Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota

Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae

Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse Thermoproteota. Despite their prevalence in high-temperature submarine communities, Thermoproteota are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the Aeropyrum-Thermodiscus-Caldisphaera. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the Aeropyrum-Thermodiscus-Caldisphaera. At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. Tiamatella incendiivivens, Hestiella acidicharens and Calypsonella navitae. A fourth genus was also identified related to Thermodiscus maritimus, for which no available sequenced genome exists. We propose the novel species Thermodiscus eudorianus to describe our high-quality Thermodiscus MAG, which represents the type genome for the genus. All three novel genera and T. eudorianus are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some Tiamatella, Calypsonella and T. eudorianus may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, Hestiella, may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family Acidilobaceae be amended to include Caldisphaera, Aeropyrum, Thermodiscus and Stetteria and the novel genera described here.

A first report on prokaryotic diversity in northwestern Arafura deep-sea sediments, Indonesia

Indonesia's deep-sea microbial communities remain poorly understood, prompting the need for comprehensive investigations. This study aimed to assess the bacterial and archaeal diversities in northwestern Arafura deep-sea sediments, spanning depths of 100 to 1,457 m using a 16S rRNA based-metagenomic sequencing approach, without technical and biological replicates. Principal component analyses based on the Bray-Curtis dissimilarity index indicated that most of the bacterial and archaeal communities were habitat-specific and influenced by depth. The most prevalent known bacterial phylotypes were detected from all samples belonging to the phylum of Desulfobacteriota, Pseudomonadota, and Firmicutes. In addition, the samples also harbored diverse members of the Archaea domain, including Crenarchaeota, Nanoarchaeota and Haloarchaeota. Notably, the sequencing data revealed the significant presence of rare prokaryotic taxa, including uncultured counterparts with less than 1% abundance. The findings suggest that novel and rare prokaryotic taxa are abundant in northwestern Arafura deep-sea ecosystem, offering unique opportunities for further bioprospecting and functional ecology studies.

Current knowledge and clinical perspectives for a unique new phylum: Nanaorchaeota

Nanoarchaea measuring less than 500 nm and encasing an average 600-kb compact genome have been studied for twenty years, after an estimated 4193-million-year evolution. Comprising only four co-cultured representatives, these symbiotic organisms initially detected in deep-sea hydrothermal vents and geothermal springs, have been further distributed in various environmental ecosystems worldwide. Recent isolation by co-culture of Nanopusillus massiliensis from the unique ecosystem of the human oral cavity, prompted us to review the evolutionary diversity of nanaorchaea resulting in a rapidly evolving taxonomiy. Regardless of their ecological niche, all nanoarchaea share limited metabolic capacities correlating with an obligate ectosymbiotic or parasitic lifestyle; focusing on the dynamics of nanoarchaea-bacteria nanoarchaea-archaea interactions at the morphological and metabolic levels; highlighting proteins involved in nanoarchaea attachment to the hosts, as well metabolic exchanges between both organisms; and highlighting clinical nanoarchaeology, an emerging field of research in the frame of the recent discovery of Candidate Phyla radiation (CPR) in human microbiota. Future studies in clinical nanobiology will expand knowledge of the nanaorchaea repertoire associated with human microbiota and diseases, to improve our understanding of the diversity of these nanoorganims and their intreactions with microbiota and host tissues.

Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speciation

Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.

Methanocaldococcus lauensis sp. nov., a novel deep-sea hydrothermal vent hyperthermophilic methanogen

Three hyperthermophilic methanogens, designated strain SG7T, strain SG1 and strain SLH, were isolated from the ABE and Tu’i Malila deep-sea hydrothermal vent fields along the Eastern Lau Spreading Center. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strains SG7T, SG1 and SLH were affiliated with the genus Methanocaldococcus within the family Methanocaldococcaceae , order Methanococcales . They shared 95.5–99.48 % 16S rRNA gene sequence similarity to other Methanocaldococcus species and were most closely related to Methanocaldococcus bathoardescens . Cells of strains SG7T, SG1 and SLH were cocci, with a diameter of 1.0–2.2 µm. The three strains grew between 45 and 93 °C (optimum, 80–85 °C), at pH 5.0–7.1 (optimum pH 6.2) and with 10–50 g l−1 NaCl (optimum 20–25 g l−1). Genome analysis revealed the presence of a 5.1 kbp plasmid in strain SG7T. Based on the results of average nucleotide identity and digital DNA–DNA hybridization analyses, we propose that strains SG1 and SG7T are representatives of a novel species, for which the name Methanocaldococcus lauensis sp. nov. is proposed; the type strain is SG7T (=DSM 109608T=JCM 39049T).

Generation and application of pseudo-long reads for metagenome assembly

BACKGROUND

Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.

RESULTS

In this study, we present a new method called PLR-GEN. It creates pseudo-long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo-long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo-long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes.

CONCLUSIONS

PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.

Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding

AIMS

The aim was to characterize indigenous microorganisms in oil reservoirs after polymer flooding (RAPF).

METHODS

The microbial communities in the crude oil phase (Oil) and in the filter-graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1~0.22 μm) were investigated by 16S rRNA gene high-throughput sequencing.

RESULTS

Indigenous microorganisms related to hydrocarbon degradation prevailed in the three phases of each well. However, obvious differences of bacterial compositions were observed among the three phases of the same well and among the same phase of different wells. The crude oil and Aqu0.22 shared many dominant bacteria. Aqu0.1 contained a unique bacterial community in each well. Most bacteria in Aqu0.1 were affiliated to culturable genera, suggesting that they may adapt to the oil reservoir environment by reduction of cell size. Contrary to the bacterial genera, archaeal genera were similar in the three phases but varied in relative abundances. The observed microbial differences may be driven by specific environmental factors in each oil well.

CONCLUSIONS

The results suggest an application potential of microbial enhanced oil recovery (MEOR) technology in RAPF. The crude oil and Aqu0.1 contain many different functional microorganisms related to hydrocarbon degradation. Both should not be overlooked when investing and exploring the indigenous microorganisms for MEOR.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work facilitates the understanding of microbial community structures in RAPF and provides information for microbial control in oil fields.

Introducing clinical nanorachaeaology: Isolation by co-culture of Nanopusillus massiliensis sp. nov

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The first ever detection in human microbiota of nanoarchaea.

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Detection and co-isolation of nanoarchaea new species in human oral microbiota.

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These data suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology.

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Extended our knowledge of human microbiota diversity.

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Opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.

Background

Nanoarchaeota, obligate symbiont of some environmental archaea with reduced genomes, have been described in marine thermal vent environments, yet never detected in hosts, including humans.

Methods

Here, using laboratory tools geared towards the detection of nanoarchaea including PCR-sequencing, WGS, microscopy and culture.

Results

We discovered a novel nanoarchaea, Nanopusillus massiliensis, detected in dental plate samples by specific PCR-based assays. Combining fluorescent in situ hybridization (FISH) with scanning electron microscopy disclosed close contacts between N. massiliensis and the archaea Methanobrevibacter oralis in these samples. Culturing one sample yielded co-isolation of M. oralis and N. massiliensis with a 606,935-bp genome, with 23.6% GC encoded 16 tRNA, 3 rRNA and 942 coding DNA sequences, of which 400 were assigned to clusters of orthologous groups.

Conclusion

The discovery of N. massiliensis, made publicly available in collection, extended our knowledge of human microbiota diversity, opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.

Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems.

Community composition and functional prediction of prokaryotes associated with sympatric sponge species of southwestern Atlantic coast

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 São 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.

The coenzyme/protein pair and the molecular evolution of life

Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.

Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents

The structure and function of microbial communities inhabiting the subseafloor near hydrothermal systems are influenced by fluid geochemistry, geologic setting and fluid flux between vent sites, as well as biological interactions. Here, we used genome-resolved metagenomics and metatranscriptomics to examine patterns of gene abundance and expression and assess potential niche differentiation in microbial communities in venting fluids from hydrothermal vent sites at the Mid-Cayman Rise. We observed similar patterns in gene and transcript abundance between two geochemically distinct vent fields at the community level but found that each vent site harbours a distinct microbial community with differing transcript abundances for individual microbial populations. Through an analysis of metabolic pathways in 64 metagenome-assembled genomes (MAGs), we show that MAG transcript abundance can be tied to differences in metabolic pathways and to potential metabolic interactions between microbial populations, allowing for niche-partitioning and divergence in both population distribution and activity. Our results illustrate that most microbial populations have a restricted distribution within the seafloor, and that the activity of those microbial populations is tied to both genome content and abiotic factors.