Article
Biodiversity Conservation
Xiuting Feng, Hongmei Li, Zenghu Zhang, Tianqi Xiong, Xiaoyong Shi, Chen He, Quan Shi, Nianzhi Jiao, Yongyu Zhang
Summary: By studying the long-term microbial degradation of kelp detritus, it was found that a significant amount of stable carbon can be stored for long-term carbon sequestration. Difficult to degrade organic carbon gradually forms during degradation, with microbial activity playing a crucial role in the carbon sequestration process.
ECOLOGICAL INDICATORS
(2022)
Article
Environmental Sciences
Ling Ding, Sen Shan, Chunle Luo, Xuchen Wang
Summary: This study investigated the concentrations and distribution of dissolved organic carbon (DOC) in the South China Sea and the western North Pacific. Laboratory experiments were conducted to determine the microbiological respiration of DOC. The findings revealed that DOC concentrations in the South China Sea varied greatly and were influenced by multiple factors. Physical mixing played a significant role in the distribution of mesopelagic DOC in the northern South China Sea basin.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Ecology
Mario Uchimiya, William Schroer, Malin Olofsson, Arthur S. Edison, Mary Ann Moran
Summary: Organic carbon transfer between surface ocean photosynthetic and heterotrophic microbes is a complex process influenced by diurnal cycles, as shown in a model community study revealing changes in diatom endometabolome and bacterial uptake transcriptome. Understanding the factors influencing metabolite release and consumption by surface ocean microbes is crucial for better constraining this globally significant carbon flux. Improved model performance was observed when active release mechanisms were incorporated, suggesting the importance of physiological balance and bacterial recognition in this process.
Article
Soil Science
Kyungjin Min, Eric Slessarev, Megan Kan, Karis McFarlane, Erik Oerter, Jennifer Pett-Ridge, Erin Nuccio, Asmeret Asefaw Berhe
Summary: Climate-smart land management practices can help in soil carbon sequestration by replacing shallow-rooted annual crop systems with deeply-rooted perennial plants. However, deep soil carbon accrual is influenced by active microbial biomass and their ability to assimilate fresh carbon at depth. Incorporating active microbial biomass, dormancy, and growth in models can improve predictions of soil's capacity to store carbon.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Microbiology
Benjamin D. D. Peterson, David P. P. Krabbenhoft, Katherine D. D. McMahon, Jacob M. M. Ogorek, Michael T. T. Tate, William H. H. Orem, Brett A. A. Poulin
Summary: The production of methylmercury (MeHg) is influenced by the bioavailability of inorganic divalent mercury (Hg(II)(i)) and the Hg-methylation capacity of the microbial community (controlled by the hgcAB gene cluster). However, the relative importance of these factors and their interaction in the environment is not well understood. Through metagenomic sequencing and a MeHg formation experiment, this study examined a wetland sulfate gradient to isolate the effects of each factor on MeHg formation. The bioavailability of Hg(II)(i) was correlated with dissolved organic matter composition, while the microbial Hg-methylation capacity was correlated with the abundance of hgcA genes. MeHg formation showed a synergistic response to both factors. Notably, hgcA sequences were found in diverse taxonomic groups, none of which contained genes for dissimilatory sulfate reduction. This research expands our understanding of the geochemical and microbial constraints on MeHg formation in natural environments and provides a framework for further mechanistic studies.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Environmental Sciences
Congcong Li, Cheng Liu, Jiaqi Liu, Changlong Feng
Summary: This study investigated the temporal dynamics of microbial communities in Biological Activated Carbon (BAC) biofilms. The results showed that microbial diversity in BAC reached its peak after 2 years and declined thereafter. The composition of microbial communities exhibited significant temporal evolution, with deterministic processes gaining importance over time and competitive relationships becoming more prevalent.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Xiaoqing Liu, Katrin Wendt-Potthoff, Johannes A. C. Barth, Kurt Friese
Summary: This study investigates the degradation of organic matter in freshwater sediments and its impact on biogeochemical dynamics and carbon burial. The study finds that degradation of organic matter is influenced by the types and sources of organic matter, leading to changes in stable isotope ratios. The results suggest that the lability of algae-derived organic matter can affect carbon burial estimation and obscure paleoenvironmental information derived from isotopic proxies.
Article
Multidisciplinary Sciences
Richard LaBrie, Berangere Pequin, Nicolas Fortin St-Gelais, Igor Yashayaev, Jennifer Cherrier, Yves Gelinas, Francois Guillemette, David C. Podgorski, Robert G. M. Spencer, Luc Tremblay, Roxane Maranger
Summary: The microbial carbon pump (MCP) hypothesis suggests that the transformation of labile dissolved organic carbon (DOC) by prokaryotes contributes to the stability of the deep ocean DOC reservoir. This study provides empirical evidence of the MCP in natural waters, showing that carbon sequestration is more efficient in deeper waters. The higher diversity of prokaryotes from the rare biosphere holds a greater metabolic potential in creating stable dissolved organic compounds.
Article
Engineering, Environmental
Jacob M. Ogorek, Ryan F. Lepak, Joel C. Hoffman, John F. DeWild, Tylor J. Rosera, Michael T. Tate, James P. Hurley, David P. Krabbenhoft
Summary: The study found that mercury concentrations in the Laurentian Great Lakes are relatively low, but game fish concentrations are close to consumption advisory limits, indicating efficient methylmercury transfer from water to game fish. The bioaccumulation factors of mercury in phytoplankton are among the highest reported in water ecosystems and are influenced by dissolved organic carbon.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Archaeology
Antonino Biagio Carbonaro, Rosario Caruso, Valentina Greco, Ola El-Aguizy, Mona Fouad Ali, Grazia Laura Gambino, Alessandro Giuffrida, Enrico Ciliberto
Summary: The study of the fractionation of stable carbon isotopes 13C and 12C has various applications, such as quality control and geographical origin analysis. This study used Isotopic Ratio Mass Spectrometry to investigate the degradation of an ancient linen textile and found that degradation contributed to the isotopic fractionation phenomenon. The measured δ13C values increased from contemporary to ancient samples.
JOURNAL OF CULTURAL HERITAGE
(2023)
Article
Multidisciplinary Sciences
Ming-Hui Wu, Sheng-Yun Chen, Jian-Wei Chen, Kai Xue, Shi-Long Chen, Xiao-Ming Wang, Tuo Chen, Shi-Chang Kang, Jun-Peng Rui, Janice E. Thies, Richard D. Bardgett, Yan-Fen Wang
Summary: Permafrost degradation alters the diversity of microbial communities in the active layer, potentially leading to carbon loss and a positive carbon feedback effect. This study provides valuable insights into the mechanisms of carbon loss in degraded permafrost, which can aid in modeling carbon emissions under future scenarios.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Environmental
Haoqun Sha, Zhenhai Liu, Yue Sun, Yuxin Wang, Xiange Wang, Jing Zheng, Yan Ma, Xiaosong He
Summary: This study found that leachate leakage enhances microbial diversity and transfers specific bacteria from landfills to groundwater, with organic matter being the key driving factor for microbial community evolution. Leachate pollution changes the assembly mechanism of microbial communities, reducing their efficiency and stability in groundwater. Microbial indicators are more sensitive to leachate leakage and can accurately identify landfills where leachate leakage occurs and other extraneous pollutants.
Article
Geochemistry & Geophysics
Christoph Spoetl, Yuri Dublyansky, Gabriella Koltai, Charlotte Honiat, Lukas Plan, Thomas Angerer
Summary: This study demonstrates that geochemical analysis of cave wall rock samples can identify hypogene karstification and provide further insights into the temperature and provenance of paleowater, as well as the source of its dissolved inorganic carbon.
Article
Engineering, Civil
Brenden Riddle, Jimmy Fox, Yi-Tin Wang, Bill Ford, Tyler Mahoney, Erik Pollock, Jason Backus, Nabil Al Aamery
Summary: Despite their importance for freshwater biogeochemical cycles and ecological restoration, there is a lack of knowledge about sediment organic matter degradation and its influence on water quality for low gradient agriculturally impacted streams. We conducted aerobic incubation experiments and found that degradation rates vary across sediment type and are influenced by the connectivity regimes of low gradient systems. The results support our hypothesis and suggest that sediment connectivity regime controls the biogeochemical cycling of the stream network.
JOURNAL OF HYDROLOGY
(2023)
Article
Chemistry, Multidisciplinary
Gabriel Dulaquais, Pierre Fourrier, Jean Francois Maguer, Corentin Denis, Matthieu Waeles, Ricardo Riso
Summary: The study focuses on the use of an extraction procedure involving the Styrene-divinylbenzene copolymer (PPL) sorbent for studying the origin and transformations of dissolved organic matter (DOM) in estuarine and coastal environments. The study investigates the fractionation effects of PPL sorbent on the size class distribution and carbon isotopic composition of DOM, revealing that the sorbent strongly fractionates DOM and has a lower affinity for aromatic compounds of marine origin. The study highlights the limitations of PPL resin extraction and emphasizes the need for careful interpretation of data solely relying on PPL extractions when studying the origin and composition of DOM.
Article
Multidisciplinary Sciences
Anirban Chakraborty, S. Emil Ruff, Xiyang Dong, Emily D. Ellefson, Carmen Li, James M. Brooks, Jayme McBee, Bernie B. Bernard, Casey R. J. Hubert
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Microbiology
Sean K. Bay, Xiyang Dong, James A. Bradley, Pok Man Leung, Rhys Grinter, Thanavit Jirapanjawat, Stefan K. Arndt, Perran L. M. Cook, Douglas E. LaRowe, Philipp A. Nauer, Eleonora Chiri, Chris Greening
Summary: The study indicates that a majority of soil bacteria can utilize trace gases as energy and carbon sources, providing a significant selective advantage in soil ecosystems with limited availability of preferred organic substrates. This has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.
NATURE MICROBIOLOGY
(2021)
Article
Ecology
Zexin Li, Donald Pan, Guangshan Wei, Weiling Pi, Chuwen Zhang, Jiang-Hai Wang, Yongyi Peng, Lu Zhang, Yong Wang, Casey R. J. Hubert, Xiyang Dong
Summary: The study revealed the global diversity and biogeography of cold seep viruses, with seep fluid flux being a major driver of viral community composition. Viruses were found to influence microbial hydrocarbon biodegradation and carbon, sulfur, and nitrogen cycling at cold seeps.
Article
Microbiology
Chuwen Zhang, Rainer U. Meckenstock, Shengze Weng, Guangshan Wei, Casey R. J. Hubert, Jiang-Hai Wang, Xiyang Dong
Summary: This study identified diverse bacterial and archaeal lineages involved in anaerobic degradation of alkanes and methylated aromatic hydrocarbons in marine sediments, including the presence of fumarate-adding enzymes (FAE). These microorganisms, found in hydrocarbon-impacted sediments, potentially degrade hydrocarbons through sulfate reduction or fermentation, expanding our understanding of the ecological roles of these organisms in marine ecosystems.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Microbiology
Wen-Li Li, Xiyang Dong, Rui Lu, Ying-Li Zhou, Peng-Fei Zheng, Dong Feng, Yong Wang
Summary: The study identified a shallow sulfate-methane transition zone (SMTZ) in cold seep areas of the South China Sea and discovered a high diversity of sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) in the cores sampled. SOB in the upper layers depended on nitrogen oxides and/or oxygen for sulfide oxidation, while SRB in the lower layers utilized the Wood-Ljungdahl pathway for CO2 fixation, sulfate reduction, and nitrogen fixation in a syntrophic or fermentative lifestyle.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Ecology
Xiyang Dong, Haoyu Lan, Liangtian Huang, Haikun Zhang, Xianbiao Lin, Shengze Weng, Yongyi Peng, Jia Lin, Jiang-hai Wang, Juan Peng, Ying Yang
Summary: This study assessed the microbial communities in surface sediments from 16 coral reef sites at different depths in the Xisha islands using gene- and genome-centric metagenomics. The results revealed the diversity and functional potential of the microbial communities, as well as the presence of antibiotic resistance genes. These findings contribute to a better understanding of the microbial ecology in reef sediments.
Article
Soil Science
Yongfeng Xu, Ying Teng, Xiyang Dong, Xiaomi Wang, Chuwen Zhang, Wenjie Ren, Ling Zhao, Yongming Luo, Chris Greening
Summary: Microcosm experiments revealed the responses of soil microbial communities to elevated H-2 levels, showing rapid growth of different hydrogenotrophic bacteria in different soils. This indicates that soils have the capability to counteract growing anthropogenic emissions of H-2.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Environmental Sciences
Haikun Zhang, Yibo Wang, Pengyuan Liu, Yanyu Sun, Xiyang Dong, Xiaoke Hu
Summary: This study investigated the distribution, hosts, and mobility potential of antibiotic resistance genes (ARGs) in the deep ocean and compared them with those in coastal waters. The results showed that deep-sea water could be a reservoir for diverse and abundant ARGs, with potential hosts mainly belonging to the Gammaproteobacteria and Alphaproteobacteria classes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Ling-Dong Shi, Xiyang Dong, Zongbao Liu, Yuchun Yang, Jih-Gaw Lin, Meng Li, Ji-Dong Gu, Li-Zhong Zhu, He-Ping Zhao
Summary: The diversity of both microorganisms and viruses in activated sludge of wastewater treatment plants plays a crucial role in controlling microbial dynamics and metabolisms. This study reveals the presence of unknown viral genera in activated sludge, indicating an unexplored reservoir for new viruses and viral diversity. The study also shows that viruses can enhance the performance of activated sludge by encoding auxiliary metabolic genes (AMGs) involved in biodegradation, but can also facilitate the spread of antibiotic resistance genes (ARGs) among microorganisms. Overall, this study highlights the mixed blessing of viruses in wastewater treatment plants and their impact on biochemical processes.
Article
Multidisciplinary Sciences
Xiyang Dong, Chuwen Zhang, Yongyi Peng, Hong-Xi Zhang, Ling-Dong Shi, Guangshan Wei, Casey R. J. Hubert, Yong Wang, Chris Greening
Summary: The authors investigate metagenomes and metatranscriptomes of diazotrophs from deep sea cold seep sediments, revealing greater phylogenetic and functional diversity than hitherto known.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Kuntong Jia, Yongyi Peng, Xueji Chen, Huahua Jian, Min Jin, Zhiwei Yi, Ming Su, Xiyang Dong, Meisheng Yi
Summary: In this study, a filamentous phage infecting Alteromonas abrolhosensis, designated phi AFP1, was isolated from the South China Sea and represented a novel genus of Inoviridae. Comparative analyses revealed that phi AFP1 could be regarded as genetic mosaics having homologous sequences with Ralstonia and Stenotrophomonas phages. The temporal transcriptome analysis of A. abrolhosensis to phi AFP1 infection revealed that 7.78% of the host genes were differentially expressed, indicating that phi AFP1 might hijack the energy of the host for the synthesis of phage proteins.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Xiyang Dong, Yongyi Peng, Muhua Wang, Laura Woods, Wenxue Wu, Yong Wang, Xi Xiao, Jiwei Li, Kuntong Jia, Chris Greening, Zongze Shao, Casey R. J. Hubert
Summary: Little is known about genetic heterogeneity within deep sea cold seep microbial populations. This study examines the intraspecies diversity patterns of 39 abundant species identified in sediment layers below the sea floor across six cold seep sites. The results reveal different evolutionary trajectories at the genomic level among these diverse populations and highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Chuwen Zhang, Xinyue Liu, Ling-Dong Shi, Jiwei Li, Xi Xiao, Zongze Shao, Xiyang Dong
Summary: Cold seeps are hydrocarbon-rich fluid escaping from the seafloor and contain high concentrations of toxic metalloid arsenic. Microbial processes can greatly alter the toxicity and mobility of arsenic and play a significant role in global arsenic biogeochemical cycling.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Multidisciplinary Sciences
Yingchun Han, Chuwen Zhang, Zhuoming Zhao, Yongyi Peng, Jing Liao, Qiuyun Jiang, Qing Liu, Zongze Shao, Xiyang Dong
Summary: Cold seeps harbor diverse and potentially useful microbes that significantly impact biogeochemical cycles. However, knowledge of the genetic diversity and repertoire of global seep microbes is limited. In this study, a comprehensive gene and genome catalog was constructed using 165 metagenomic datasets from 16 cold seep sites, revealing a large number of novel species and providing valuable insights into the functions of cold seep microbiomes.
Article
Microbiology
Xiyang Dong, Chuwen Zhang, Wenli Li, Shengze Weng, Weizhi Song, Jiangtao Li, Yong Wang
Summary: Despite being geographically distant, similar microbial community patterns dominated by Gammaproteobacteria, Bacteroidota, and Candidatus Patescibacteria were observed in multiple deep-sea vent fields. These microbes, such as metabolically flexible Gammaproteobacteria, utilize sulfur, iron, and hydrogen as electron donors for chemolithoautotrophic growth. Furthermore, lateral gene transfer of functional genes central to energy metabolism was identified among community members within the same class, shedding light on microbial ecology and evolution in inactive seafloor sulfide deposits.
FEMS MICROBIOLOGY ECOLOGY
(2021)
