Branched glycerol dibiphytanyl glycerol tetraethers (bGDGTs) are known as bacterial lipids that occur widely in terrestrial environments, particularly in anaerobic peat bogs and soil. We examined the abundance and distribution of bGDGTs in both core (C) and polar (P) lipid fractions from the water column and surface sediments in the lower Pearl River (PR) and its estuary using two extraction methods (sonication vs. Bligh and Dyer). A number of soil samples in the lower PR drainage basin were also collected and extracted for bGDGTs using the sonication method. The results showed aquatic production of bGDGTs as supported by substantial abundances of P-bGDGTs in the water column and sediment samples. The bGDGT-based proxies (BIT, CBT, and MBT) were not affected by the method of extraction when C-bGDGTs were analyzed; in such case, the pHCBT of the sediments reflected the soil pH of the lower PR drainage basin, and the temperature close to the annual mean air temperature (MAT) in the lower PR basin. On the other hand, the P-bGDGT-derived proxies were inconsistent between the two methods. The P-bGDGTs (particularly those extracted using the sonication method) may not be reliable indicators of annual MATs.
Surprisingly high rates of microbial respiration have recently been reported in hadal trench sediment, yet the potentially active microorganisms and specific microbe–microbe relationships in trench sediment are largely unknown. We investigated the bulk and active prokaryotic communities and co-occurrence interactions of different lineages in vertically sectioned sediment cores taken from the deepest points of the Mariana and Mussau Trenches. Analysis on species novelty revealed for the first time the high rate of novel lineages in the microbial communities of the hadal trenches. Using 95, 97, and 99% similarity as thresholds, averagely 22.29, 32.3, and 64.1% of total OTUs retrieved from sediments of the two trenches were identified as the potentially novel lineages, respectively. The compositions of the potentially active communities, revealed via ribosomal RNA (rRNA), were significantly different from those of bulk communities (rDNA) in all samples from both trenches. The dominant taxa in bulk communities generally accounted for low proportions in the rRNA libraries, signifying that the abundance was not necessarily related to community functions in the hadal sediments. The potentially active communities showed high diversity and composed primarily of heterotrophic lineages, supporting their potential contributions in organic carbon consumption. Network analysis revealed high modularity and non-random co-occurrence of phylogenetically unrelated taxa, indicating highly specified micro-niches and close microbial interactions in the hadal sediments tested. Combined analysis of activity potentials and network keystone scores revealed significance of phyla Chloroflexi and Gemmatimonadetes, as well as several potentially alkane-degrading taxa in maintaining microbial interactions and functions of the trench communities. Overall, our results demonstrate that the hadal trenches harbor diverse, closely interacting, and active microorganisms, despite the extreme environmental conditions.
A novel heterotrophic, Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain NBT06-6, was isolated from the deep seawater in the New Britain Trench and characterized phylogenetically and phenotypically. Optimal bacterial growth occurred at 35 °C (range 22-41 °C), at pH 6 (4-8) and with 4 % (w/v) NaCl (0-10 %). The strain grew at hydrostatic pressures of 0.1-100 MPa (optimum, 0.1 MPa) at 35 °C. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain NBT06-6 belonged to the genus Corynebacterium, with the highest sequence similarity (97.9 %) to Corynebacterium imitans, and shared low 16S rRNA gene sequence similarities (<97.0 %) with other type strains. The major respiratory menaquinones were MK-8(H2) and MK-9(H2). The polar lipids were diphosphatidyglycerol, phosphatidylglycerol, phosphatidylinositol, three unidentified aminoglycolipids and four unidentified glycolipids. The major fatty acids detected were C18 : 1ω9c, C16 : 0 and C15 : 0. Strain NBT06-6 contained meso-diaminopimelic acid and mycolic acids in its cell wall, and mannose, galactose, glucose, arabinose and ribose as major whole-cell sugars. The G+C content of the genomic DNA was 65.1 mol%. The digital DNA-DNA hybridization value and the average nucleotide identity between strain NBT06-6 and C. imitans were 24.5±2.4 and 81.9 %, respectively. The combined genotypic and phenotypic data indicated that strain NBT06-6 represents a novel species of the genus Corynebacterium, for which the name Corynebacterium hadale sp. nov. is proposed, with the type strain NBT06-6 (=MCCC 1K03347=DSM 105365).
Background The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms. Results We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts’ nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat. Conclusion Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.
The Three Gorges Dam (TGD) of the Yangtze River, China, is one of the largest irrigation and hydroelectric engineering projects in the world. The effects of huge man-made projects like TGD on fauna and macrophyte are obvious, mainly through changes of water dynamics and flow pattern; however, it is less clear how microorganisms respond to such changes. This research was aimed to examine differences in microbial diversity at different seasons and locations (in front of and behind the TGD). In addition, differences between particle-attached and free-living communities were also examined. The community structures of total and potentially active microorganisms in the water columns behind and Production and hosting by Elsevier available at www.sciencedirect.com China University of Geosciences (Beijing) GEOSCIENCE FRONTIERS journal homepage: www.elsevier.com/locate/gsf GEOSCIENCE FRONTIERS 3 (3) (2012) 335e349 in front of the TGD were analyzed with the DNA-and RNA-based 16S rRNA gene phylogenetic approaches over three different seasons. Clone libraries of 16S rRNA genes were prepared after amplification from extracted DNA and, for some samples, after preparing cDNA from extracted rRNA. Differences were observed between sites at different seasons and between free-living and particle-attached communities. Both bacterial and archaeal communities were more diverse in summer than in winter, due to higher nutrient levels and warmer temperature in summer than in winter. Particle-attached microorganisms were more diverse than free-living communities, possibly because of higher nutrient levels and heterogeneous geochemical micro-environments in particles. Spatial variations in bacterial community structure were observed, i.e., the water reservoir behind the TGD (upstream) hosted more diverse bacterial populations than in front of the dam (downstream), because of diverse sources of sediments and waters from upstream to the reservoir. These results have important implications for our understanding of responses of microbial communities to environmental changes in river ecosystems affected by dam construction. ª 2011, China University of Geosciences (Beijing) and Peking University. Production and hosting by Elsevier B.V. All rights reserved.
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