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Deep-sea eukaryotic microorganisms play a vital role in degrading organic matter and geochemically cycling elements in the deep ocean. However, the impact of sampling methods on detection of these microorganisms under high hydrostatic pressure remains uncertain. In this study, we compared a traditional water sampling method using a Niskin bottle, an in situ microbial filtration and fixation method (ISMIFF), and a multiple in situ nucleic acid collection (MISNAC) method to exhibit differences in the community structures that were collected at ~590–3100 m in the South China Sea (SCS). The classification and biodiversity indices of 18S rDNA Illumina sequencing reads from the V9 variation region revealed higher diversity for MISNAC DNA absorption column samples compared to others. Importantly, the relative abundance of Ciliophora (19.49%), Copepoda (23.31%), and Diplonemea (10.67%) was higher in MISNAC adsorption column samples, while Retaria (48.86%) were dominant in the MISNAC membrane samples. This indicates that MISNAC columns might collect more DNA in situ for the naked protists, while Retaria with a carbonate shell were more likely retained on the membrane. In conclusion, MISNAC is an effective method for DNA collection of deep-sea eukaryotic microorganisms and provides valuable materials for studying deep-sea microbial ecosystems. [ABSTRACT FROM AUTHOR]

Summary: Reduced substrates produced by the serpentinization reaction under hydration of olivine may have fuelled biological processes on early Earth. To understand the adaptive strategies and carbon metabolism of the microbes in the serpentinizing ecosystems, we reconstructed 18 draft genomes representing dominant species of Omnitrophicaeota, Gammaproteobacteria and Methanobacteria from the Manleluag serpentinizing spring in Zambales, Philippines (hyperalkaline and rich in methane and hydrogen). Phylogenomics revealed that two genomes were affiliated with a candidate phylum NPL‐UPA2 and the references of all our genomes were derived from ground waters, hot springs and the deep biosphere. C1 metabolism appears to be widespread as most of the genomes code for methanogenesis, CO oxidation and CO2 fixation. However, likely due to the low CO2 concentration and election acceptors, the biomass in the spring was extremely low (<103 cell/ml). Various Na+ and K+ transporters and Na+‐driving ATPases appear to be encoded by these genomes, suggesting that nutrient acquisition, bioenergetics and normal cytoplasmic pH were dependent on Na+ and K+ pumps. Our results advance our understanding of the metabolic potentials and bioenergetics of serpentinizing springs and provide a framework of the ecology of early Earth. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Bacteria produce metamorphosis-associated contractile (MAC) structures to induce larval metamorphosis in Hydroides elegans. The distribution and diversity of mac gene homologs in marine environments are largely unexplored. In the present study mac genes were examined in marine environments by analyzing 101 biofilm and 91 seawater metagenomes. There were more mac genes in biofilms than in seawater, and substratum type, location, or sampling time did not affect the mac genes in biofilms. The mac gene clusters were highly diverse and often incomplete while the three MAC components co-occurred with other genes of different functions. Genomic analysis of four Pseudoalteromonas and two Streptomyces strains revealed the mac genes transfers among different microbial taxa. It is proposed that mac genes are more specific to biofilms; gene transfer among different microbial taxa has led to highly diverse mac gene clusters; and in most cases, the three MAC components function individually rather than forming a complex. [ABSTRACT FROM AUTHOR]

Highlights: [•] Adverse effects of antifouling compound butenolide were studied using marine medaka. [•] The active ingredient in SeaNine 211, DCOIT, was employed as positive control. [•] Butenolide induced transient, reversible biological effects on marine medaka. [•] Lower toxicity of butenolide on marine biota highlights its promising application. [•] The increased sensitivity of male medaka addresses the gender difference. [ABSTRACT FROM AUTHOR]

Background: The International Association for the Study of Lung Cancer (IASLC) proposed a novel grading system for invasive lung adenocarcinoma, but lymphatic invasion was not evaluated. Meanwhile, the scope of lymph node dissection in part-solid invasive lung adenocarcinoma (PSILA) is still controversial. Therefore, this study aims to explore preoperative risk factors for lymph node metastasis in PSILA, to provide reference for intraoperative dissection of lymph nodes., Methods: From 2018 to 2020, clinical data of patients (stage cN0) consecutively diagnosed as PSILA were retrospectively analyzed and classified according to the novel grading system. Logistic regression was conducted to screen the clinicopathological factors of lymph node metastasis in PSILA., Results: A large cohort of 960 patients with PSILA who underwent lobectomy or sub-lobectomy were enrolled. By logistic regression analyses, solid part size, bronchial cutoff sign, spiculation, and carbohydrate antigen 199 (CA199) were eventually identified as independent risk factors for lymph node metastasis, based on which a nomogram was built to preoperatively predict the risk of lymph node metastasis [area under the receiver operating characteristic curve (AUC)=0.858; concordance index = 0.857; best cutoff, 0.027]. This suggests that intraoperative systematic lymph node dissection is recommended when the predicted risk value exceeds 0.027. Reproducibility of the novel grading system was verified., Conclusions: The novel IASLC grading system was applicative in real world. The nomogram for preoperative prediction of lymph node metastasis may provide reference for the lymph node dissection strategy during PSILA surgeries., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Gao, Wang, Zuo, Zhang and Zhang.)

BACKGROUND Benign retrosternal thyroid goiters can become large enough to compress the trachea and result in tracheomalacia and stenosis. This retrospective study from a single surgical center aimed to study the surgical management of 48 patients with retrosternal goiter and tracheal stenosis diagnosed and treated from January 2017 to December 2021. MATERIAL AND METHODS All preoperative contrast-enhanced CT scans showed retrosternal goiter and tracheal stenosis. RG was classified into type I in 28 patients, type II in 12 patients, and type III in 8 patients. TS was classified into grade I in 31 patients, grade II in 11 patients, and grade III in 6 patients. All patients were referred for surgery. Clinicopathologic features and surgical outcomes were recorded. RESULTS All operations were successfully performed. There were 41 patients with transcervical incision, 4 with cervical incision+sternotomy, 2 with cervical incision and thoracoscopic surgery, and 1 with cervical incision and surgery via the subxiphoid approach. Two patients presented recurrent laryngeal nerve injury. One patient showed short-term hand and foot numbness. The patients were pathologically diagnosed as simple nodular goiter (n=27), nodular goiter combined with cystic change (n=6), adenomatous nodular goiter (n=10), and thyroid adenoma (n=5). There was no prominent tumor recurrence or gradual TS remission. CONCLUSIONS This study has highlighted that patients with retrosternal goiter and tracheal stenosis may have comorbidities and require a multidisciplinary approach to management. The choice of anesthesia, surgical approach, and maintenance of the airway during and after surgery should be individualized.

Purpose: Immune checkpoint inhibitors (ICIs) have been successfully used in many clinical trials related to immunotherapy. This study aimed to investigate the clinical efficacy of ICIs and prognostic factors in patients with resectable non-small cell lung cancer (NSCLC) following neoadjuvant therapy in the real world., Methods: A total of 170 consecutive patients were finally selected and divided into two groups: the preoperative chemotherapy group (n = 91) and the chemo-immunotherapy group (n = 79). The primary endpoint was disease-free survival (DFS). The secondary endpoints were pathological response, clinical response, pathological nodal disease, and ability of multivariate Cox regression analysis to predict survival. Survival was estimated using Kaplan-Meier method and compared using log-rank test., Results: There was a statistically significant difference in DFS between the two groups (log-rank test, P = 0.019). Multivariate Cox regression analysis showed that maximum tumor diameter (P = 0.016), higher lymph node stage (ypN1, P = 0.016; ypN2, P <0.001), and major pathological response not achieved (non-major pathological response [MPR], P = 0.011) were independent prognostic factors for worse DFS., Conclusion: Neoadjuvant chemo-immunotherapy yields better effects in pathological and clinical response than chemotherapy alone, which is also associated with longer DFS in the treatment of locally advanced NSCLC. Moreover, a larger tumor specimen diameter, higher ypN staging, and non-MPR after neoadjuvant therapy were associated with worse prognosis.

Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes and candidate phyla Patescibacteria and Marinimicrobia. Distinct dominant groups in the microbial communities were observed in trench-axis sediment (water depth >8,600 m), compared to the slopes of the Challenger Deep. A sampling site at the northern slope was enriched with archaea from mesophilic Euryarchaeota Marine Group II (MGII) as a biomarker of specific geochemical setting. Among archaeal community, Thaumarchaeota represented by Nitrosopumilus were dominant in the upper layers and diminished drastically in the deeper layers. " Ca . Woesearchaeota", however, became the dominant group in the deeper layers. Overall, our study provides a better understanding on the pattern of the microbial communities in the deepest hadal sediments on Earth, and highlights the extraordinary diversity still waiting to be discovered., Competing Interests: The authors declare that they have no competing interests.

Marine organisms in intertidal zones are subjected to periodical fluctuations and wave activities. To understand how microbes in intertidal biofilms adapt to the stresses, the microbial metagenomes of biofilms from intertidal and subtidal zones were compared. The genes responsible for resistance to metal ion and oxidative stresses were enriched in both 6-day and 12-day intertidal biofilms, including genes associated with secondary metabolism, inorganic ion transport and metabolism, signal transduction and extracellular polymeric substance metabolism. In addition, these genes were more enriched in 12-day than 6-day intertidal biofilms. We hypothesize that a complex signaling network is used for stress tolerance and propose a model illustrating the relationships between these functions and environmental metal ion concentrations and oxidative stresses. These findings show that bacteria use diverse mechanisms to adapt to intertidal zones and indicate that the community structures of intertidal biofilms are modulated by metal ion and oxidative stresses.

A Gram-negative, obligately anaerobic, non-spore-forming, long rod-shaped bacterium strain P2(T) was isolated from the offshore mangrove sediment of the South China Sea. Growth was observed at between 22 and 39 °C, with an optimum at 35 °C. The pH range for growth was 5.0-8.5, with an optimum around pH 7.0-7.5. Salt tolerance was determined between 0.2 and 3.5% (w/v), optimum at 0.5-1.0%. Catalase and oxidase activities were negative. Strain P2(T) utilized cysteine, lactate, pyruvate, yeast extract or H(2)/CO(2)+acetate as electron donors, and sulfate or sulfite as electron acceptors. Metabolism was strictly fermentative. The main organic fermentation products were propionate, acetate and succinate. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P2(T) formed a distinct evolutionary lineage within the family Marinilabiliaceae. Strain P2(T) was most closely related to members of the genera Alkaliflexus (92.0% 16S rRNA gene sequence similarity), Marinilabilia (91.7%) and Anaerophaga (89.9%) of the family Marinilabiliaceae. The DNA G+C content of the novel strain was 44.2 ± 1.0 mol%. The dominant fatty acids of strain P2(T) were iso-C(15:0) (33.5%), anteiso-C(15:0) (18.9%), C(16:0) (5.4%), C(16:0) 3-OH (7.7%) and iso-C(17:0) 3-OH (13.3%). The respiratory quinone was menaquinone 7 (100% of total quinone) and the major polar lipid was phosphatidylethanolamine. Strain P2(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of phylogenetic, phenotypic and physiological evidence, a novel genus, Mangroviflexus, is proposed to harbour strain P2(T) ( = CGMCC 1.5167(T) = DSM 24214(T)) which is described as the type strain of a novel species, Mangroviflexus xiamenensis gen. nov., sp. nov.

A taxonomic study was carried out on strain P1(T), which was isolated from mangrove sediment samples collected from Qinglan Port (Hainan, China). Cells were curved rods, that were motile, with a single polar flagellum. The strain was non-spore-forming with a cell size of 0.6×1.5-2.2 µm. Catalase and oxidase activities were not detected. Growth was observed in the temperature range 22-44 °C (optimum, 35-40 °C) and pH range 5.5-8.5 (optimum, pH 7.0). NaCl was required for growth and tolerated at up to 3.5% (w/v) (optimum, 0.5%). Strain P1(T) utilized hydrogen, succinate, L-malate, citrate, oxalate, DL-lactate, pyruvate, or cysteine as electron donors, and sulfate or sulfite as electron acceptors. Fermentation products from pyruvate were acetate, H(2) and CO(2). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P1(T) formed a distinct evolutionary lineage within the family Desulfovibrionaceae. Strain P1(T) was most closely related to members of the genera Desulfovibrio (92.0-94.3% 16S rRNA gene sequence similarity), Desulfocurvus (91.1%), Bilophila (87.9%) and Lawsonia (86.0%) of the family Desulfovibrionaceae. The DNA G+C content of strain P1(T) was 64.5 mol% and the major cellular fatty acids were iso-C(15:0) (18.8%), anteiso-C(15:0) (5.0%), C(16:0) (14.2%) and iso-C(17:1)ω9c (24.4%). The predominant menaquinone was MK-7 (97%). Major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Strain P1(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain P1(T) represents a novel species of a new genus, for which the name Desulfobaculum xiamenensis gen. nov., sp. nov. is proposed. The type strain of Desulfobaculum xiamenensis is P1(T) (=CGMCC 1.5166(T)=DSM 24233(T)).

Anaerophaga sp. strain HS1 was isolated from offshore hot spring sediment in Xiamen, China. It was identified as a novel, moderately thermophilic, strictly anaerobic bacterium affiliated with the family Marinilabiaceae and showed xylanase activity. Here, we describe the 3.88-Mb draft genome sequence of Anaerophaga sp. strain HS1 and the annotation analysis of related xylanase genes.

Thermococcus sp. strain 4557 is a hyperthermophilic anaerobic archaeon isolated from the deep-sea hydrothermal vent Guaymas Basin site in the Gulf of California at a depth of 2,000 m. Here, we present the complete genome sequence of Thermococcus sp. 4557, which consists of a single circular chromosome of 2,011,320 bp with a G+C content of 56.08%.