Yu-Shih Lin

Yu-Shih Lin
National Sun Yat-sen University | NSYSU · Department of Oceanography

PhD

About

88
Publications
9,245
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1,410
Citations
Introduction
Additional affiliations
December 2012 - present
National Sun Yat-sen University
Position
  • Professor

Publications

Publications (88)
Article
Shallow-water hydrothermal plumes concomitantly host both photosynthetic and chemoautotrophic organisms in a single biotope. Yet, rate measurements to quantify the contributions of different autotrophic activity types are scarce. Herein, we measured the light and dark dissolved inorganic carbon (DIC) uptake rates in the plume water of the Kueishant...
Article
A mesophilic, hydrogenotrophic methanogen, strain FWC-SCC2T, was isolated from deep-sea sediments collected by a real-time video multiple-corer at the C5-6 station near a cold seep at Four-Way Closure Ridge region during R/V Ocean Researcher III ORIII-1900 cruise in 2015. The cells were irregular cocci, non-motile and 0.8-1.2 µm in diameter. The me...
Article
Large eutrophic river plumes can lead to hypoxic near-bottom water during summer. However, how the carbonate system in this stratified water column varies at a daily to weekly scale is still unclear. At the end of the first severe El Niño Southern Oscillation event in the 21st century during 2015/2016, high temperature, high salinity water was obse...
Article
The particulate organic matter (POM) of shallow-water hydrothermal fields has been studied in the context of food web reconstruction, but the processes governing its biogeochemistry and dynamics are poorly explored. Here, we investigate the POM in the Kueishantao hydrothermal field using chemical and hydrodynamic approaches. The depletion of total...
Article
Full-text available
Sediment community oxygen consumption (SCOC) rates provide important information about biogeochemical processes in marine sediments and the activity of benthic microorganisms and fauna. Therefore, several databases of SCOC data have been compiled since the mid-1990s. However, these earlier databases contained much less data records and were not fre...
Article
Basin models can simulate geological, geochemical and geophysical processes and potentially also the deep biosphere, starting from a burial curve, assuming a thermal history and utilising other experimentally obtained data. Here we apply basin modelling techniques to model cell abundances within the deep coalbed biosphere off Shimokita Peninsula, J...
Article
Full-text available
With large topographic gradients, rifted basins serve as efficient traps for particulate matter from adjacent lands and the ocean surface. However, the fate of organic carbon in the sediment, mostly unaltered by the hydrothermal activities known to occur in young rifts, remains poorly understood. In this study, we present an examination of diagenet...
Article
Full-text available
Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotro...
Article
In this study, lignin-derived phenols, stable carbon isotopes and bulk elemental compositions were determined along the length of two sediment cores (C1 and C2) from the Andong salt marsh, which is located southwest of Hangzhou Bay, China. The purpose of this study was to determine the short-term changes and their implications along sediment profil...
Data
Odds ratios for the 37 single-copy housing-keeping genes between individual metagenomes and the average metagenome.
Data
Chao1 and Inverse Simpson estimators as a function of depth. Data points are mean values based on rarefaction at a standardized sequence count (n = 10,008) with bars indicating 95% confidence intervals.
Data
(a) Proportions of 16S rRNA gene amplicons related to methanogens and ANME members in environmental and incubated samples. (b) PCoA analysis for community variance among environmental and incubated samples.
Data
Relative abundances of gene families listed in Figure 3B. Abundances were calculated as read count per gene per base of gene length, and shown as a proportion against the abundance of the universal single-copy gene encoding RNA polymerase subunit B (rpoB).
Data
Accumulations of 13CO2 over time for incubations with different treatments. The dotted lines represent the regression of data points with R2 values shown in color corresponding to individual replicates or control.
Data
Phylogenetic tree of mcrA genes. Sequences retrieved from the metagenomes with a length of >300 bp are labeled in blue, whereas sequences previously reported for other cores in LGHMVs are labeled in green. The accession numbers of reference sequences are in brackets.
Article
Full-text available
Terrestrial mud volcanoes (MVs) are an important natural source of methane emission. The role of microbial processes in methane cycling and organic transformation in such environments remains largely unexplored. In this study, we aim to uncover functional potentials and community assemblages across geochemical transitions in a ferruginous, sulfate-...
Article
Lignin oxidation products, δ¹³C values, C/N ratios and particle size were used to investigate the sources, distribution and chemical stability of sedimentary organic matter (OM) along the Andong salt marsh located in the southwestern end of Hangzhou Bay, China. Terrestrial OM was highest at the upper marshes and decreased closer to the sea, and the...
Article
Methylated amines and sulfides are ubiquitous organic nitrogen and sulfur compounds in the marine environment and could serve as important energy substrates to methanogens inhabiting anoxic sediments. However, their abundance and isotopic values remain largely unconstrained in marine sediments. In this study, we investigated the distribution of tri...
Article
Subsurface sediments are among the largest, but also among the least understood ecosystems on Earth. However, novel analytical methods are contributing to constrain uncertainties regarding this unique environment. Here, the microbial community in subsurface sediments was investigated along a transect through the Benguela upwelling system from the o...
Article
Dissolved organic matter (DOM) in marine sediment pore waters derives largely from decomposition of particulate organic matter and its composition is influenced by various biogeochemical and oceanographic processes in yet undetermined ways. Here, we determine the molecular inventory of pore water DOM in marine sediments of contrasting depositional...
Article
Full-text available
Ocean margin sediments have been considered as important sources of dissolved organic carbon (DOC) to the deep ocean, yet the contribution from advective settings has just started to be acknowledged. Here we present evidence showing that near-surface heating of sediment in the Guaymas Basin, a young extensional depression, causes mass production an...
Article
Full-text available
Hydrocarbon vents have recently been reported to contribute considerable amounts of dissolved organic carbon (DOC) to the oceans. Many such hydrocarbon vents widely exist in the northern South China Sea (NSCS). To investigate if these hydrocarbon vent sites release DOC, we used a real-time video multiple-corer to collect bottom seawater and surface...
Article
Full-text available
Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was ind...
Article
Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carb...
Article
Full-text available
Amino sugars are quantitatively significant constituents of soil and marine sediment, but their sources and turnover in environmental samples remain poorly understood. The stable carbon isotopic composition of amino sugars can provide information on the lifestyles of their source organisms and can be monitored during incubations with labeled substr...
Article
Low-molecular-weight (LMW) alcohols are produced during the microbial degradation of organic matter from precursors such as lignin, pectin, and carbohydrates. The biogeochemical behavior of these alcohols in marine sediment is poorly constrained but potentially central to carbon cycling. Little is known about LMW alcohols in sediment pore waters be...
Data
Low-molecular-weight (LMW) alcohols are produced during the microbial degradation of organic matter from precursors such as lignin, pectin, and carbohydrates. The biogeochemical behavior of these alcohols in marine sediment is poorly constrained but potentially central to carbon cycling. Little is known about LMW alcohols in sediment pore waters be...
Article
The detection of intact phospholipids (PLs) in sedimentary extracts using liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) is commonly limited by ion suppression caused by complex matrices; the effect typically cannot be satisfactorily reduced using traditional column chromatographic cleanup procedures. We therefore imple...
Article
Ethane and propane are low molecular weight hydrocarbons observed widely at trace levels in cold marine sediments where thermogenic sources are considered insignificant, but their biological sources remain poorly constrained. In this study, several C-2 and C-3 compounds including alkenes, alcohols, thiols and carboxylic acids with a C-2 or C-3 skel...
Article
To understand Holocene climate evolutions in low-latitude region of the western Pacific, paired δ18O and Mg/Ca records of planktonic foraminifer Globigerinoides ruber (250-300 μm, sensu stricto, s.s.) from a marine core ORI715-21 (121.5° E, 22.7° N, water depth 760 m) underneath the Kuroshio Current (KC) off eastern Taiwan were analyzed. Over the p...
Article
Full-text available
Sediments of coastal upwelling areas are generally characterised by a high content of organic carbon that is mainly degraded via anaerobic microbial processes including sulfate reduction as a major terminal oxidation step. Despite the high importance of sulfate reduction in these sediments, the identity of sulfate-reducing bacteria (SRB) has remain...
Article
Full-text available
The methane-rich, hydrothermally heated sediments of the Guaymas Basin are inhabited by thermophilic microorganisms, including anaerobic methane-oxidizing archaea (mainly ANME-1) and sulfate-reducing bacteria (e.g., HotSeep-1 cluster). We studied the microbial carbon flow in ANME-1/ HotSeep-1 enrichments in stable-isotope-probing experiments with a...
Article
The membrane lipids diglycosyl-glycerol dibiphytanyl glycerol tetraethers (2G-GDGTs) in marine subsurface sediments are believed to originate from uncultivated benthic archaea, yet the production of 2G-GDGTs from subseafloor samples has not been demonstrated in vitro. In order to validate sedimentary biosynthesis of 2G-GDGTs, we performed a stable...
Article
Hydroxylated glycerol dialkyl glycerol tetraethers (hydroxy-GDGTs) were detected in marine sediments of diverse depositional regimes and ages. Mass spectrometric evidence, complemented by information gleaned from two-dimensional (2D) 1H–13C nuclear magnetic resonance (NMR) spectroscopy on minute quantities of target analyte isolated from marine sed...
Article
Molecular hydrogen (H2) is a central metabolite that couples organic matter degradation and terminal electron-accepting processes. H2 levels in natural environments are often regulated by microbial syntrophy; therefore, pore-water H2 concentration is a useful parameter for studying biogeochemical processes in sediments. However, little is known abo...
Technical Report
Integrated ocean Drilling Program (IODP) Expedition 337 was the first expedition dedicated to subseafloor microbiology that used riser drilling technology. IODP drill Site C0020 is located in a forearc basin formed by the subduction of the Pacific plate off the Shimokita Peninsula at a water depth of 1180 m. Seismic profiles strongly suggested the...
Data
Hydroxylated glycerol dialkyl glycerol tetraethers (hydroxy-GDGTs) were detected in marine sediments of diverse depositional regimes and ages. Mass spectrometric evidence, complemented by information gleaned from two-dimensional (2D) 1H-13C nuclear magnetic resonance (NMR) spectroscopy on minute quantities of target analyte isolated from marine sed...
Article
Glycolipids are prominent constituents in the membranes of cells from all domains of life. For example, diglycosyl-glycerol dibiphytanyl glycerol tetraethers (2Gly-GDGTs) are associated with methanotrophic ANME-1 archaea and heterotrophic benthic archaea, two archaeal groups of global biogeochemical importance. The hydrophobic biphytane moieties of...
Article
Full-text available
In anoxic environments, volatile methylated sulfides like methanethiol (MT) and dimethyl sulfide (DMS) link the pools of inorganic and organic carbon with the sulfur cycle. However, direct formation of methylated sulfides from reduction of dissolved inorganic carbon has previously not been demonstrated. When studying the effect of temperature on hy...
Article
We present high resolution profiles for the methane concentration and the carbon isotope composition of methane from surface sediments and from the sediment–water transition in the Black Sea. At shallow water sites methane migrates from the sediment into the water column, and the magnitude of this upward migrating flux depends on the depth of the s...
Article
Full-text available
We have studied the effects of slow infiltration of oxygen on microbial communities in refrigerated legacy samples from ocean drilling expeditions. Storage was in heat-sealed, laminated foil bags with a N2 headspace for geomicrobiological studies. Analysis of microbial lipids suggests that Bacteria were barely detectable in situ but increased remar...
Data
We have studied the effects of slow infiltration of oxygen on microbial communities in refrigerated legacy samples from ocean drilling expeditions. Storage was in heat-sealed, laminated foil bags with a N2 headspace for geomicrobiological studies. Analysis of microbial lipids suggests that Bacteria were barely detectable in situ but increased remar...
Data
We present high resolution profiles for the methane concentration and the carbon isotope composition of methane from surface sediments and from the sediment-water transition in the Black Sea. At shallow water sites methane migrates from the sediment into the water column, and the magnitude of this upward migrating flux depends on the depth of the s...
Article
Glycolipids are prominent constituents in the membranes of cells from all domains of life. For example, diglycosyl-glycerol dibiphytanyl glycerol tetraethers (2Gly-GDGTs) are associated with methanotrophic ANME-1 archaea and heterotrophic benthic archaea, two archaeal groups of global biogeochemical importance. The hydrophobic biphytane moieties of...
Article
In anoxic environments, volatile methylated sulfides like methanethiol (MT) and dimethyl sulfide (DMS) link the pools of inorganic and organic carbon with the sulfur cycle. However, direct formation of methylated sulfides from reduction of dissolved inorganic carbon has previously not been demonstrated. When studying the effect of temperature on hy...
Article
Full-text available
A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H2 and CO2, which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both th...
Conference Paper
Full-text available
We investigated the phylogenic and geochemical characteristics of biogenic coalbed methane (CBM) in the Indiana part of the Illinois Basin to identify the organisms responsible for methane generation and to determine the biogeochemical constraints on production of methanogenic substrates, such as H 2 and CO 2. 16S rRNA analysis of in-situ microbial...
Article
This study examines the relationships between topography and spatial variations in groundwater and soil morphology within the multi-step Taoyuan–Hukou Tableland in northwest Taiwan. Several different geomorphological and pedological approaches were jointly undertaken, including analyses of a digital elevation model (DEM), a reclassified soil map, f...
Article
We present a new high precision analytical method for the determination of Mg/Ca and Sr/Ca ratios in carbonates using an inductively coupled plasma quadrupole mass spectrometer (ICP-QMS) with a 650-W cold plasma technique and a desolvation introduction system. Signal intensities are detected in pulse-counting mode and Mg/Ca and Sr/Ca ratios are cal...