Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents.

The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization.

BACKGROUND: The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. RESULTS: Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. CONCLUSIONS: The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.

Multiple Nucleocapsid Structural Forms of Shrimp White Spot Syndrome Virus Suggests a Novel Viral Morphogenetic Pathway.

White spot syndrome virus (WSSV) is a very large dsDNA virus. The accepted shape of the WSSV virion has been as ellipsoidal, with a tail-like extension. However, due to the scarcity of reliable references, the pathogenesis and morphogenesis of WSSV are not well understood. Here, we used transmission electron microscopy (TEM) and cryogenic electron microscopy (Cryo-EM) to address some knowledge gaps. We concluded that mature WSSV virions with a stout oval-like shape do not have tail-like extensions. Furthermore, there were two distinct ends in WSSV nucleocapsids: a portal cap and a closed base. A C14 symmetric structure of the WSSV nucleocapsid was also proposed, according to our Cryo-EM map. Immunoelectron microscopy (IEM) revealed that VP664 proteins, the main components of the 14 assembly units, form a ring-like architecture. Moreover, WSSV nucleocapsids were also observed to undergo unique helical dissociation. Based on these new results, we propose a novel morphogenetic pathway of WSSV.

Prevalence, complete genome, and metabolic potentials of a phylogenetically novel cyanobacterial symbiont in the coral-killing sponge, Terpios hoshinota.

Terpios hoshinota is an aggressive, space-competing sponge that kills various stony corals. Outbreaks of this species have led to intense damage to coral reefs in many locations. Here, the first large-scale 16S rRNA gene survey across three oceans revealed that bacteria related to the taxa Prochloron, Endozoicomonas, SAR116, Ruegeria, and unclassified Proteobacteria were prevalent in T. hoshinota. A Prochloron-related bacterium was the most dominant and prevalent cyanobacterium in T. hoshinota. The complete genome of this uncultivated cyanobacterium and pigment analysis demonstrated that it has phycobiliproteins and lacks chlorophyll b, which is inconsistent with the definition of Prochloron. Furthermore, the cyanobacterium was phylogenetically distinct from Prochloron, strongly suggesting that it should be a sister taxon to Prochloron. Therefore, we proposed this symbiotic cyanobacterium as a novel species under the new genus Candidatus Paraprochloron terpiosi. Comparative genomic analyses revealed that 'Paraprochloron' and Prochloron exhibit distinct genomic features and DNA replication machinery. We also characterized the metabolic potentials of 'Paraprochloron terpiosi' in carbon and nitrogen cycling and propose a model for interactions between it and T. hoshinota. This study builds a foundation for the study of the T. hoshinota microbiome and paves the way for better understanding of ecosystems involving this coral-killing sponge.

A multi-step nitrifying microbial enrichment to remove ammonia and nitrite in brackish aquaculture systems.

One of the most important advancements in harnessing the biological nitrification in the field is enrichment solution of nitrifying microbial consortia. In the current study, we developed an improved multi-step enrichment to amplify a targeted microbial consortium from a sediment sample collected in tropical mangrove, Vietnam. The results showed that it took 122 culturing days with five unique continuous enrichment steps, the microbial consortium consumed total 5665 mgN L-1. Relative substrate removal rate increased rapidly from 0.114 mgN L-1 h-1 at the end of the first-step enrichment up to 3.58 mgN L-1 h-1 at the end of the fifth-step enrichment. High-throughput sequencing revealed that Nitrospirae, Proteobacteria and Bacteroidetes were the dominant taxa at the phylum level while Nitrospira, Marinobacter, Denitromonas and Nitrosomonas were the dominant taxa at the genus level in the enriched consortia. A pilot-scale experiment for shrimp cultivation of L. vannamei in 84 day-period proved the efficiency of Total ammonium nitrogen and nitrite removal in the consortium-activated treatment was much higher than the control.

Spatiotemporal Changes in the Bacterial Community of the Meromictic Lake Uchum, Siberia.

Lake Uchum is a newly defined meromictic lake in Siberia with clear seasonal changes in its mixolimnion. This study characterized the temporal dynamics and vertical profile of bacterial communities in oxic and anoxic zones of the lake across all four seasons: October (autumn), March (winter), May (spring), and August (summer). Bacterial richness and diversity in the anoxic zone varied widely between time points. Proteobacteria was the dominant bacterial phylum throughout the oxic and anoxic zones across all four seasons. Alphaproteobacteria (Loktanella) and Gammaproteobacteria (Aliidiomarina) exhibited the highest abundance in the oxic and anoxic zone, respectively. Furthermore, there was a successional shift in sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria in the anoxic zone across the seasons. The most dominant SRB, Desulfonatronovibrio sp., is likely one of the main producers of hydrogen sulfide (H2S) and typically accumulates the most H2S in winter. The representative anoxygenic phototrophic bacterial group in Lake Uchum was purple sulfur bacteria (PSB). PSB were dominant (60.76%) in summer, but only had 0.2-1.5% relative abundance from autumn to spring. Multivariate analysis revealed that the abundance of these SRB and PSB correlated to the concentration of H2S in Lake Uchum. Taken together, this study provides insights into the relationships between changes in bacterial community and environmental features in Lake Uchum.

Spatial and cross-seasonal patterns of coral diseases in reefs of Taiwan: high prevalence and regional variation.

Although research on coral diseases is increasing worldwide, it remains limited in Taiwan. Taiwan is located at the Tropic of Cancer and contains both tropical and subtropical reefs. We conducted spatial and cross-seasonal surveys in Taiwan in 2018 and identified 7 types of disease and nondisease lesions and 6 potential factors influencing coral health. The overall mean prevalence of disease and nondisease lesions varied considerably across the reef regions, and host susceptibility differed among the coral taxa. The overall mean prevalence of disease and nondisease lesions was highest in Kenting (mean ± SEM: 8.58 ± 1.81%) and lowest on the Southern Islands (2.12 ± 0.73%). Although the prevalence of diseases did not differ significantly between the seasons, cyanobacteria-related diseases-including black band disease (BBD), BBD-like syndrome, and other cyanobacterial syndromes-were slightly more prevalent in autumn than in spring. Furthermore, 3 of the potential factors influencing coral health (i.e. turf algae, bioeroding sponges, and coral bleaching) were strong predictors of disease and nondisease lesion prevalence. These results advance our understanding of coral disease ecology in Taiwan and highlight the need for further research on the correlations between diseases, hosts, and environment.

Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia.

A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01T were non-motile, cocci and 0.8-1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01T was methanol. The temperature range of growth for strain SY-01T was from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0-1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01T was 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01T was most closely related to Methanolobus zinderi SD1T (97.3 % 16S rRNA gene sequence similarity), and had 95.5-97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01T and DSM 21339T was computed using average nucleotide identity and digital DNA-DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01T represents a novel species of the genus Methanolobus, and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01T (=BCRC AR10051T=NBRC 113166 T=DSM 107642T).

Taxonomy based performance metrics for evaluating taxonomic assignment methods.

BACKGROUND: Metagenomics experiments often make inferences about microbial communities by sequencing 16S and 18S rRNA, and taxonomic assignment is a fundamental step in such studies. This paper addresses the weaknesses in two types of metrics commonly used by previous studies for measuring the performance of existing taxonomic assignment methods: Sequence count based metrics and Binary error measurement. These metrics made performance evaluation results biased, less informative and mutually incomparable. RESULTS: We investigated weaknesses in two types of metrics and proposed new performance metrics including Average Taxonomy Distance (ATD) and ATD_by_Taxa, together with the visualized ATD plot. CONCLUSIONS: By comparing the evaluation results from four popular taxonomic assignment methods across three test data sets, we found the new metrics more robust, informative and comparable.

ENVirT: inference of ecological characteristics of viruses from metagenomic data.

BACKGROUND: Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databases to first estimate an average genome length of a viral community before being able to estimate other parameters, such as viral richness. Although this approach has been widely used, it can adversely skew results since the majority of viruses are yet to be catalogued in databases. RESULTS: In this paper, we present ENVirT, a method for estimating the richness of novel viral mixtures, and for the first time we also show that it is possible to simultaneously estimate the average genome length without a priori information. This is shown to be a significant improvement over database-dependent methods, since we can now robustly analyze samples that may include novel viral types under-represented in current databases. We demonstrate that the viral richness estimates produced by ENVirT are several orders of magnitude higher in accuracy than the estimates produced by existing methods named PHACCS and CatchAll when benchmarked against simulated data. We repeated the analysis of 20 metavirome samples using ENVirT, which produced results in close agreement with complementary in virto analyses. CONCLUSIONS: These insights were previously not captured by existing computational methods. As such, ENVirT is shown to be an essential tool for enhancing our understanding of novel viral populations.

Coralloluteibacterium stylophorae gen. nov., sp. nov., a new member of the family Lysobacteraceae isolated from the reef-building coral Stylophora sp.

A bacterial strain, designated Sty a-1T, was isolated from a reef-building coral Stylophora sp., collected off coast of Southern Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain Sty a-1T were Gram-staining-negative, aerobic, poly-ß-hydroxybutyrate accumulating, motile by means of flagella, non-spore forming, straight rod-shaped and colonies were yellow and circular. Growth occurred at 15-40 °C (optimum, 30-35 °C), at pH 6-10 (optimum, pH 6.5-8) and with 0-7% NaCl (optimum, 2-3%). The predominant fatty acids were iso-C15:0, iso-C17:1 ω9c, summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) and iso-C17:0. The major isoprenoid quinone was Q-8 and the DNA G+C content was 68.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an uncharacterized aminophospholipid and three uncharacterized lipids. The major polyamines were spermidine, putrescine and homospermidine. Phylogenetic analyses based on 16S rRNA and four housekeeping gene sequences (recA, atpD, rpoA and rpoB) showed that strain Sty a-1T forms a distinct lineage with respect to closely related genera in the family Lysobacteraceae, most closely related to Lysobacter, Silanimonas, Arenimonas and Luteimonas and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 95%. On the basis of the genotypic and phenotypic data, strain Sty a-1T represents a novel genus and species of the family Lysobacteraceae, for which the name Coralloluteibacterium stylophorae gen. nov., sp. nov. is proposed. The type strain is Sty a-1T (= BCRC 80968T = LMG 29479T = KCTC 52167T).

Thalassotalea coralli sp. nov., isolated from the torch coral Euphyllia glabrescens.

Strain Eup a-8T, isolated from a torch coral Euphyllia glabrescens, was characterized using a polyphasic taxonomy approach. Cells of strain Eup a-8T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, poly-ß-hydroxybutyrate-containing, rod-shaped and formed white colonies. Optimal growth occurred at 25-30 °C, pH 7-8, and in the presence of 2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Eup a-8T belonged to the genus Thalassotalea and showed the highest levels of sequence similarity with respect to Thalassotalea ganghwensis JC2041T (97.1 %). Strain Eup a-8T contained C17 : 1ω8c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C14 : 0 and iso-C16 : 0 as the predominant fatty acids. The only isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and one uncharacterized phospholipid. Genomic DNA G+C content of strain Eup a-8T was 41.5 mol%. The DNA-DNA hybridization value for strain Eup a-8T with Thalassotalea ganghwensis JC2041T was less than 70 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain Eup a-8T should be classified as a novel species of the genus Thalassotalea, for which the name Thalassotalea coralli sp. nov. is proposed. The type strain is Eup a-8T (=BCRC 80967T=LMG 29478T=KCTC 52169T).

Litoribrevibacter euphylliae sp. nov., isolated from the torch coral Euphyllia glabrescens.

Strain Eup a-2T, isolated from the torch coral Euphyllia glabrescens, was characterized using a polyphasic taxonomy approach. Cells of strain Eup a-2T were Gram-negative, aerobic and motile by three polar flagella and formed translucent colonies. Optimal growth occurred at 25 °C, pH 6-8 and in the presence of 2-4 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Eup a-2T belonged to the genus Litoribrevibacter and showed the highest levels of sequence similarity with respect to Litoribrevibacter albus Y32T (97.8 %). Strain Eup a-2T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the predominant fatty acids. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphophatidylglycerol. Genomic DNA G+C content of strain Eup a-2T was 49.1 mol%. The DNA-DNA hybridization value for strain Eup a-2T with L. albus Y32T was less than 30 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain Eup a-2T should be classified as a novel species of the genus Litoribrevibacter, for which the name Litoribrevibactereuphylliae sp. nov. is presented. The type strain is Eup a-2T (=BCRC 81004T=LMG 29725T=KCTC 52438T).

Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia.

A psychrotolerant, methylotrophic methanogen, strain YSF-03T, was isolated from the saline meromictic Lake Shira in Siberia. Cells of strain YSF-03T were non-motile, irregular cocci and 0.8-1.2 µm in diameter. The methanogenic substrates utilized by strain YSF-03T were methanol and trimethylamine. The temperature range of growth for strain YSF-03T was from 0 to 37 °C. The optimum growth conditions were 30-37 °C, pH 7.0-7.4 and 0.17 M NaCl. The G+C content of the genome of strain YSF-03T was 41.3 mol%. Phylogenetic analysis revealed that strain YSF-03T was most closely related to Methanolobus profundi MobMT (98.15 % similarity in 16S rRNA gene sequence). Genome relatedness between strain YSF-03T and MobMT was computed using the Genome-to-Genome Distance Calculator and average nucleotide identity, which gave values of 23.5 and 79.3 %, respectively. Based on the morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain YSF-03T represents a novel species of the genus Methanolobus, for which the name Methanolobus psychrotolerans sp. nov. is proposed. The type strain is YSF-03T (=BCRC AR10049T=DSM 104044T=NBRC 112514T).

The effects of contemporary selection and dispersal limitation on the community assembly of acidophilic microalgae.

Extremophilic microalgae are primary producers in acidic habitats, such as volcanic sites and acid mine drainages, and play a central role in biogeochemical cycles. Yet, basic knowledge about their species composition and community assembly is lacking. Here, we begin to fill this knowledge gap by performing the first large-scale survey of microalgal diversity in acidic geothermal sites across the West Pacific Island Chain. We collected 72 environmental samples in 12 geothermal sites, measured temperature and pH, and performed rbcL amplicon-based 454 pyrosequencing. Using these data, we estimated the diversity of microalgal species, and then examined the relative contribution of contemporary selection (i.e., local environmental variables) and dispersal limitation on the assembly of these communities. A species delimitation analysis uncovered seven major microalgae (four red, two green, and one diatom) and higher species diversity than previously appreciated. A distance-based redundancy analysis with variation partitioning revealed that dispersal limitation has a greater influence on the community assembly of microalgae than contemporary selection. Consistent with this finding, community similarity among the sampled sites decayed more quickly over geographical distance than differences in environmental factors. Our work paves the way for future studies to understand the ecology and biogeography of microalgae in extreme habitats.

CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.

BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains. RESULTS: Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome. CONCLUSIONS: The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.

Endozoicomonas acroporae sp. nov., isolated from Acropora coral.

Strain Acr-14T, isolated from Acropora coral, was characterized by using a polyphasic taxonomy approach. Cells of strain Acr-14T were Gram-stain-negative, aerobic, non-motile, poly-ß-hydroxybutyrate-accumulating, rod-shaped and formed creamy white colonies. Optimal growth occurred at 30 °C, pH 7 and in the presence of 2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Acr-14T belonged to the genus Endozoicomonas and was most closely related to Endozoicomonas atrinae WP70T with sequence similarity of 96.7 %. Strain Acr-14T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the predominant fatty acids. The predominant isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain Acr-14T was 49.1 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrated that strain Acr-14T should be classified as a novel species of the genus Endozoicomonas, for which the name Endozoicomonas acroporae sp. nov. is presented. The type strain is Acr-14T (=BCRC 80922T=LMG 29482T=KCTC 42901T).

Thalassotalea euphylliae sp. nov., isolated from the torch coral Euphyllia glabrescens.

Strain Eup-16T, isolated from the torch coral Euphyllia glabrescens, was characterized using a polyphasic taxonomy approach. Cells of strain Eup-16T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, contained poly-ß-hydroxybutyrate, rod-shaped and formed pale yellow colonies. Optimal growth occurred at 25-30 °C, pH 7.5-9 and in the presence of 1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Eup-16T belonged to the genus Thalassotalea and was most closely related to Thalassotalea montiporae CL-22T with sequence similarity of 98.4 %. Strain Eup-16T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C16 : 0 and C17 : 1ω8c as the predominant fatty acids. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of strain Eup-16T was 43.2 mol%. The DNA-DNA hybridization value for strain Eup-16T with T. montiporae CL-22T was less than 34 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain Eup-16T should be classified as a representative of a novel species of the genus Thalassotalea, for which the name Thalassotalea euphylliae sp. nov. is presented. The type strain is Eup-16T (=BCRC 80910T=LMG 29001T=KCTC 42743T).

Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness.

BACKGROUND: Estimating the number of different species (richness) in a mixed microbial population has been a main focus in metagenomic research. Existing methods of species richness estimation ride on the assumption that the reads in each assembled contig correspond to only one of the microbial genomes in the population. This assumption and the underlying probabilistic formulations of existing methods are not useful for quasispecies populations where the strains are highly genetically related. RESULTS: On benchmark data sets, our estimation method provided accurate richness estimates (< 0.2 median estimation error) and improved the precision of ViQuaS by 2%-13% and F-score by 1%-9% without compromising the recall rates. We also demonstrate that our estimation method can be used to improve the precision and F-score of ShoRAH by 0%-7% and 0%-5% respectively. CONCLUSIONS: The proposed probabilistic estimation method can be used to estimate the richness of viral populations with a quasispecies behavior and to improve the accuracy of the quasispecies spectra reconstructed by the existing methods ViQuaS and ShoRAH in the presence of a moderate level of technical sequencing errors. AVAILABILITY: http://sourceforge.net/projects/viquas/.

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics.

BACKGROUND: Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. RESULTS: In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. CONCLUSIONS: Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.