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Made available in DSpace on 2021-06-25T15:06:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-05 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Prokaryotes contribute to the health of marine sponges. However, there is lack of data on the assembly rules of sponge-associated prokaryotic communities, especially for those inhabiting biodiversity hotspots, such as ecoregions between tropical and warm temperate southwestern Atlantic waters. The sympatric species Aplysina caissara, Axinella corrugata, and Dragmacidon reticulatum were collected along with environmental samples from the north coast of SAo Paulo (Brazil). Overall, 64 prokaryotic phyla were detected; 51 were associated with sponge species, and the dominant were Proteobacteria, Bacteria (unclassified), Cyanobacteria, Crenarchaeota, and Chloroflexi. Around 64% and 89% of the unclassified operational taxonomical units (OTUs) associated with Brazilian sponge species showed a sequence similarity below 97%, with sequences in the Silva and NCBI Type Strain databases, respectively, indicating the presence of a large number of unidentified taxa. The prokaryotic communities were species-specific, ranging 56%-80% of the OTUs and distinct from the environmental samples. Fifty-four lineages were responsible for the differences detected among the categories. Functional prediction demonstrated that Ap. caissara was enriched for energy metabolism and biosynthesis of secondary metabolites, whereas D. reticulatum was enhanced for metabolism of terpenoids and polyketides, as well as xenobiotics' biodegradation and metabolism. This survey revealed a high level of novelty associated with Brazilian sponge species and that distinct members responsible from the differences among Brazilian sponge species could be correlated to the predicted functions. Sao Paulo State Univ, Inst Biosci, Coastal Campus Sao Vicente, Sao Paulo, Brazil Univ Estado Rio De Janeiro, Biol Inst Roberto Alcantara Gomes, Dept Genet, Rio De Janeiro, Brazil Univ Sao Paulo, Biosci Inst & NP Biomar, Dept Physiol, Ctr Marine Biol, Sao Paulo, Brazil Sao Paulo State Univ, Inst Biosci, Coastal Campus Sao Vicente, Sao Paulo, Brazil FAPESP: 2016/17189-7 FAPESP: 2017/10157-5 FAPESP: 2018/12937-0 FAPESP: 2017/11380-0

Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes1–5. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)6–8. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that—to our knowledge—have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead—depending on the choice of species and conserved genes used to build the phylogeny—supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota–Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal ‘eukaryome’ in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer. Comparative analysis of 162 genomes of Asgard archaea results in six newly proposed phyla, including a deep branch that is provisionally named Wukongarchaeota, and sheds light on the evolutionary history of this clade.

Targeted ‘omics’ research for seaweeds, utilizing various computational and informatics frameworks, has the potential to rapidly develop our understanding of biological processes at the molecular level and contribute to solutions for the most pressing environmental and social issues of our time. Here, a systematic review into the current status of seaweed omics research was undertaken to evaluate the biological diversity of seaweed species investigated (red, green and brown phyla), the levels to which the work was undertaken (from full genome to transcripts, proteins or metabolites) and the field of research to which it has contributed. We report that from 1994 to 2021 the majority of seaweed omics research has been performed on the red seaweeds (45% of total studies), with more than half of these studies based upon two genera Pyropia and Gracilaria. A smaller number of studies examined brown seaweed (key genera Saccharina and Sargassum) and green seaweed (primarily Ulva). Overall, seaweed omics research is most highly associated with the field of evolution (46% of total studies), followed by the fields of ecology, natural products and their biosynthesis, omics methodology and seaweed–microbe interactions. Synthesis and specific outcomes derived from omics studies in the red seaweeds are provided. Together, these studies have provided a broad-scale interrogation of seaweeds, facilitating our ability to answer fundamental queries and develop applied outcomes. Crucial to the next steps will be establishing analytical tools and databases that can be more broadly utilized by practitioners and researchers across the globe because of their shared interest in the key seaweed genera.

From a morphological point of view, placozoans are among the most simple free-living animals. This enigmatic phylum is critical for our understanding of the evolution of animals and their cell types. Their millimeter-sized, disc-like bodies consist of only three cell layers that are shaped by roughly seven major cell types. Placozoans lack muscle cells and neurons but are able to move using their ciliated lower surface and take up food in a highly coordinated manner. Intriguingly, the genome of Trichoplax adhaerens, the founding member of the enigmatic phylum, has disclosed a surprising level of genetic complexity. Moreover, recent molecular and functional investigations have uncovered a much larger, so-far hidden cell-type diversity. Here, we have extended the microanatomical characterization of a recently described placozoan species—Hoilungia hongkongensis. In H. hongkongensis, we recognized the established canonical three-layered placozoan body plan but also came across several morphologically distinct and potentially novel cell types, among them novel gland cells and “shiny spheres”-bearing cells at the upper epithelium. Thus, the diversity of cell types in placozoans is indeed higher than anticipated.

Years of intense research have shown that the assembly of peptidoglycan, the extracellular mesh-like polymer surrounding the bacterial cell, is incredibly complex. It requires a suite of reactions catalyzed by dynamic macromolecular protein complexes whose localization and activity should be finely regulated in space and time. In this review, we focus on the main developments reported over the last five years for the assembly of peptidoglycan in Firmicutes, a bacterial phylum that comprises monoderm bacteria and that encompasses well studied bacterial models with different cell shapes and lifestyles.

The Amoebozoa, a group containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics/transcriptomics to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (64) and human pathogen genera (51) associated with the Amoebozoa. Using single cell genomics/transcriptomics we were able to determine up to 24 potential endosymbiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multi-drug resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.

The virosphere is fascinatingly vast and diverse, but as mandatory intracellular parasites, viral particles must reach the intracellular space to guarantee their species' permanence on the planet. While most known viruses that infect animals explore the endocytic pathway to enter the host cell, a diverse group of ancient viruses that make up the phylum Nucleocytoviricota appear to have evolved to explore new access' routes to the cell's cytoplasm. Giant viruses of amoeba take advantage of the phagocytosis process that these organisms exploit a lot, while phycodnavirus must actively break through a algal cellulose cell wall. The mechanisms of entry into the cell and the viruses themselves are diverse, varying in the steps of adhesion, entry, and uncoating. These are clues left by evolution about how these organisms shaped and were shaped by convoluting with eukaryotes.

Background Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria. Results Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal pathogens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria. Conclusions Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.

Pathogenic bacteria and antibiotic resistance genes (ARGs) in urban landscape waters may pose a potential threat to human health. However, the investigation of their occurrence in the urban landscape waters replenished by reclaimed water (RW) and surface water (SW) is still insufficient. The water samples collected from six urban landscape waters replenished by RW or SW were used to analyze bacterial diversity using high-throughput sequencing of 16S rRNA gene and to detect 18 ARGs and 2 integron-integrase genes by means of quantitative PCR array. Results indicated that Proteobacteria was the dominant phylum in all six urban landscape waters. The bacterial species richness was lower in urban landscape waters replenished by RW than that by SW. Sulfonamide resistance genes (sulI and sulIII) were the major ARGs in these urban landscape waters. No significant difference in the relative abundance of sulfonamide resistance genes, tetracycline resistance genes, and most of beta-lactam resistance genes was observed between RW-replenished and SW-replenished urban landscape waters. By contrast, the relative abundance of blaampC gene and qnrA gene in RW-replenished urban landscape waters was significantly higher than that in SW-replenished urban landscape waters (p < 0.05), which suggested that use of RW may increase the amount of specific ARGs to urban landscape waters. Interestingly, among six urban landscape waters, RW-replenished urban landscape waters had a relatively rich variety of ARGs (12-15 of 18 ARGs) but a low relative abundance of ARGs (458.90-1944.67 copies/16S × 106). The RW replenishment was found to have a certain impact on the bacterial diversity and prevalence of ARGs in urban landscape waters, which provide new insight into the effect of RW replenishment on urban landscape waters.

A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100–200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C8–C17 alkanes and up to 28% degradation of C18–C33 alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.

Candidatus phylum Eremiobacterota (formerly WPS-2) is an as-yet-uncultured bacterial clade that takes its name from Ca. Eremiobacter, an Antarctic soil aerobe proposed to be capable of a novel form of chemolithoautotrophy termed atmospheric chemosynthesis, that uses the energy derived from atmospheric H(2)-oxidation to fix CO(2) through the Calvin-Benson-Bassham (CBB) cycle via type 1E RuBisCO. To elucidate the phylogenetic affiliation and metabolic capacities of Ca. Eremiobacterota, we analysed 63 public metagenome-assembled genomes (MAGs) and nine new MAGs generated from Antarctic soil metagenomes. These MAGs represent both recognized classes within Ca. Eremiobacterota, namely Ca. Eremiobacteria and UBP9. Ca. Eremiobacteria are inferred to be facultatively acidophilic with a preference for peptides and amino acids as nutrient sources. Epifluorescence microscopy revealed Ca. Eremiobacteria cells from Antarctica desert soil to be coccoid in shape. Two orders are recognized within class Ca. Eremiobacteria: Ca. Eremiobacterales and Ca. Baltobacterales. The latter are metabolically versatile, with individual members having genes required for trace gas driven autotrophy, anoxygenic photosynthesis, CO oxidation, and anaerobic respiration. UBP9, here renamed Ca. Xenobia class. nov., are inferred to be obligate heterotrophs with acidophilic adaptations, but individual members having highly divergent metabolic capacities compared to Ca. Eremiobacteria, especially with regard to respiration and central carbon metabolism. We conclude Ca. Eremiobacterota to be an ecologically versatile phylum with the potential to thrive under an array of “extreme” environmental conditions.

The quality and safety of the aquatic products have gradually become the focus of global attention. In this study, the environmental eukaryotic and fungi communities in pond-cultured grass carp (Ctenopharyngodon idellus) and the koi carp (Cyprinus carpio L.) were investigated. For comparative analysis, the alpha diversity shows that the environmental microbial abundance in the koi carp groups were higher than that in the grass carp groups, while beta diversity reveals that the differences of the microbial community composition and structures in the grass carp groups were significantly higher than those in the koi carp groups. Meanwhile, the environmental microbial diversity of grass carp groups was higher than that of koi carp groups at phylum level, but showed no significant difference at genus level. Additionally, the dominant total phyla were Opisthokonta, Stramenopiles plusAlveolates plusRhizaria, Archaeplastida, Cryptophyceae, and Centrohelida for the 18S rRNA gene and Ciliophora, Chlorophyta, and Ascomycota for the ITS2 rRNA gene in both of the two carp groups. Additionally, annotation analysis showed that the biomarkers in the grass carp groups are significantly higher than those of the koi carp groups. Furthermore, the functional prediction of Funguild showed significant difference in outputs, while similarity in trophic modes and guild types between the two carp groups. Meanwhile, the total relative abundances of animal pathogen, fungal parasite, and plant pathogen were extremely similar between the two carp groups. Surprisingly, one pathogenic fungus of genus Fusarium was identified in both the environments of two carp groups based on filtered operational taxonomic unit tables. Overall, this is the first robust report to understand the characteristics of environmental eukaryotic microorganisms and fungi in the edible and ornamental carps. Our results also provide the basic data for the prevention of fungal diseases and the healthy culture of the carps.

Abuse of antibiotics in aquaculture have been alarming and might aggravate spread of resistance genes in the environment. Holistic ARGs proliferation checks require deeper analyses of coupled absolute abundances in 16S rRNA bacteria communities at the phylum level to detect biomarkers. Sulfanilamide (sul) and copper II sulfate (CuSO4 II) were, therefore, designed and added as separate or combined treatments in 9 replicate engineered goldfish tanks comprising 3 individual sul, 3 CuSO4 II, 3 (sul + CuSO4 II) combinations, and 3 controls within 180 days. The DNA from water and fish guts was sequenced under qPCR to determine 16S rRNA bacteria biomarkers co-occurring with the correspondent ARGs. Combined chemical addition at 0.8–1.5 mg sul + 0.5–1.0 mg CuSO4 II/3 L of tank waters reduced sequenced 16S rRNA bacteria absolute abundances in fish gut and water samples while portraying the biomarkers. Absolute abundances of the entire 16S rRNA bacteria was higher in fish guts (3.4 × 1014–4.9 × 108 copies/g) than water samples (1.5 × 109–2.6 × 1015 copies/L), respectively. Much as sul 1(log) were dominant over intl 1(log) genes, and their fundamental profiles were also higher in the fish guts than water samples; the Spearman’s correlation analyses revealed positive relationship (p Proteobacteria (10–50:15–65%) > Planktomycetes (10–52:8–25%) featured prominently based on LEfSe use as the hot-spotted biomarkers, hence justifying its higher prospects towards innovative environmental microbiological and biotechnological studies.

The genus Rickettsia belongs to the Proteobacteria phylum and these bacteria infect animals and humans causing a range of diseases worldwide. The genus is divided into 4 groups and despite the publ...

A new way to “see” color Color perception is an important aspect of the way many organisms navigate their world. The ability to perceive color has thus far thought to depend on the presence of either eyes or minimally receptive cells containing opsin receptor genes. Ghosh et al. show that foraging Caenorhabditis elegans roundworms, which do not have eyes or opsins, can distinguish a blue color indicative of a toxin released by bacterial mats (see the Perspective by Neal and Vosshall). They suggest that the worms do this through the detection of the ratio between blue and amber light, a process dependent on at least two cellular stress-response genes. Different strains of C. elegans responded to different ratios, suggesting that this pathway plays an ecological role. Science , this issue p. 1059 ; see also p. 995

Background Within tropical shallow-water coral reefs, marine sponges provide microhabitats for a wide range of fauna. Although there have been numerous studies and reports of symbiotic relationships amongst sponges and their associated fauna, those pieces of information are isolated and disconnected. For this reason, based on the available literature, we compiled a species-interaction dataset of coral reef marine sponge-associated fauna known to date. New information We introduce a dataset that includes 67 literature items that report 101 species of sponge hosts clustered in 12 Orders having a host/guest interaction with 284 guest species from six Phyla present in the Northwestern Tropical Atlantic coral reefs. This dataset consists of two types of information: 1. Machine-readable data and 2. Human-readable data. These two types of coding improve the scope of the dataset and facilitate the link between machine platforms and human-friendly displays. We also created an interactive visualisation of the species-interactions dataset and of a dynamic Chord Diagram of the host-guest species connections to generate a user-friendly link between the user and the dataset.

Analysis of milk micrbiomes from healthy cows and cows with different (clinical and subclinical) forms of mastitis was performed at two farms of the Central Russia. An increase in the operational taxonomic units (OTUs) of bacteria of the phylum Proteоbacteria belonging primarily to Pseudomonadales, Burkholderiales, as well as Streptococcaceae, Staphylococcaceae, and Bacillaceae in the animals with mastitis was detected. The Planococcaceae OTU percentage decreased. The ratio of rarely presented OTUs also changed in the milk of animals with mastitis.

Sponges accommodate a diverse group of microorganisms with varied metabolic capabilities. The bacterial associates of sponges are widely studied while our understanding of archaeal counterparts is scanty. In the present study, we report the archaeal associates of two sponges, Pseudoceratina purpurea (NCBI barcode: KX454492) and Cinachyra sp. (NCBI barcode: KX454495), found in the coral reef ecosystems of Gulf of Mannar, India. Archaea in the water column was predominated by members of class Halobacteria of Phylum Euryarchaeota (97%) followed by a minor fraction (3%) of Nitrosopumilus sp. of phylum Thaumarchaeota. Interestingly, Thaumarchaeota was identified as the sole archaeal population associated with the two sponges studied, among which Nitrosopumilus sp. occuppied 80 and 100% of the sequences in the clone library of P. purpurea and Cinachyra sp. respectively. Other archaea found in the P. purpurea were Nitrososphaera (10%) and unclassified ones (10%). The study identified Nitrosopumilus sp. as a unique symbiotic archaeon of sponges, P. purpurea and Cinachyra sp. The existence of host driven factors in selecting specific associates from a diverse group of archaea in the environment may need further investigations.

Studies on marine fungi (termed as ‘marine-derived fungi’ in this paper) have been significantly increasing worldwide because of the critical role displayed by marine fungi in the marine ecosystem and their potential as sources of bioactive compounds. Korea is surrounded by three seas containing abundant marine resources. In this review, to facilitate research and applications of marine fungi, we summarized previously studied marine fungi in Korea focusing on published research articles in peer-reviewed journals over the last two decades. Approximately 79% of the studies (66 articles) were published in the 2010s and described a total of 818 strains (isolates) of 266 species belonging to 3 phyla, 8 classes, 21 orders, 43 families, and 76 genera. The most prevalent fungi belong to the genera Penicillium/Eupenicillium/Talaromyces, accounting for 40.2% of all species (107 species), followed by Aspergillus/Eurotium/Neosartorya (13.9%, 37 strains). Approximately 67% of fungal strains were originated from the eastern (44.6%, 365 strains) and western coasts (22.1%, 181 strains), and their main isolation sources were coastal plants/halophytes, marine animals, sediment, and marine algae. More than 35% of the strains (292 strains) produced novel and/or bioactive compounds with enzymatic, antimicrobial, antioxidant, anti-cancer, anti-inflammatory, anti-diabetic, or multi-functional activities. This review provides insights into current knowledge and future perspectives regarding marine-derived fungi in Korea.

Describing diet-related effects on the gut microbiome is essential for understanding its interactions with fat and/or sugar-rich diets to promote obesity-related metabolic diseases. Here, we sequenced the V3-V4 hypervariable region of the bacterial 16S rRNA gene to study the composition and dynamics of the gut microbiome of adult mice fed diets rich in fat and/or sugar, at 9 and 18 weeks of diet. Under high-fat, high-sugar diet, the abundances of Tuzzerella and Anaerovorax were transiently increased at 9 weeks, while Lactobacillus remained elevated at 9 and 18 weeks. The same diet decreased the abundances of Akkermansia, Paludicola, Eisenbergiella, and Butyricicoccus at 9 and 18 weeks, while Intestinimonas and UCG-009 of the Butyricicoccaceae family responded only at 18 weeks. The high-fat diet decreased the abundances of UBA1819 at 9 weeks, and Gastranaerophilales, Clostridia UCG-014, and ASF356 at 9 and 18 weeks. Those of Marvinbryantia, Harryflintia, Alistipes, Blautia, Lachnospiraceae A2, Eubacterium coprostanoligenes group, and Eubacterium brachy group were lowered only at 18 weeks. Interestingly, these genera were not sensitive to the high-sugar diet. The mouse gut microbiome was differentially affected by diets rich in fat or fat and sugar. The differences observed at 9 and 18 weeks indicate a progressive microbiome response.

The ongoing biotechnological revolution is rooted in our knowledge of enzymes. However, metagenomics is showing how little we know about Earth's enzyme repertoire. Deep sequencing has revolutionized our view of the tree of life. The genomes of newly‐discovered organisms are replete with novel sequences, emphasizing the trove of enzyme structures and functions waiting to be explored by biochemists. Here, we sought to draw attention to the vastness of the “enzymatic dark matter” within the tree of life by placing enzymological knowledge in the context of phylogeny. We used kinetic parameters from the BRaunschweig ENzyme DAtabase (BRENDA) as our proxy for enzymological knowledge. Mapping 12,677 BRENDA entries onto the phylogenetic tree revealed that 55% of these data were from eukaryotes, even though they are the least diverse part of the tree. At the next taxonomic level, only four of 18 archaeal phyla and 24 of 111 bacterial phyla are represented in the BRENDA dataset. One phylum, the Proteobacteria, accounts for over half of all bacterial entries. Similarly, the supergroup Amorphea, which includes animals and fungi, contains over half the data on eukaryotes. Many major taxonomic groups are notable for their complete absence from BRENDA, including the ultra‐diverse bacterial Candidate Phyla Radiation. At the species level, five mammals (including human) contribute 15% of BRENDA entries. The taxonomic bias in enzymology is strong, but in the era of gene synthesis we now have the tools to address it. Doing so promises to enrich our biochemical understanding of life and uncover powerful new biocatalysts.

Benthos is an organism that lives on the bottom of the waters, both in the form of animals and plants, living on the surface and on the bottom of the waters. This study aims to determine the diversity of macrozoobenthic species in the Barumun River, Pinang City. The research starts from December 2020 to February 2021. Macrozoobenthic sampling using Surber net and Ekman Grab based on substrate differences in the riverbed. Macrozoobenthos found in the Barumun River in Pinang City consists of two phyla, namely Arthropoda and Molluscs. The phylum Arthropods found are from the class of insects belonging to the genera Hydropsyche, Polycentropus, psephenus, Dryops, Anthopotamu, Acroneuria and Triops. The phylum Molluscs found were from the Bilvavia class which belonged to the Corbicula genus and from the Gastropod class of the Genera Melanoides and Melanatria. The highest macrozoobenthic abudance at each station was Polycentropus (65,67 ind L) and Potadoma (265,67 ind L). The highest macrozoobenthic abudance found was Melanatria at (633,67 ind L) based on the vulnerability index value (H) (2,087 – 1,003) dominance index (C) (0133 -0,389) and evenness index (E) (0,365-0,603) Barumun River Kota Pinang is included in the good condition category with high species diversity. The physical and chemical factors of the waters are able to support macrozoobenthic life.

Cryptic species are morphologically identical but genetically distinct, and are prominent across numerous phyla. The coexistence of such closely related species on local scales would seem to run counter to traditional coexistence and competition theory; it has been hypothesized as a consequence of differences in their resource use or tolerances to environmental conditions. We developed an individual-based model of a community of three cryptic Litoditis marina (nematode) species, to understand how individual-level interspecific and intraspecific interactions might explain the coexistence of these closely related species. The model incorporates individuals' reproduction, competition, dispersal and resource use. Data characterizing the cryptic species (growth rates, dispersal ability, competitive interactions and responses to changing environmental conditions) were obtained from laboratory experiments involving both mono- and multispecific nematode cultures, and are used to parameterize the model. Simulation studies are used to investigate which individual-level mechanisms of dispersal and interaction lead to the characteristic population-level patterns observed experimentally. Our results highlight the key role of intraspecific competition in mediating dispersal and therefore co-occurrence of the cryptic species. The differences in dispersal also influence the response of the cryptic species to competition, a combination of factors that provides an explanation for their co-occurrence. These results provide insights into how changes in individual-level processes can be amplified to affect population-level co-occurrence.

The unicellular trypanosomatids belong to the phylum Euglenozoa and all known species are obligate parasites. Distinct lineages infect plants, invertebrates, and vertebrates, including humans. Genome data for marine diplonemids, together with freshwater euglenids and free-living kinetoplastids, the closest known nonparasitic relatives to trypanosomatids, recently became available. Robust phylogenetic reconstructions across Euglenozoa are now possible and place the results of parasite-focused studies into an evolutionary context. Here we discuss recent advances in identifying the factors shaping the evolution of Euglenozoa, focusing on ancestral features generally considered parasite-specific. Remarkably, most of these predate the transition(s) to parasitism, suggesting that the presence of certain preconditions makes a significant lifestyle change more likely.

Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health., Metagenomics and electron microscopy are combined to analyse the diversity of episymbiotic CPR bacteria and DPANN archaea in eight groundwater communities.

Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

Once the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.

An understanding of the annual variations in the phytoplankton community in freshwater lakes, and of the drivers responsible for these variations, is essential for lake management. In this study we collected and analyzed seasonal samples of phytoplankton and assessed environmental variables in Nansi Lake from 2011 to 2015, in order to identify the seasonal dynamics of the phytoplankton community and the main drivers in each phylum. The results showed that phytoplankton diversity in Nansi Lake followed annual cycles, which were interrupted by a water diversion in 2013. The disruption of equilibrium was clearly demonstrated by the Shannon���Wiener diversity index, Pielou���s evenness index, and Simpson���s dominance index, whereas the species richness and abundance showed resilience, maintaining regular annual cycles. The dominant species were frequently Synedra acus K��tz (Bacillariophyta), Closterium gracile Br��b (Chlorophyta), and Scenedesmus quadricauda Br��b (Chlorophyta) in summer and autumn. Non-metric multidimensional scaling (NMDS) analysis suggested that the phytoplankton was most widely distributed in summer, when conditions were more conducive to phytoplankton growth and reproduction. Redundancy analysis (RDA) indicated that the main drivers for the phytoplankton community varied in different taxonomic units. Specifically, the NP ratio and permanganate index (CODMn) had significant effects on Chlorophyta, whereas pH, dissolved oxygen (DO), and transparency significantly influenced Bacillariophyta. This study highlights the importance of seasonal phytoplankton succession and the need for identification of the main drivers in each phylum in order to achieve more effective control of phytoplankton blooms in freshwater lakes.

Flowers secrete nutrient-rich exudates that support the growth of an assemblage of microorganisms, including both beneficial and pathogenic members, most of which belong to the phylum Proteobacteria. Given the potential role of the microbiome in plant health, manipulating the microbiome to promote growth of beneficial members holds promise in controlling plant diseases. In this study, we inoculated four different bacterial strains that were originally isolated from apple stigmas, alone or in mixtures of increasing complexity, onto apple flowers during bloom. We tested whether such treatments would influence fire blight occurrence, a disease caused by Erwinia amylovora, and whether we could detect a shift in the structure of the microbiome due to the treatments. We show that various inoculations did influence the occurrence of fire blight, although the level of disease suppression was dependent upon specific bacterial strains. Furthermore, treatments using different strains or strain mixtures predominantly resulted in increased representation of the inoculated strains, suggesting that disease suppression was due to an alteration of the stigma microbiome structure. Compared with treatments using single strains, a Pantoea–Pseudomonas strain mixture produced a homogeneous microbiome structure with less interflower variability. Findings from this study suggest that the microbiome on the flower stigma can be manipulated through microbial inoculation. Due to flowers’ short life span yet important role in plant disease infection, even a short-term influence on microbiome composition may result in significant decreases in disease susceptibility.

Invertebrate animals comprise more than 95% of the animal kingdom's species and approximately 40 separate phyla. Yet, invertebrates are an artificial taxon, in which all members simply possess a single negative trait: they lack a vertebral column (backbone). In fact, some invertebrates are more closely related to vertebrates than to their "fellow" invertebrates. For the purpose of this veterinary article, we have elected to review a handful of important groups: Coelenterates, Gastropods, Cephalopods, Chelicerates, Crustaceans, Insects, and Echinoderms. We have primarily included behaviors that may have an impact on clinical case outcome, or be of interest to the veterinary clinician.

Ticks can transmit numerous pathogens and harbor diverse microbial communities. Considerable progress has been made in the characterization of the bacterial profiles of ticks, whereas other members of tick microbiota (such as fungi and viruses) and the functional characteristics of ticks warrant further exploration. To investigate the taxonomic and functional profiles and explore potential pathogens they were carrying, samples of different developmental stages and of both sexes of Haemaphysalis longicornis were collected in the present study and the metagenomic deep sequencing method was applied. Metagenomic deep sequencing results revealed that bacteria were predominant, followed by fungi, viruses, archaea and metazoans. Proteobacteria was the dominant phylum in the microbiota of H. longicornis. The abundance of microbial species varied significantly among groups, the bacteria of nymphs and female adults demonstrated unique characteristics, and the microbial community of males overlapped with those of nymphs and females. Functional annotation results demonstrated that the metagenomic sequences of the three groups were classified under metabolism, genetic information processing, environmental information processing and cellular processes. Differences in functional characteristics were observed in both the pathways composition and abundance of carbohydrate-active enzymes. Furthermore, whole metagenome sequencing helped to elucidate the diversity of pathogens carried by H. longicornis, which may facilitate further research attempting to prevent and control tick-borne diseases.

Fermented foods play an important role in the daily life and diet of the populations in Congo. Among these fermented foods, there is Pilipili or fermented pepper which is consumed without prior cooking. The microorganisms present are eaten alive. Few studies have been carried out on these microorganisms which may have beneficial effects on health. This study aimed to investing taxonomic diversity of bacterial communities in 3 samples of fermented peppers produced in 3 distinct areas of Brazzaville. To do this investigation, Illumina Miseq sequencing of 16S rRNA gene was used. The results showed that the number of identified operational taxonomic units (OTUs) ranged from 156 to 392. All OTUs belong to the domain of Bacteria and could be categorized into 21 Phyla, 36 Classes, 58 Orders, 100 Families and 171 genera. Firmicutes and Proteobacteria were the main dominant phyla of the total phyla present with a relative abundance of 89.12% and 8.08%, respectly. At the class level, Bacili were dominant in EB1 (99.50%), EB3 (85.32%) and EB2 (42.29%) while Clostridia in EB2 (40.10%). Lactobacillus, Clostridium sensu stricto and Frutobacillus were the dominant genera in the sample EB1, EB2 and EB3, respectively. The hierarchical classification showed that the samples EB1 and EB2 form the same group and EB3 is unique. Principal component analysis showed that the younger EB3 and EB2 samples were more diverse than the older EB1 sample. This study is a first in Congo on the diversity of fermented pepper using Illumina Miseq. It has shown that this food is very diverse and can be a source for the isolation of bacteria with biotechnological potential.

We evaluated the fungal diversity in two lakes on the South Shetland Islands, using DNA metabarcoding through high-throughput sequencing (HTS). A microcosm experiment was deployed for two consecutive years in lakes on Deception and King George islands to capture potential decomposer freshwater fungi. Analyses of the baits revealed 258,326 DNA reads distributed in 34 fungal taxa of the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota and Rozellomycota. Tetracladium marchalianum, Tetracladium sp., Rozellomycota sp., Fungal sp. 1 and Fungal sp. 2 were the most common taxa detected. However, the majority of the communities comprised intermediate and rare taxa. Both fungal communities displayed moderate indices of diversity, richness and dominance. Only six taxa were detected in both lakes, including the most dominant T. marchalianum and Tetracladium sp. The high numbers of reads of the known aquatic saprotrophic hyphomycetes T. marchalianum and Tetracladium sp. in the baits suggest that these fungi may digest organic material in Antarctic lakes, releasing available carbon and nutrients to the other aquatic organisms present in the complex lake food web. Our data confirm that the use of cotton baits together with HTS approaches can be appropriate to study the diversity of resident freshwater fungi present in Antarctic lakes.

Knowledge about the impact of altitude and ethnicity on human oral microbiota is currently limited. To obtain the baseline of normal salivary microbiota, we analyzed the bacteria and fungi composition in Tibetan (HY group) and Han population (CD group) living at different altitudes by using next-generation sequencing (NGS) technology combined with PICRUSt and FUNGuild analyses. There were significant differences in oral microbiota composition between the two groups at phylum and genus levels. At the phylum level, the HY group had higher relative abundances of Firmicutes and Ascomycota, whereas the Bacteroidetes and Basidiomycota in the CD group were richer. These changes at the phylum level reflected different dominant genus compositions. Compared with the Han population, Candida, Fusarium, Zopfiella, Streptococcus, Veillonella and Rothia in Tibetan were higher. Surprisingly, the Zopfiella was found almost exclusively in the Tibetan. The PICRUSt and FUNGuild analysis also indicated that the function of the bacterial and fungal communities was altered between the two groups. In conclusion, our results suggest that there are significant differences in oral microbial structure and metabolic characteristics and trophic modes among Tibetan and Han population living at different altitudes. We first established the oral microbiota framework and represented a critical step for determining the diversity of oral microbiota in the Tibetan and Han population.

Eukaryotic microplankton plays an important role in water biotic community and in maintaining the stability of water ecosystems. Environmental DNA metabarcoding provides the opportunity to integrate traditional and emerging approaches to discover more new species, and develop molecular biotic indices that can be more rapidly, frequently, and robustly used in water quality assessments. In order to examine assemblages of eukaryotic microplankton in lower reaches of Qiantang River, ITS gene metabarcoding technology based on environmental DNA was carried out. As a result, various species of phytoplankton, fungi and zooplankton were annotated on. More phylum, classes and specieses of eukaryotic phytoplankton and zooplankton were found after compared communities taxa based on metabarcoding with that obtained from morphological examination. Nevertheless, Chlorophyceae was the most common assemblage both identified by using these two methods, also Mesocyclops leuckarti and Acanthocyclops bicuspidatus were both found to be the dominant species of Cyclopoida in the river. Additionally, the reads proportions of phytoplankton and zooplankton at the three freshwater sampling sites (Tonglu, Fuyang and Wenyan) decreased as temperature drop. Meanwhile, twenty classes of fungi were annotated on, of which the community characteristic was first researched in the river. There were significant spatial differences in values of Chao1 index for eukaryotic microplankton. Cluster analysis and Non-metric multidimensional scaling ordination further confirmed that the community composition of eukaryotic microplankton at class level for Jiashao-September sample had the most dissimilarity with the others.

This study was carried out at Mahallet Ziad wastewater treatment plant in El-Gharbia Province during a period extending between Feb. 2018 and Jan. 2019. Major planktonic groups and certain physico-chemical parameters were investigated monthly at this water plant to elucidate its performance efficiency in treating and enhancing the wastewater. It was apparently that protozoa and rotifers represent the major groups in that wastewater treatment plant. Protozoa are represented by three major phyla (Sarcodina, Mastigophorea and Ciliophora) where the ciliated protozoans prevail the other two phyla. The numerical densities of sessile peritrich ciliates were less abundant than other ciliated protozoan types (crawling and swimming ciliates). It was proved that the maximal and minimal numerical densities of total protozoans of the present investigation exhibited 6956 and 1716x 102/L during March and December, respectively. Simultaneously, the uppermost numerical values of sarcodines, flagellates and ciliates were 565, 2211 and 56312/L during May, February and April, while the lowest ones were 30, 87 and 1716x 102/L on September, July and December, respectively. Different types of protozoan were proved to be significantly influenced to varying levels with certain physico-chemical parameters. From the technological point of view, it was proved that the performing efficiency of the activated sludge of the present study is more or lessparallel to those of other wastewater treatment plants in different provinces of Egypt which gives an indication that there is a critical strategic need for the government to have more treated water to be used in agricultural and industrial activities.

Large amounts of detrital organic matter and osmolytes accumulate in the sediments of hadal trenches (>6000 m depth) due to the funnelling effect. It is still unknown whether there are novel active microbes that depend on specific carbon sources in extreme and isolated environments. In this study, we present a novel active bacterial phylum, Candidatus Tianyabacteria in the FCB superphylum, which was enriched in sediments collected from the Challenger Deep. Genome binning resulted in high-quality Ca. Tianyabacteria genomes representing two Ca. Tianyabacteria lineages (L1 and L2) in sediments 0-21 cm below the surface (cmbsf); L1 tends to be abundant in the upper layers (0-9 cmbsf), and L2 seems to be more prevalent in the deeper layers (12-21 cmbsf). Gene annotation and transcriptomics results indicate that the two lineages might import and catalyse amino acids and myo-inositol into central carbon metabolism for a heterotrophic lifestyle. Probably due to differences in environmental oxygen levels, the L2 genomes harbour gene clusters responsible for denitrification and fermentation, while the L1 genomes encode octahaem cytochrome c and multicopper oxidase using unknown substrates. The Ca. Tianyabacteria are thus novel heterotrophic organisms that participate in processes of carbon, nitrogen and organic osmolyte cycling in hadal sediments.

Background. A comprehensive understanding of the commensal microflora and its relation to health is essential for preventing and combating diseases. The aim of this study was to examine the structure of the oral microbiome by using different sequencing technologies. Material and Methods. Five preschool children with no symptoms of oral and systemic diseases were recruited. Samples of saliva were collected. A 468 bp insert size library was constructed on the MiSeq platform and then subjected to 300 bp paired-end sequencing. Libraries with longer insert sizes, including a full-length 16S rDNA gene, were sequenced on the PacBio RS II platform. Results. A total of 122.6 Mb of raw data, including 244,967 high-quality sequences, were generated by the MiSeq platform, while 134.6 Mb of raw data, including 70,030 high-quality reads, were generated by the PacBio RS II platform. Clustering of the unique sequences into OTUs at 3% dissimilarity resulted in an average of 225 OTUs on the MiSeq platform; however, the number of OTUs generated on the PacBio RS II platform was 449, far greater than the number of OTUs generated on the MiSeq platform. A total of 437 species belonging to 10 phyla and 60 genera were detected by the PacBio RS II platform, while 163 species belonging to 12 phyla and 72 genera were detected by the MiSeq platform. Conclusions. The oral microflora of healthy Chinese children were analyzed. Compared with traditional 16S rRNA sequencing technology, the PacBio system, despite providing a lower amount of clean data, surpassed the resolution of the MiSeq platform by improving the read length and annotating the nucleotide sequences at the species or strain level. This trial is registered with NCT02341352.

Bacteria are divided primarily into monoderms (with one cell membrane, and usually Gram-positive, due to a thick peptidoglycan layer) and diderms (with two cell membranes, and mostly Gram-negative, due to a thin peptidoglycan layer sandwiched between the two membranes). Photosynthetic species are spread among the taxonomic groups, some having type I reaction centers (RCI in monoderm phylum Firmicutes; and diderm phyla Acidobacteria and Chlorobi), others with type II reaction centers (RCII in monoderm phylum Chloroflexi; and diderm taxa Gemmatimonadetes, and alpha-, beta-, and gamma-Proteobacteria), and some containing both (RCI and RCII, only in diderm phylum Cyanobacteria). In most bacterial phylograms, photosystem types and diderm taxa are polyphyletic. A more parsimonious arrangement, which is supported by photosystem evolution, as well as additional sets of molecular characters, suggests that endosymbiotic events resulted in the formation of the diderms. In the model presented, monoderms readily form a monophyletic group, while diderms are produced by at least two endosymbiotic events, followed by additional evolutionary changes.

Cell coverings can be observed in all major groups of organisms, which include animals, plants, fungi, protists and prokaryotes. They play a key role in assuring cell survival or adaptation to certain environmental conditions. Since the term algae refers to a polyphyletic and very artificial group, the cell coverings of these organisms are very diverse in molecular composition and with different arrangements. Differences have taxonomic value since they allow microalgae phyla or even minor taxonomic groups, such as classes, orders or families, to be distinguished. Understanding the structure of cell coverings is also fundamental for the use of microalgae to obtain products of commercial value. Despite its importance, the composition and architecture of microalgae coverings is still poorly understood, especially considering the great diversity of organisms. Diatom frustules are the most studied coverings due their uses in areas of bio- and nanotechnology. There is a lack of information about the cell wall, lorica, periplast, amphiesma and scales. This study is a review with the aim of synthesizing literature information on microalgae cell coverings to describe their compositions, arrangements, functions and industrial uses.

Truffles are included among the most expensive fungi around the world. Around 180 truffle species have been described worldwide, and more than 50 species have been recorded from China. However, so far, the influence of provenances on truffle morphology, phylogeny, and bacterial and fungal microbiome community structure of both peridium and gleba has been scarcely studied. The rare excavated Chinese truffle Tuber pseudobrumale, known previously only from its type collection, was investigated in different collections from Yunnan and Sichuan provinces located in southwestern China. The microbiome showed differences at the phylum and order levels according to their provenances and compartments (gleba or peridium). For the first time, yeasts and filamentous fungi associated with truffles were studied using a metagenomic approach. Sixty-one fungal genera were identified by Illumina high throughput sequencing, belonging to 48 families, 37 orders, 20 classes, and 11 phyla were recorded. The non-metric multi-dimensional scaling plots (NDMS) showed different patterns for bacteria and fungi. In bacteria, both compartments and provenances were grouped in different clusters, while fungi grouped together more by provenance than by compartments. These changes were recorded along with macro- and micromorphological variations of the ascomata in the different collections. This integral study demonstrates for the first time that the provenances originate conspicuous intraspecific variations in T. pseudobrumale in terms of morphology and microbiome community structure in peridium and gleba, despite strong genetic consistency.

The gut microbiome provides ecological information about host animals, but we still have limited knowledge of the gut microbiome, particularly for animals inhabiting remote locations, such as Antarctica. Here, we compared fecal microbiota between southern elephant seals (Mirounga leonina) and Weddell seals (Leptonychotes weddelli), that are top predatory marine mammals in the Antarctic ecosystem, using 16S rRNA amplicon sequencing and assessed the relationships of the gut microbial communities to functional profiles using gut metabolite analysis. The bacterial community did not differ significantly by host species or sex at the phylum level, but the distinction at the family level was obvious. The family Ruminococcaceae (Firmicutes) was more abundant in southern elephant seals than in Weddell seals, and the families Acidaminococcaceae (Firmicutes) and Pasteurellaceae (Gammaproteobacteria) were uniquely present in Weddell seals. The fecal bacterial community structure was distinctively clustered by host species, with only 6.7% of amplicon sequence variants (ASVs) shared between host species. This result implies that host phylogeny rather than other factors, such as diet or age, could be the major driver of fecal microbiotic diversification. Interestingly, there was no apparent sex effect on bacterial community structure in Weddell seals, but the effect of sex was pronounced in adult southern elephant seals mainly due to the prevalence of Edwardsiella sp., suggesting that extreme sexual dimorphism may modulate the gut microbiota of southern elephant seals. Unlike the clear distinction in the taxonomic composition of fecal bacterial communities, there were no discernible differences in the profiles of potential microbial functions and gut metabolites between host species or sexes, indicating that functional redundancy dominates the gut microbiota of seals surveyed in this study.

In this research, an analysis of the social component of the history in Filosofía de larealidad histórica is carried out, based on a study of the Zubirian foundations with which IgnacioEllacuría builds the second chapter of this work. In order to show its originality and trace a pathto the main categories of this subject. En esta investigación se realiza un análisis de la componente social de la historia dela Filosofía de la realidad histórica, a partir de un estudio de los fundamentos zubirianos con los queIgnacio Ellacuría construye el capítulo segundo de esta obra. Con el objetivo de evidenciar suoriginalidad y trazar una ruta de acceso a las principales categorías de esta temática.

International audience; Microbial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare organisms such as Candidate Phyla Radiation bacteria (CPR) and enigmatic entities such as aster-like nanoparticles (ALNs). Here, a reactor was inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4°C for 31 months and enriched for ALNs, diverse Planctomycetes, and CPR bacteria. We reconstructed draft genomes and predicted metabolic traits for 12 diverse Planctomycetes and 9 CPR bacteria, some of which are likely representatives of undescribed families or genera. One CPR genome representing the little-studied lineage "Candidatus Peribacter" was curated to completion (1.239 Mbp) and unexpectedly encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some planctomycetes and CPR bacteria were active under the culture conditions, accounting for ;30% and ;1% of RNA reads mapping to the genome set, respectively. We also reconstructed genomes and obtained transmission electron microscope images for numerous viruses, including one with a .300-kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes are central players in a subsystem that includes ALNs, symbiotic CPR bacteria, and viruses. IMPORTANCE Laboratory incubations of natural microbial communities can aid in the study of member organisms and their networks of interaction. This is particularly important for understudied lineages for which key elements of basic biology are still emerging. Using genomics and microscopy, we found that members of the bacterial lineage Planctomycetes may be central players in a subset of a freshwater lake microbiome that includes other bacteria, archaea, viruses, and mysterious entities, called aster-like nanoparticles (ALNs), whose origin is unknown. Our results help constrain the possible origins of ALNs and provide insight into possible interactions within a complex lake ecosystem. KEYWORDS CPR bacteria, aster-like nanoparticles, lake microbiome, metagenomics, viruses F reshwater lakes host diverse microbial communities that likely control ecosystem biogeochemistry (1, 2). Here, we established a laboratory culture based on an inoculum from Lake Fargette, France, a site chosen as part of a parallel study of enigmatic aster-like nanoparticles (ALNs) (3, 4). ALNs are enigmatic, organic, femtoplankton entities that exhibit bloom-like behavior in various freshwater and coastal environments (3, 4). In this experiment, Editor

Rapid bacterial growth depends on the speed at which ribosomes can translate mRNA into proteins. mRNAs that encode successive stretches of proline can cause ribosomes to stall, substantially reducing translation speed. Such stalling is especially detrimental for species that must grow and divide rapidly. Here we focus on di-prolyl motifs (XXPPX) and ask whether their incidence varies with growth rate. To find out we conducted a broad survey of such motifs in >3000 bacterial genomes across 36 phyla. Indeed, fast-growing species encode fewer motifs than slow-growing species, especially in highly expressed proteins. We also found many di-prolyl motifs within thermophiles, where prolines can help maintain proteome stability. Moreover, bacteria with complex, multicellular lifecycles also encode many di-prolyl motifs. This is especially evident in the slow-growing phylum Myxococcota. Bacteria in this phylum encode many serine-threonine kinases, and many di-prolyl motifs at potential phosphorylation sites within these kinases. Serine-threonine kinases are involved in cell signaling and help regulate developmental processes linked to multicellularity in the Myxococcota. Altogether, our observations suggest that weakened selection on translational rate, whether due to slow or thermophilic growth, may allow di-prolyl motifs to take on new roles in biological processes that are unrelated to translational rate.

The Postojna-Planina Cave System (PPCS) in central Slovenia is a globally exceptional site of subterranean biodiversity, comprised of many interconnected caves with cumulative passage length exceeding 34 km. Two rivers sink into the caves of the PPCS, called the Pivka and Rak, and join underground into Unica River, which emerges to the surface. The studies of fauna of PPCS began in the 19th century with the first scientific descriptions of specialized cave animals in the world, making it “the cradle of speleobiology”. Currently, the species list of PPCS contains 116 troglobiotic animal species belonging to eight phyla, confirming its status as the richest in the world. Of these, 47 species have been scientifically described from the PPCS, and more than 10 await formal taxonomic descriptions. We expect that further sampling, detailed analyses of less studied taxa, and the use of molecular methods may reveal more species. To keep the cave animals’ checklist in PPCS up-to-date, we have supplemented the printed checklist with an online interface. As the revised checklist is a necessary first step for further activities, we discuss the importance of PPCS in terms of future research and conservation.

Summary We present HoPhage (Host of Phage) to identify the host of a given phage fragment from metavirome data at the genus level. HoPhage integrates two modules using a deep learning algorithm and a Markov chain model, respectively. HoPhage achieves 47.90% and 82.47% mean accuracy at the genus and phylum levels for ∼1-kb long artificial phage fragments when predicting host among 50 genera, representing 7.54–20.22% and 13.55–24.31% improvement, respectively. By testing on three real virome samples, HoPhage yields 81.11% mean accuracy at the genus level within a much broader candidate host range. Availability and implementation HoPhage is available at http://cqb.pku.edu.cn/ZhuLab/HoPhage/data/ Supplementary information Supplementary data are available at Bioinformatics online.

To understand the relationship between the community structure of bacteria and soil environment, the diversity and composition of soil bacterial communities were investigated, based on 16S rRNA gene clone library, in three different sampling sites (SP1, SP2 and SP3) in the Bortala and Jinghe River basins of Ebinur Lake Wetland. The results showed that the diversity of bacteria among plots was SP2 > SP3 > SP1, and the richness was SP3 > SP2 > SP1. Community composition analysis of bacteria showed that Proteobacteria and Bacteroides accounted for 49.7% and 53.7%, respectively, making them the most dominant phyla observed. In SP1, Proteobacteria was the most dominant phylum, followed by Bacteroides. In SP2 and SP3, Bacteroides was the most dominant phylum, followed by Proteobacteria. At subphyla level, Gammaproteobacteria, Alphaproteobacteria and Deltaproteobacteria accounted for 50%, 51.0%, and 42.2% of the Proteobacteria of SP1, SP2, and SP3, respectively. Betaproteobacteria and Epsilonproteobacteria were found only in SP3. RDA results showed that SOM, SM and EC were the main soil environmental factors affecting bacterial community structure.

Chaetognaths (arrow worms) are an enigmatic group of transparent planktonic invertebrates and play an important role in the marine food web. Their morphological and developmental features have raised extensive debates since the discovery of the phylum in the 18th century. Uncertainty in the phylogenetic placement of certain chaetognath species still exists and is puzzling many scientists who have tried to clarify this task. Studies using a portion of both small subunit ribosomal ribonucleic acid (SSU rRNA) and large subunit ribosomal ribonucleic acid (LSU rRNA) genes when integrated with conventional taxonomy were contributed to resolve taxonomical issues in this group. Here we present the first phylogenetic study of Chaetognatha based on a portion of mitochondrial cytochrome oxidase I (COI) gene and compare our results with the earlier morphological and molecular evolutionary hypotheses. This study includes 16 extant species, representing 8 genera and 6 of which are among the 9 extant families. We recommend the following clade structure for the phylum: Aphragmophora comprising Sagittidae with Pterosagittidae and Krohnittidae included in the Sagittidae and Phragmophora comprising Eukrohniidae, Spadellidae, and Heterokrohniidae. Phylogenetic analyses also supported the division of Phragmophora into two monophyletic groups: the Monophragmophora and Biphragmophora. Moreover, Ctenodontina/Flabellodontina and Syngonata/Chorismogonata suborders were not validated. Precise phylogenetic investigations using various molecular markers and specimens from diverse regions are definitely needed to provide an exact evolutionary concept on this phylum.