Article
Microbiology
Qi-Yun Liang, Jin-Yu Zhang, Daliang Ning, Wen-Xing Yu, Guan-Jun Chen, Xuanyu Tao, Jizhong Zhou, Zong-Jun Du, Da-Shuai Mu
Summary: Inhibiting sulfate-reducing bacteria (SRB) has shown various effects on microbial community properties and coexistence patterns, indicating the importance of SRB in organic matter (OM) degradation. Suppression of SRB resulted in decreased relative abundances of several bacterial families and altered network and community assembly processes. These findings highlight the essential role of SRB in OM degradation.
Article
Environmental Sciences
Zhe Zhou, Susann Henkel, Sabine Kasten, Moritz Holtappels
Summary: Permeable sandy sediments on the global continental shelf play a crucial role in regulating organic matter and nutrient cycling in the coastal ocean. This study investigated the biogeochemical processes in North Sea sands under porewater advection and changing redox conditions. The results showed that Fe(III) oxyhydroxides served as the major electron acceptors during anoxic incubation, and Fe(II) in the solid phase acted as a rechargeable redox battery. Furthermore, excessive phosphorus release occurred after the release of Fe(II), potentially increasing net benthic phosphorus efflux under variable redox conditions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Tiantian Yu, Weichao Wu, Wenyue Liang, Yinzhao Wang, Jialin Hou, Yunru Chen, Marcus Elvert, Kai-Uwe Hinrichs, Fengping Wang
Summary: Experimental findings show that cellulose, lignin, casein and oleic acid can stimulate the growth of uncultured bacteria in aquatic environments and these bacteria have the ability to degrade these organic compounds. These results provide new insights into the ecological functions and metabolic features of uncultured bacteria in aquatic environments.
Article
Environmental Sciences
Margaux Durand, David Touchette, Ya-Jou Chen, Elisse Magnuson, Jessica Wasserscheid, Charles W. Greer, Lyle G. Whyte, Ianina Altshuler
Summary: Global warming-induced sea ice loss has increased Arctic maritime traffic, which in turn increases the risk of ecosystem contamination from fuel spills and nutrient loading. A study was conducted to assess the impact of marine diesel on bacterial metabolic activity and diversity in Northwest Passage beach sediments. The results showed that higher temperatures and nutrients stimulated microbial activity, while diesel reduced it. Diesel exposure also significantly decreased microbial diversity and selectively enriched for the Psychrobacter genus. The study also identified microbial communities with stress response, aromatic compound, and ammonia assimilation metabolisms that were enriched in diesel-contaminated environments.
MARINE POLLUTION BULLETIN
(2023)
Article
Microbiology
Jing-Yi Zhang, Zheng-Han Lian, Manik Prabhu Narsing Rao, Pandeng Wang, Lan Liu, Bao-Zhu Fang, Meng -Meng Li, Ze-Tao Liu, Ai-Ping Lv, Sha Tan, Lei Dong, Jia-Ling Li, Jian-Yu Jiao, Wen-Jun Li
Summary: Microbes in the marine environment are widely distributed and most of them have not yet been cultured. Drying treatments can alter the cultivated microbial diversity, and some potential novel species can only be cultured from drying-treated samples. Drying treatments have different effects on different genera, and they play a significant role in the separation of microbial communities at a cultivation temperature of 28 degrees Celsius.
MICROBIOLOGICAL RESEARCH
(2023)
Review
Ecology
Brett J. Baker, Kathryn E. Appler, Xianzhe Gong
Summary: Metagenomic approaches are transforming our understanding of microbial communities in marine sediments, revealing new lineages with unknown ecological roles and distinct phyla. Uncultured bacteria and archaea in sediments play key roles in mediating previously undescribed steps in carbon and nutrient cycling, advancing our knowledge of global ocean processes.
ANNUAL REVIEW OF MARINE SCIENCE, VOL 13, 2021
(2021)
Article
Environmental Sciences
Zhenhan Li, Wenqiang Zhang, Baoqing Shan
Summary: We studied the distribution and sources of polycyclic aromatic hydrocarbons (PAHs) and organic matter (OM) in sediments from two rivers in North China. The results showed a significant positive correlation between PAHs and OM in the sediments, with higher concentrations detected downstream of areas affected by human activity. Petroleum, coal, and wood combustion were identified as the main sources of PAHs in the sediments, while terrestrial and aquatic higher plants, soil, and sewage discharge contributed to the OM content. OM accumulated and aged along the river, leading to stronger adsorption of PAHs.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biology
Santina Soru, Patrizia Stipcich, Giulia Ceccherelli, Claudia Ennas, Davide Moccia, Antonio Pusceddu
Summary: Marine heatwaves (MHWs) intensification due to global warming not only affects species and communities but also alters sediment biogeochemistry and energy transfer towards higher trophic levels. The study found that MHWs enhance organic loads, increase phytopigment contents in the short term but decrease to initial levels in the longer term. The nutritional quality of organic matter decreases with time, suggesting a decrease in ecosystem functioning. The intensification of MHWs will have significant impacts on coastal biogeochemistry and benthic communities.
Article
Environmental Sciences
David A. Aromokeye, Graciana Willis-Poratti, Lea C. Wunder, Xiuran Yin, Jenny Wendt, Tim Richter-Heitmann, Susann Henkel, Susana Vazquez, Marcus Elvert, Walter Mac Cormack, Michael W. Friedrich
Summary: The colonization of newly ice-free areas by marine benthic organisms intensifies the burial of macroalgae detritus in surface sediments, affecting early diagenetic processes like microbial iron reduction in Potter Cove. Under scenarios of global warming, the active microbial populations identified will expand their environmental function, facilitating organic matter remineralization and increasing the release of iron and CO2 from sediments. Such indirect consequences of glacial retreat may be relevant for the assessment of future nutrient and carbon fluxes on a regional scale.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Geochemistry & Geophysics
S. Bruggmann, S. Severmann, J. McManus
Summary: Concentrations and isotope ratios of chromium (Cr) in marine sediment can be used to reconstruct ocean biogeochemical conditions. The study examines the differences in Cr concentrations between oxic and anoxic sediments, finding that Cr concentrations are lower in oxic sediments. It also highlights the strong dependence of Cr on sedimentary redox conditions and biological productivity.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2023)
Article
Environmental Sciences
Philip A. Pika, Dominik Hulse, Timothy I. Eglinton, Sandra Arndt
Summary: The degradation of organic matter (OM) in marine sediments is vital for understanding global biogeochemical cycling, with OM reactivity at its core. By using benthic diffusive oxygen uptake (DOU) rates as a proxy, we determined OM reactivities in marine sediments inversely. The reactivities varied significantly, ranging from high in polar regions to extremely low in the South Pacific. Furthermore, we developed transfer functions that can estimate OM reactivity based on DOU, OM content, and water depths, and used one of these functions to create the first global maps of benthic OM reactivity.
GLOBAL BIOGEOCHEMICAL CYCLES
(2023)
Article
Environmental Sciences
Yu Hu, Juan Chen, Chao Wang, Peifang Wang, Han Gao, Jingjing Zhang, Bo Zhang, Ge Cui, Dan Zhao
Summary: This study investigated the removal of HBCD from contaminated sediment under different hydrodynamic conditions and revealed that microbial debromination was an important process for HBCD removal. The dynamic water conditions resulted in higher sediment redox potential, which decreased the abundance of organohalide-respiring bacteria and hindered the microbial degradation of HBCD.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Meng-Meng Chen, Fang-Hong Nie, Aftab Qamar, Di-hua Zhu, Yao Hu, Min Zhang, Qing-Lang Song, Hong-Ying Lin, Zhi-Bao Chen, Su-Qing Liu, Jin-Jun Chen
Summary: Microplastics extracted from mangrove sediments were found to have an impact on the diversity and composition of microbial communities, as well as on the nitrification function of these communities.
BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY
(2022)
Article
Environmental Sciences
Honghong Guo, Jie Gu, Xiaojuan Wang, Zilin Song, Jing Yu, Liusheng Lei
Summary: This study found that bamboo charcoal and bamboo vinegar have significant effects on organic matter degradation and methane emissions during composting, with bamboo vinegar being the most effective treatment for controlling methane emissions. Both bamboo charcoal and bamboo vinegar can enhance metabolism associated with organic matter degradation and reduce methane metabolism.
ENVIRONMENTAL POLLUTION
(2021)
Review
Microbiology
Peter Q. Fischer, Irene Sanchez-Andrea, Alfons J. M. Stams, Laura Villanueva, Diana Z. Sousa
Summary: Methanol is a ubiquitous compound in marine sediments, serving as a carbon and energy source for various microorganisms that compete for it using different biochemical pathways. Current knowledge provides insight into the sources of methanol, the ecology of methanol-utilizing microorganisms, and their metabolism, but the unknown diversity of methanol utilizers in marine sediments remains to be explored through metagenomic analysis.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Jeffrey J. Marlow, Amit Kumar, Brandon C. Enalls, Linda M. Reynard, Noreen Tuross, Gregory Stephanopoulos, Peter Girguis
BIOTECHNOLOGY AND BIOENGINEERING
(2018)
Editorial Material
Oceanography
Nicole A. Raineault, Katherine L. C. Bell, Peter Girguis
DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
(2018)
Article
Oceanography
Anna P. M. Michel, Scott D. Wankel, Jason Kapit, Zoe Sandwith, Peter R. Girguis
DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY
(2018)
Article
Geochemistry & Geophysics
Aude Picard, Amy Gartman, David R. Clarke, Peter R. Girguis
GEOCHIMICA ET COSMOCHIMICA ACTA
(2018)
Article
Multidisciplinary Sciences
Elizabeth Trembath-Reichert, Sunita R. Shah Walter, Marc Alec Fontanez Ortiz, Patrick D. Carter, Peter R. Girguis, Julie A. Huber
Summary: The study of microbial biomass production in cool, oxic basement fluids from the western flank of the Mid-Atlantic Ridge indicates a microbial community capable of synthesizing carbon and nitrogen under dynamic conditions. Bicarbonate incorporation rates were highest in isolated fluids, suggesting a potential strategy for supplementing ancient and recalcitrant dissolved organic carbon in the globally distributed subseafloor crustal environment.
Article
Microbiology
Jeffrey Marlow, Rachel Spietz, Keun-Young Kim, Mark Ellisman, Peter Girguis, Roland Hatzenpichler
Summary: The study revealed that the proportion of active microbial cells decreases rapidly with depth in salt marsh sediment, with a shift in the most prominent active community members from the surface layer to deeper layers. Microbe-mineral relationships were found to be dynamic and context-dependent arbiters of biogeochemical cycling.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jeffrey J. Marlow, Daniel Hoer, Sean P. Jungbluth, Linda M. Reynard, Amy Gartman, Marko S. Chavez, Mohamed Y. El-Naggar, Noreen Tuross, Victoria J. Orphan, Peter R. Girguis
Summary: The study suggests that carbonate rocks in marine methane seeps host methane-oxidizing microbial communities with substantial methanotrophic potential. Laboratory experiments showed that carbonates from Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured so far. The research highlights the importance of rock-hosted methanotrophy as a significant contributor to marine methane consumption.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Andre Luiz de Oliveira, Jessica Mitchell, Peter Girguis, Monika Bright
Summary: The study presents the high-quality draft genome of the giant tubeworm Riftia pachyptila, revealing signs of reductive evolution and evolutionary adaptations to the vent environment and endosymbiosis. The conservation of developmental gene repertoire in the gutless tubeworm and the role of innate immune system in establishing symbiosis are highlighted. The research bridges four decades of physiological research in Riftia and sheds new light on development, whole organism functions, and evolution in the giant tubeworm.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Isabel R. Baker, Bridget E. Conley, Jeffrey A. Gralnick, Peter R. Girguis
Summary: Some bacteria and archaea have evolved the ability to use extracellular electron transfer (EET) as a means of energy metabolism. The MtrCAB system, which transfers electrons from metabolic substrates to electron acceptors outside the cell, has been found in a diverse range of bacteria. These findings highlight the broad relevance of EET to different taxa and biogeochemical cycles in our biosphere and provide a foundation for further research on its evolution and role in Earth's redox landscape.
Article
Microbiology
Yunha Hwang, Peter R. Girguis
Summary: This study investigated the population-level genetic diversity of marine microbes and found differences in genetic diversification between different ocean basins, potentially due to variations in nutrient availability and environmental fluctuations.
Article
Marine & Freshwater Biology
Jacob P. Beam, Alexander B. Michaud, David T. Johnston, Peter R. Girguis, David Emerson
Summary: Coastal sediments are important sources of dissolved iron (dFe) that contribute to the iron supply in the adjacent open ocean. The sedimentary dFe flux is influenced by a complex interplay of microbial activities, including reduction-oxidation condition, Fe and S cycling, and benthic fauna bio-mixing and bio-irrigation. The study found that bottom water oxygen concentration affects iron dynamics, and bioturbation plays a crucial role in increasing poorly crystalline Fe(III)-oxides within sediments while reducing Fe(II) flux. These results highlight the significance of bioturbation for sedimentary Fe-cycling and demonstrate the complex response to hypoxia involving both animal behavior and microbial response.
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Article
Ecology
Jay T. Osvatic, Benedict Yuen, Martin Kunert, Laetitia Wilkins, Bela Hausmann, Peter Girguis, Kennet Lundin, John Taylor, Guillaume Jospin, Jillian M. Petersen
Summary: Chemosynthetic symbioses between bacteria and invertebrates are found worldwide and are important for understanding the evolutionary transitions between shallow and deep waters. The Lucinidae family, with representatives in both shallow and deep seas, has colonized the deep sea independently, allowing for the study of microbial symbionts' role in adaptation. Metagenomic analyses of deep-water lucinid species revealed symbiont switching near deep-sea hydrothermal vents and cold seeps, highlighting the importance of symbiont metabolic capabilities in the adaptation to challenging deep-sea habitats.
Article
Multidisciplinary Sciences
Tori M. Hoehler, Dylan J. Mankel, Peter R. Girguis, Thomas M. McCollom, Nancy Y. Kiang, Bo Barker Jorgensen
Summary: We investigated the connection between biological energy utilization rates and the biomass sustained by this energy utilization at both organism and biosphere levels. By compiling a dataset consisting of over 10,000 measurements of metabolic rates from more than 2,900 species, and quantifying energy utilization rates on a biomass-normalized basis for different components of the biosphere, we found that energy utilization rates vary greatly. The correlation between mass-normalized energy utilization rates and biomass carbon turnover rates suggests global mean turnover rates for terrestrial soil biota, marine water column biota, and marine sediment biota.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Yunha Hwang, Simon Roux, Clement Coclet, Sebastian J. E. Krause, Peter R. Girguis
Summary: Metagenomics and Hi-C proximity-ligation sequencing have revealed that viruses can interact with distantly related microbial hosts in dense microbial communities. The study focused on a biomass dense, deep-sea hydrothermal mat and found evidence of viral interactions with hosts across microbial domains, particularly between known syntrophic partners. This phenomenon was also observed in diverse ecosystems that harbor syntrophic biofilms. The findings suggest that viral entry into non-primary host cells may be common in densely populated ecosystems, impacting syntrophic microbes and enhancing resilience against viruses through CRISPR-mediated inter-population augmentation.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Isabel R. Baker, Bridget E. Conley, Jeffrey A. Gralnick, Peter R. Girguis
Summary: The study reveals that genes encoding the EET system MtrCAB are widespread in diverse bacteria, highlighting the ubiquity and potential impact of EET in our biosphere. These genes have been mainly disseminated through horizontal transfer, with changes observed in different lineages indicating adaptations to changing environments.
Article
Geochemistry & Geophysics
Xinze Lu, Geoffrey J. Gilleaudeau, Brian Kendall
Summary: The Late Ordovician mass extinction is the first major extinction event in the Phanerozoic, but the reasons for the decline in global biodiversity before the extinction are not well understood.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2024)
Article
Geochemistry & Geophysics
Junyao Kang, Daniel D. Gregory, Benjamin Gill, Shiqiang Huang, Changxin Lai, Zhaoshan Chang, Huan Cui, Ivan Belousov, Shuhai Xiao
Summary: Sedimentary pyrite is an important geological archive, but it can be altered by diagenetic and hydrothermal processes. This study successfully trained machine learning algorithms to distinguish pyrite origins using trace element data. The approach was validated and applied to identify the origins of pyrite in two sedimentary successions in South China.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2024)