereas myxozoans, as most metazoan species, have circular chromosomes. In this work, we determined the structure of the mt genome of P. hydriforme, using Illumina and Oxford Nanopore Technologies reads, and showed that it is circular. This suggests that P. hydriforme is not nested within Medusozoa, as this would entail linearization followed by recirculation. Instead, our results support the view that P. hydriforme is a sister clade to Myxozoa, and mt linearization in the lineage leading to medusozoans occurred after the divergence of Myxozoa + P. hydriforme. Detailed analyses of the assembled P. hydriforme mt genome show that: (1) it is encoded on a single circular chromosome with an estimated size of ∼93,000 base pairs, making it one of the largest metazoan mt genomes; (2) around 78% of the genome encompasses a noncoding region composed of several repeat types; (3) similar to Myxozoa, no mt tRNAs were identified; (4) the codon TGA is a stop codon and does not encode for tryptophan as in other cnidarians; (5) similar to myxozoan mt genomes, it is extremely fast evolving.

Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

Phylogenomic tree reconstruction has recently become a routine and critical task to elucidate the evolutionary relationships among bacterial species. The most widely used method utilizes the concatenated core genes, universally present in a single-copy throughout the bacterial domain. In our previous study, a bioinformatics pipeline termed Up-to-date Bacterial Core Genes (UBCG) was developed with a set of bacterial core genes selected from 1,429 species covering 28 phyla. In this study, we revised a new bacterial core gene set, named UBCG2, that was selected from the more extensive genome sequence set belonging to 3,508 species spanning 43 phyla. UBCG2 comprises 81 genes with nine Clusters of Orthologous Groups of proteins (COGs) functional categories. The new gene set and complete pipeline are available at http://leb.snu.ac.kr/ubcg2 .

Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutakedominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.

Biofilm formation and microbial adhesion are two related and complex phenomena. These phenomena are known to play an important role in microbial life and various functions with positive and negative aspects. Actinobacteria have wide distribution in aquatic and terrestrial ecosystems. This phylum is very large and diverse and contains two important genera Streptomyces and Mycobacteria. The genus Streptomyces is the most biotechnologically important, while the genus Mycobacteria contains the pathogenic species of Mycobacteriaceae. According to the literature, the majority of studies carried out on actinomycetes are focused on the detection of new molecules. Despite the well-known diversity and metabolic activities, less attention has been paid to this phylum. Research on adhesion and biofilm formation is not well developed. In the present review, an attempt has been made to review the literature available on the different aspects on biofilm formation and adhesion of Actinobacteria. We focus especially on the genus Streptomyces. Furthermore, a brief overview about the molecules and structures involved in the adhesion phenomenon in the most relevant genus is summarized. We mention the mechanisms of quorum sensing and quorum quenching because of their direct association with biofilm formation.

Alterations in the gut immune axis under hypobaric hypoxia (HH) exposure may be a consequence of microbial dysbiosis. The mechanism of induction of gut inflammation by alterations in gut bacterial and viral populations has not been discovered meticulously. Here we used whole-genome and 16S rRNA sequencing to characterize the taxonomic and functional shifts in the faecal microbiome after HH exposure. Ten faecal samples from unexposed and HH exposed (3 days, 7 days and 14 days) Sprague–Dawley rats were analyzed. 16S rRNA sequencing was conducted on Illumina MiSeq platform using universal primers and analysed using QIIME (Greengenes database). WGS sequencing was done on Illumina HiSEQ 2500 platform and analysed using MOCAT2 (eggNOG database). HH exhibited an overarching effect on taxonomic and functional gene composition. A significant change in α-diversity at phylum level and β-diversity at phylum and genus level were observed between control and HH exposed groups. Significant (p

The rapid spread of multi-drug resistant microbes has lead researchers to discover natural alternative remedies such as antimicrobial peptides (AMPs). In the first line of defense, AMPs display a broad spectrum of potent activity against multi-resistant pathogenic bacteria, viruses, fungi, and even cancer. AMPs can be further characterised into families according to amino acid composition, secondary structure, and function. However, despite recent advancements in rapid computational methods for AMP prediction from various mammalian, aquatic, and terrestrial species, there is limited information regarding their presence, functional roles, and family type from marine macroalgae. In this paper, we present a promising two-tier ensemble of heterogeneous machine learning models that integrates seven well-known machine learning classifiers to predict AMPs from macroalgae. The first tier of the ensemble consists of a suite of binary classifiers that identify AMPs from protein sequence data which are then forwarded to a second-tier multi-class ensemble to characterise their functional family type. The two-tier ensemble was successfully used to identify 39 putative AMP sequences in 12 macroalgae species from three different phyla groups. The approach we describe is not limited to AMPs and can also be applied to search sequence data for other types of proteins.

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, “subdivision 23”) and Ca. Polarisedimenticola (“subdivision 22”), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

Objective: Microorganisms play an important role in all ecosystem processes and a growing body of molecular and ecological evidence has shown that microbial biodiversity is much more diverse and complex than previously anticipated. This study aimed to determine the prokaryotic microorganisms present in Gokceada Salt Lake Lagoon. Materials and Methods: A metabarcoding approach was used to determine the microbial diversity in Gokceada Salt Lake Lagoon. Results: 16S rDNA targeted sequencing revealed 5 Archaea and 31 Bacteria species and Archaea represented 63.2%. The most frequent Archaea genus was Halorubrum, which belongs to the Euryarchaeota phylum, and the dominant species of Bacteria was Halomonas sulfidaeris (Proteobacteria phylum). Conclusion: This work will contribute to our understanding of the microbial community structure and composition in coastal lagoons. Hovewer, further surveys will improve our knowledge on microbiota in Gokceada Salt Lake Lagoon.

A total of 137 strains of mesophilic and psychrotolerant hydrocarbon-oxidizing bacteria have been isolated from three regions of the Sea of Japan exposed to different levels of anthropogenic pollution. The taxonomic affiliations of the culturable bacteria from surface waters and bottom sediments that are involved in the biodegradation of petroleum hydrocarbons in these regions have been identified. The isolated microorganisms belong to the phyla Actinobacteria, Firmicutes, and Proteobacteria. The hydrocarbon-oxidizing ability of the bacteria Okibacterium sp., Lechevalieria flava, Patulibacter sp., P. minatonensis, Gracilibacillus massiliensis, Thalassobacillus sp., Virgibacillus dokdonensis, Chryseomicrobium amylolyticum, Jeotgalibacillus marinus, Moraxella osloensis, Idiomarina maritima, and I. piscisalsi has been recorded for the first time. The results we obtained extend our knowledge about the potential of biodegradation of pollutants by members of certain taxa in the marine environment.

Lolium perenne L. and Sorghum sudanense (Piper) Stapf. are 2 common forages fed to blue sheep (Pseudois nayaur Hodgson, 1833) in captivity. However, the effect of these 2 forages on the gastrointestinal microbiota is largely unknown. We analyzed the diversity of the microbiota in the feces of captive blue sheep fed with L. perenne (group F1) and S. sudanense (group F2) by 16S rRNA sequencing. A total of 20 major phyla and 29 genera fecal bacterial communities were detected in the 2 groups. The F1 and F2 groups shared common microbiota at the phylum level, which mainly consisted of Firmicutes and Bacteroidetes. Ruminococcaceae_UCG-005, Eubacterium_coprostanoligenes_group, Ruminococcaceae_UCG-013, and Ruminococcaceae_UCG-010 were the top 4 dominant taxa at the genus level. The percentage of Ruminococcaceae_UCG-010 was significantly higher in the F2 group (∼2.75-fold) than in F1 group. The diversity and abundance of the microbial community in F2 was higher than that in F1. Although both of L. perenne and S. sudanense affect the metabolism of the gastrointestinal microbiota of blue sheep, the S. sudanense improves more aspects of metabolism and biogenesis. In summary, our results demonstrated that L. perenne and S. sudanense affect blue sheep gastrointestinal microbiota in different ways. But S. sudanense efficiently improved the gastrointestinal microbiota of blue sheep.

Host manipulation has already been documented in several distinct host–parasite associations, covering all major phyla of living organisms. While in animals we know that several species have the ability to manipulate their hosts for the benefit of the parasite, in arthropopathogenic fungi there is very little knowledge about possible behavioral manipulation. We report for the first time the interaction between the araneopathogenic fungus genus Gibellula Cavara and the spider Macrophyes pacoti Brescovit, Oliveira, Sobczak and Sobczak, 2019 (Anyphaenidae) in addition to investigating the potential change in behavior of spiders infected by the parasitic fungus. We also investigated whether the rainfall regime influences the abundance of infected spiders and the parasitism rate by the araneopathogenic fungus. Our results corroborated our hypothesis that the fungus induces vertical segregation in the spider population, inducing infected spiders to be at higher heights than uninfected ones. Dead infected spiders were found in a stretched position that probably helps in fixing the carcass on the leaves by increasing the contact surface between the host and the substrate. Our results also confirm the positive relationship between the rainy season and the greater number of parasitized spiders and the parasitism rate.

High-throughput sequencing of 16S rRNA genes was used to investigate the taxonomic diversity of the bacterial community inhabiting the fruiting bodies of the myxomycete Lycogala еpidendrum. Members of 31 bacterial genera belonging to six phyla were revealed. The phylum Proteobacteria predominated in the microbiome, with Pseudomonas and Luteibacter as predominant genera. Analysis of the taxonomic diversity of bacterial communities revealed significantly lower diversity in the L. epidendrum community, compared to those of brushwood and litter adjacent to the fruiting bodies. This is an indication of a selective role of the myxomycete fruiting body in respect to the phylum Proteobacteria and especially to the genera Pseudomonas and Luteibacter.