MASH-Ocean 1.0: Interactive platform for investigating microbial diversity, function, and biogeography with marine metagenomic data.

A large number of oceanic metagenomic data and environmental metadata have been published. However, most studies focused on limited ecosystems using different analysis tools, making it challenging to integrate these data into robust results and comprehensive global understanding of marine microbiome. Here, we constructed a systematic and quantitative analysis platform, the Microbiome Atlas/Sino-Hydrosphere for Ocean Ecosystem (MASH-Ocean: https://www.biosino.org/mash-ocean/), by integrating global marine metagenomic data and a unified data processing flow. MASH-Ocean 1.0 comprises 2147 metagenomic samples with five analysis modules: sample view, diversity, function, biogeography, and interaction network. This platform provides convenient and stable support for researchers in microbiology, environmental science, and biogeochemistry, to ensure the integration of omics data generated from hydrosphere ecosystems, to bridge the gap between elusive omics data and biological, ecological, and geological discovery, ultimately to foster the formation of a comprehensive atlas for aquatic environments.

Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis.

Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.

The Cambrian microfossil Qingjiangonema reveals the co-evolution of sulfate-reducing bacteria and the oxygenation of Earth's surface.

Sulfate reduction is an essential metabolism that maintains biogeochemical cycles in marine and terrestrial ecosystems. Sulfate reducers are exclusively prokaryotic, phylogenetically diverse, and may have evolved early in Earth's history. However, their origin is elusive and unequivocal fossils are lacking. Here we report a new microfossil, Qingjiangonema cambria, from ∼518-million-year-old black shales that yield the Qingjiang biota. Qingjiangonema is a long filamentous form comprising hundreds of cells filled by equimorphic and equidimensional pyrite microcrystals with a light sulfur isotope composition. Multiple lines of evidence indicate Qingjiangonema was a sulfate-reducing bacterium that exhibits similar patterns of cell organization to filamentous forms within the phylum Desulfobacterota, including the sulfate-reducing Desulfonema and sulfide-oxidizing cable bacteria. Phylogenomic analyses confirm separate, independent origins of multicellularity in Desulfonema and in cable bacteria. Molecular clock analyses infer that the Desulfobacterota, which encompass a majority of sulfate-reducing taxa, diverged ∼2.41 billion years ago during the Paleoproterozoic Great Oxygenation Event, while cable bacteria diverged ∼0.56 billion years ago during or immediately after the Neoproterozoic Oxygenation Event. Taken together, we interpret Qingjiangonema as a multicellular sulfate-reducing microfossil and propose that cable bacteria evolved from a multicellular filamentous sulfate-reducing ancestor. We infer that the diversification of the Desulfobacterota and the origin of cable bacteria may have been responses to oxygenation events in Earth's history.

Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle.

Photosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction center appears in at least six Myxococcota families from three classes, suggesting vertical inheritance of these genes from an early common ancestor, with multiple independent losses in other lineages. Analysis of metatranscriptomic datasets indicate that the putative myxococcotal photosynthesis genes are actively expressed in various natural environments. Furthermore, heterologous expression of myxococcotal pigment biosynthesis genes in a purple bacterium supports that the genes can drive photosynthetic processes. Given that predatory abilities are thought to be widespread across Myxococcota, our results suggest the intriguing possibility of a chimeric lifestyle (combining predatory and photosynthetic abilities) in members of this phylum.

A systematic analysis of marine lysogens and proviruses.

Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.

Renaissance for magnetotactic bacteria in astrobiology.

Capable of forming magnetofossils similar to some magnetite nanocrystals observed in the Martian meteorite ALH84001, magnetotactic bacteria (MTB) once occupied a special position in the field of astrobiology during the 1990s and 2000s. This flourish of interest in putative Martian magnetofossils faded from all but the experts studying magnetosome formation, based on claims that abiotic processes could produce magnetosome-like magnetite crystals. Recently, the rapid growth in our knowledge of the extreme environments in which MTB thrive and their phylogenic heritage, leads us to advocate for a renaissance of MTB in astrobiology. In recent decades, magnetotactic members have been discovered alive in natural extreme environments with wide ranges of salinity (up to 90 g L-1), pH (1-10), and temperature (0-70 °C). Additionally, some MTB populations are found to be able to survive irradiated, desiccated, metal-rich, hypomagnetic, or microgravity conditions, and are capable of utilizing simple inorganic compounds such as sulfate and nitrate. Moreover, MTB likely emerged quite early in Earth's history, coinciding with a period when the Martian surface was covered with liquid water as well as a strong magnetic field. MTB are commonly discovered in suboxic or oxic-anoxic interfaces in aquatic environments or sediments similar to ancient crater lakes on Mars, such as Gale crater and Jezero crater. Taken together, MTB can be exemplary model microorganisms in astrobiology research, and putative ancient Martian life, if it ever occurred, could plausibly have included magnetotactic microorganisms. Furthermore, we summarize multiple typical biosignatures that can be applied for the detection of ancient MTB on Earth and extraterrestrial MTB-like life. We suggest transporting MTB to space stations and simulation chambers to further investigate their tolerance potential and distinctive biosignatures to aid in understanding the evolutionary history of MTB and the potential of magnetofossils as an extraterrestrial biomarker.

Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution.

It has been proposed that early bacteria, or even the last universal common ancestor of all cells, were thermophilic. However, research on the origin and evolution of thermophily is hampered by the difficulties associated with the isolation of deep-branching thermophilic microorganisms in pure culture. Here, we isolate a deep-branching thermophilic bacterium from a deep-sea hydrothermal vent, using a two-step cultivation strategy ("Subtraction-Suboptimal", StS) designed to isolate rare organisms. The bacterium, which we name Zhurongbacter thermophilus 3DAC, is a sulfur-reducing heterotroph that is phylogenetically related to Coprothermobacterota and other thermophilic bacterial groups, forming a clade that seems to represent a major, early-diverging bacterial lineage. The ancestor of this clade might be a thermophilic, strictly anaerobic, motile, hydrogen-dependent, and mixotrophic bacterium. Thus, our study provides insights into the early evolution of thermophilic bacteria.

Key Molecules in Bladder Cancer Affect Patient Prognosis and Immunotherapy Efficacy: Further Exploration for CNTN1 and EMP1.

PURPOSE: Immunotherapy has been widely used in bladder cancer (BCa) in recent years and has significantly improved the prognosis of patients with BCa. However, further identification of immunotherapy-sensitive individuals to improve the efficacy of immunotherapy remains an important unmet need. MATERIALS AND METHODS: The key genes were screened and identified from Gene Expression Omnibus database and The Cancer Genome Atlas database to construct the risk prediction function (risk scores). Real-time polymerase chain reaction, immunohistochemistry, and IMvigor210 data sets were used to verify the roles of key molecules and efficacy of risk scores. The biologic function of CNTN1 and EMP1 was further explored through cell proliferation experiments. RESULTS: Five key genes, CNTN1, MAP1A, EMP1, MFAP5, and PTGIS, which were significantly related to the prognosis and immune checkpoint molecules of patients, were screened out. CNTN1 and EMP1 were further experimentally confirmed for their significant tumor-promoting effects. Besides, the constructed risk scores on the basis of these five key genes can accurately predict the prognosis and immunotherapy efficacy of patients with BCa. Interestingly, the high-risk patients identified by the risk scores have significantly worse prognosis and immunotherapy effects than low-risk patients. CONCLUSION: The key genes we screened can affect the prognosis of BCa, tumor microenvironment immune infiltration, and the efficacy of immunotherapy. The risk scores tool we constructed will contribute to the development of individualized treatment for BCa.

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment.

Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution, and ecological functions remains poorly constrained. Here, we present the largest dataset of Bathyarchaeia metagenome assembled genome to date and reclassify Bathyarchaeia into eight order-level units corresponding to the former subgroup system. Highly diversified and versatile carbon metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ~3.3 billion years, followed by three major diversifications at ~3.0, ~2.5, and ~1.8 to 1.7 billion years, likely driven by continental emergence, growth, and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ~300 million years perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary history of Bathyarchaeia potentially has been shaped by geological forces, which, in turn, affected Earth's surface environment.

Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments.

BACKGROUND: A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited. RESULTS: Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete ß-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, 13C-labeled acetate was produced in the incubations when 13C-labeled dissolved inorganic carbon was provided. CONCLUSIONS: Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.

Treatment options and prognostic risk factors for urachal carcinoma: A multicetnter retrospective study.

PURPOSE: Urachal carcinoma (UC) is a rare genitourinary cancer with an insidious onset, high risk of recurrence, and a poor prognosis. Surgical resection alone has difficulty in controlling the tumor. We aim to explore treatment options and prognostic risk factors for UC based on a multicenter cohort and long-term follow-up database. MATERIALS AND METHODS: The clinical data, treatment and follow-up results of 163 patients with UC in 6 medical centers were analyzed retrospectively. Kaplan-Meier analysis and a Cox proportional hazards model were used to assess the treatment options and prognostic risk factors for UC. RESULTS: Kaplan-Meier analysis showed no difference in the 5-year recurrence-free survival rate (P =0.282) or overall survival rate (P =0.673) between extended partial cystectomy (EPC) and radical cystectomy (RC) for patients at stage III and below. Whether bilateral pelvic lymph nodes were dissected was also not significantly correlated with the patient's recurrence (P =0.921) or prognosis (P =0.741). Postoperative adjuvant chemotherapy significantly reduced the recurrence rate of patients with stage Ⅲb or below (P =0.005). Combined treatment of postoperative recurrence patients prolonged the survival time of patients compared with single chemotherapy or conservative treatment (34.022±5.031 vs. 12.837±2.349 or 6.192±0.875 months, P <0.001). Kaplan-Meier and univariate Cox regression analyses showed that age >55 years, Sheldon stage, carbohydrate antigen 19-9 (CA19-9) >9.935 U/mL, carbohydrate antigen 72-4 (CA724) >6.02 U/mL, and postoperative adjuvant chemotherapy were closely related to the overall survival and recurrence-free survival of patients (P <0.05). Multivariate Cox proportional hazard regression confirmed that the Sheldon stage and CA724 >6.02 U/mL were independent recurrence risk factors. CONCLUSIONS: EPC or RC provides similar oncologic results for UC, but bilateral pelvic lymph node dissection is not necessary in early-stage patients. Postoperative adjuvant chemotherapy can significantly reduce the recurrence rate, and combination therapy may provide better survival outcomes. CA724 can predict tumor recurrence or metastasis at an early stage.

Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics.

Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. Bathyarchaeia, which are among the most abundant microorganisms in marine sediment, have been proposed to mediate anaerobic lignin degradation. However, the mechanism of bathyarchaeial lignin degradation remains unclear. Here, we report an enrichment culture of Bathyarchaeia, named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001 (Ca. B. ligniniphilus), from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions. Ca. B. ligniniphilus possesses and highly expresses novel methyltransferase 1 (MT1, mtgB) for transferring methoxyl groups from lignin monomers to cob(I)alamin. MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages. Heterologous expression of the mtgB gene confirmed O-demethylation activity. The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments, and they were highly expressed in coastal sediments from the East China Sea. These findings suggest that Bathyarchaeia, capable of O-demethylation via their novel and specific methyltransferases, are ubiquitous in coastal sediments.

Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.

Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.

Isolation of a Novel Thermophilic Methanogen and the Evolutionary History of the Class Methanobacteria.

Methanogens can produce methane in anaerobic environments via the methanogenesis pathway, and are regarded as one of the most ancient life forms on Earth. They are ubiquitously distributed across distinct ecosystems and are considered to have a thermophilic origin. In this study, we isolated, pure cultured, and completely sequenced a single methanogen strain DL9LZB001, from a hot spring at Tengchong in Southwest China. DL9LZB001 is a thermophilic and hydrogenotrophic methanogen with an optimum growth temperature of 65 °C. It is a putative novel species, which has been named Methanothermobacter tengchongensis-a Class I methanogen belonging to the class Methanobacteria. Comparative genomic and ancestral analyses indicate that the class Methanobacteria originated in a hyperthermal environment and then evolved to adapt to ambient temperatures. This study extends the understanding of methanogens living in geothermal niches, as well as the origin and evolutionary history of these organisms in ecosystems with different temperatures.

Rad54L promotes bladder cancer progression by regulating cell cycle and cell senescence.

Bladder cancer (BCa) is the most prevalent cancer of the urinary system, but its pathogenesis is still poorly understood. Several reports have suggested that gene damage repair is highly correlated with tumor development and drug resistance, in which homologous recombination repair gene Rad54L seems to play an important role, through yet unclear mechanisms. Therefore, this study stratified cancer patients by Rad54L expression in BCa tissue, and high Rad54L expression was associated with a poor prognosis. Mechanistically, we demonstrate that high Rad54L expression promotes abnormal bladder tumor cell proliferation by changing the cell cycle and cell senescence. In addition, this study also suggests that Rad54L may be associated with p53, p21, and pRB in BCa tissue. In summary, this study exposes Rad54L as potential a prognostic biomarker and precision treatment target in BCa.

Optimization of prostate cancer patient lymph node staging via the integration of neutrophil-lymphocyte ratios, platelet-lymphocyte ratios, and 68 Ga-PSMA-PET-derived SUVmax values.

BACKGROUND: At present, standardized parameters for quantitatively evaluating 68 Ga-PSMA-PET/CT outcomes when diagnosing lymph node metastasis in prostate cancer patients are lacking. Inflammatory hematological biomarkers offer value as robust predictors of certain cancer-related outcomes. The present study was thus developed to explore approaches to improving the utility of 68 Ga-PSMA-PET/CT for diagnosing lymph node metastasis through the combined evaluation of inflammatory hematological markers in prostate cancer patients. METHODS: Pretreatment patient details including age, initial TPSA levels, hematological findings, biopsy pathology results (Gleason score and ISUP grouping), radical pathology results, and imaging details were collected. Optimal cutoff values for each predictor then being determined based upon Youden's index, with univariate and multivariate analyses were then used to identify independent predictors of lymph node metastasis and used to construct a nomogram. RESULT: Independent predictors of lymph node metastasis in this patient cohort included SUVmax (odds ratio [OR]: 30.549, 95% confidence interval [CI]: 10.855-85.973, p < 0.001), neutrophil-lymphocyte ratio (OR:8.221, 95%CI: 1.335-50.614, p = 0.023), platelet-lymphocyte ratio (OR:8.221, 95% CI: 1.335-50.614, p = 0.023), initial TPSA (OR:2.761, 95% CI: 1.132-6.733, p = 0.026), and clinical T-stage (T3 vs. T2, OR:11.332, 95% CI:3.929-32.681, p < 0.001; T4 vs. T2, OR:9.101, 95% CI:1.962-42.213, p = 0.005), with corresponding optimal cutoff values of 2.3 (area under the curve [AUC]: 0.873, sensitivity: 0.736, specificity: 0.902), 1.72 (AUC: 0.558, sensitivity: 0.529, specificity: 0.643), 83.305 (AUC: 0.651, sensitivity: 0.299, specificity: 0.979), and 21.875 (AUC: 0.672, sensitivity: 0.736, specificity: 0.601). Subsequent nomogram construction was associated with good predictive ability, with a C-index of 0.887(95% CI: 0.793-0.981) and an AUC of 0.924 (95% CI: 0.882-0.965). CONCLUSION: SUVmax, the neutrophil-lymphocyte ratio, the platelet-lymphocyte ratio, initial TPSA, and clinical T-stage represent valuable independent predictors of lymph node metastasis in prostate cancer patients, offering an opportunity to further optimize lymph node staging for these patients.

Clinical implications of 3D printing technology in preoperative evaluation of partial nephrectomy. / 3D打印技术应用于肾部分切除术术前评估中的临床意义.

OBJECTIVES: Renal cancer is a common malignancy of the urinary system, and the partial nephrectomy is a common surgical modality for early renal cancer. 3D printing technology can create a visual three-dimensional model by using 3D digital models of the patient's imaging data. With this model, surgeons can perform preoperative assessment to clarify the location, depth, and blood supply of the tumor, which helps to develop preoperative plans and achieve better surgical outcomes. In this study, the R.E.N.A.L scoring system was used to stratify patients with renal tumors and to explore the clinical application value of 3D printing technology in laparoscopic partial nephrectomy. METHODS: A total of 114 renal cancer patients who received laparoscopic partial nephrectomy in Xiangya Hospital from June 2019 to December 2020 were enrolled. The patients were assigned into an experimental group (n=52) and a control group (n=62) according to whether 3D printing technology was performed, and the differences in perioperative parameters between the 2 groups were compared. Thirty-nine patients were assigned into a low-complexity group (4-6 points), 32 into a moderate-complexity group (7-9 points), and 43 into a high-complexity group (10-12 points) according to R.E.N.A.L score, and the differences in perioperative parameters between the experimental group and the control group in each score group were compared. RESULTS: The experimental group had shorter operative time, renal ischemia time, and postoperative hospital stay (all P<0.05), less intraoperative blood loss (P=0.047), and smaller postoperative blood creatinine change (P=0.032) compared with the control group. In the low-complexity group, there were no statistically significant differences between the experimental group and the control group in operation time, renal ischemia time, intraoperative blood loss, postoperative blood creatinine changes, and postoperative hospital stay (all P>0.05). In the moderate- and high- complexity groups, the experimental group had shorter operative time, renal ischemia time, and postoperative hospital stay (P<0.05 or P<0.001), less intraoperative blood loss (P=0.022 and P<0.001, respectively), and smaller postoperative blood creatinine changes (P<0.05 and P<0.001, respectively) compared with the control group. CONCLUSIONS: Compared with renal tumor patients with R.E.N.A.L score<7, renal cancer patients with R.E.N.A.L score≥7 may benefit more from 3D printing assessment before undergoing partial nephrectomy.

Draft Genome Sequences of Four Bacterial Strains Isolated from Sediment of the South China Sea.

Here, we report the draft genome sequences of four bacterial isolates from sediment of the South China Sea. Three of the isolates belong to the class Alphaproteobacteria and encode complete SoxXAYZBCD gene clusters, related to thiosulfate oxidation, while one isolate belongs to the class Opitutae and possesses a total of 397 carbohydrate active enzymes (CAZymes), related to predicted polysaccharide degradation.

Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners.

The metabolism of methane in anoxic ecosystems is mainly mediated by methanogens and methane-oxidizing archaea (MMA), key players in global carbon cycling. Viruses are vital in regulating their host fate and ecological function. However, our knowledge about the distribution and diversity of MMA viruses and their interactions with hosts is rather limited. Here, by searching metagenomes containing mcrA (the gene coding for the α-subunit of methyl-coenzyme M reductase) from a wide variety of environments, 140 viral operational taxonomic units (vOTUs) that potentially infect methanogens or methane-oxidizing archaea were retrieved. Four MMA vOTUs (three infecting the order Methanobacteriales and one infecting the order Methanococcales) were predicted to cross-domain infect sulfate-reducing bacteria. By facilitating assimilatory sulfur reduction, MMA viruses may increase the fitness of their hosts in sulfate-depleted anoxic ecosystems and benefit from synthesis of the sulfur-containing amino acid cysteine. Moreover, cell-cell aggregation promoted by MMA viruses may be beneficial for both the viruses and their hosts by improving infectivity and environmental stress resistance, respectively. Our results suggest a potential role of viruses in the ecological and environmental adaptation of methanogens and methane-oxidizing archaea.

Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes.

The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.