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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]

Objective: This is a retrospective study of adverse events associated with preoperative computed tomography (CT)–guided hookwire or coil localisation. We analysed the experience and process flaws in resecting ground-glass nodules (GGNs) through video-assisted thoracoscopic surgery (VATS) and determined the remedial strategy. Methods: Adverse events were evaluated in 40 patients with 45 GGNs who underwent CT-guided hookwire or coil localisation before VATS. For lesions not successfully marked or detected, palpation, resection of the highly suspected area, segmentectomy or lobectomy was performed. Results: Among all adverse events, 15 were dislodgement of the marking materials, 5 were breakaway of the marking materials, 7 were > 2 cm distance between the lesions and the tips, 3 was marking material across the two adjacent lobes, 15 were pneumothorax and 2 were certain parts of marking materials stuck into the chest wall. All GGNs were resected successfully. 20 lesions were detected by palpation. 9 GGNs were discovered after the resection of highly suspected areas. Segmentectomies and lobectomies were performed directly on 7 and 9 GGNs, respectively. Conclusions: When adverse events occur, a second intraoperative localisation, by resecting the highly suspected area either through non-anatomical resection (wedge resection) or anatomical resection (segmentectomy or lobectomy) using the VATS should be considered the alternatives for GGNs localization. [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]

β-thymosins, a family of highly conserved peptides, play a vital role in wound-healing, angiogenesis, antimicrobial process and antiviral immunity. Three novel β-thymosin-repeat proteins, named mjthm4, mjthm3 and mjthm2, were cloned from Marsupenaeus japonicus using expressed sequence tags (EST) from suppression subtractive hybridization. The mjthm4, mjthm3 and mjthm2 cDNAs possessed open reading frames that encoded 166, 128 and 90 amino acid residue polypeptides and contained four, three and two β-thymosin actin binding modules, respectively. Blast analysis demonstrated that mjthm4, mjthm3 and mjthm2 shared high homology with known invertebrate multi-repeat β-thymosins. These proteins are ubiquitously expressed in all of the examined tissues, and the transcriptional levels were highest in the intestine. Further investigation revealed that mjthm4, mjthm3 and mjthm2 were remarkably up-regulated 6 h after WSSV infection. Moreover, while mjthm4 transcriptional levels displayed no changes, mjthm3 and mjthm2 levels decreased in the virus-resistant shrimps. The results indicate that mjthm4, mjthm3 and mjthm2 are novel multi-repeat β-thymosin homologues, have a close relationship with WSSV infection, and might contribute to a better understanding of host defense and/or virus invasion interactions in shrimps. [ABSTRACT FROM AUTHOR]

The low biomass in environmental samples is a major challenge for microbial metagenomic studies. The amplification of a genomic DNA was frequently applied to meeting the minimum requirement of the DNA for a high-throughput next-generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms is examined. The DNA template of 10 pg in each reaction of the MALBAC amplification may generate enough DNA for Illumina sequencing. Using 10 pg and 100 pg templates for each reaction set, the MALBAC kit shows a stable and homogeneous amplification as indicated by the highly consistent coverage of the reads from the two amplified samples on the contigs assembled by the original unamplified sample. Although GenomePlex whole genome amplification kit allows one to generate enough DNA using 100 pg of template in each reaction, the minority of the mixed bacterial species is not linearly amplified. For both of the kits, the GC-rich regions of the genomic DNA are not efficiently amplified as suggested by the low coverage of the contigs with the high GC content. The high efficiency of the MALBAC kit is supported for the amplification of environmental microbial DNA samples, and the concerns on its application are also raised to bacterial species with the high GC content. [ABSTRACT FROM AUTHOR]