Articles | Volume 18, issue 6
https://doi.org/10.5194/bg-18-2091-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-18-2091-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
23 Mar 2021
Research article |
| 23 Mar 2021
| 23 Mar 2021
Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments
Michal Elul
CORRESPONDING AUTHOR
Department of Earth and Environmental Science, Ben-Gurion University
of the Negev, Beer Sheva, Israel
Maxim Rubin-Blum
Israel Oceanographic and Limnological Research, Haifa, Israel
Zeev Ronen
Department of Environmental Hydrology and Microbiology, The
Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev,
Sede Boker Campus, Israel
Itay Bar-Or
Central Virology Laboratory, Ministry of Health, Sheba Medical
Center, Ramat Gan, Israel
Werner Eckert
Israel Oceanographic & Limnological Research, The Yigal Allon
Kinneret Limnological Laboratory, Migdal, Israel
Orit Sivan
Department of Earth and Environmental Science, Ben-Gurion University
of the Negev, Beer Sheva, Israel
Related authors
Hanni Vigderovich, Werner Eckert, Michal Elul, Maxim Rubin-Blum, Marcus Elvert, and Orit Sivan
Biogeosciences, 19, 2313–2331, https://doi.org/10.5194/bg-19-2313-2022, https://doi.org/10.5194/bg-19-2313-2022, 2022
Short summary
Short summary
Anaerobic oxidation of methane (AOM) is one of the major processes limiting the release of the greenhouse gas methane from natural environments. Here we show that significant AOM exists in the methane zone of lake sediments in natural conditions and even after long-term (ca. 18 months) anaerobic slurry incubations with two stages. Methanogens were most likely responsible for oxidizing the methane, and humic substances and iron oxides are likely electron acceptors to support this oxidation.
Ilil Levakov, Zeev Ronen, Tuvia Turkeltaub, and Ofer Dahan
EGUsphere, https://doi.org/10.5194/egusphere-2022-1179, https://doi.org/10.5194/egusphere-2022-1179, 2022
Preprint withdrawn
Short summary
Short summary
This study presents a novel approach for in-situ large-scale remediation of contaminated unsaturated zone and groundwater. Flow and transport models were calibrated against continuously monitored data, enabling evaluation of the required conditions for optimal contaminate removal. The results enabled realistic data-based predictions of the time frame that is required to attain full contaminant removal through efficient and low-cost in-situ treatment technique.
Hanni Vigderovich, Werner Eckert, Michal Elul, Maxim Rubin-Blum, Marcus Elvert, and Orit Sivan
Biogeosciences, 19, 2313–2331, https://doi.org/10.5194/bg-19-2313-2022, https://doi.org/10.5194/bg-19-2313-2022, 2022
Short summary
Short summary
Anaerobic oxidation of methane (AOM) is one of the major processes limiting the release of the greenhouse gas methane from natural environments. Here we show that significant AOM exists in the methane zone of lake sediments in natural conditions and even after long-term (ca. 18 months) anaerobic slurry incubations with two stages. Methanogens were most likely responsible for oxidizing the methane, and humic substances and iron oxides are likely electron acceptors to support this oxidation.
Ofer Dahan, Idan Katz, Lior Avishai, and Zeev Ronen
Hydrol. Earth Syst. Sci., 21, 4011–4020, https://doi.org/10.5194/hess-21-4011-2017, https://doi.org/10.5194/hess-21-4011-2017, 2017
Short summary
Short summary
In situ bioremediation of a perchlorate-contaminated vadose zone was conducted through infiltration of electron-donor-enriched water. A vadose zone monitoring system (VMS) provided real-time tracking of the hydraulic and chemical conditions across the unsaturated zone. Variations in concentration profiles of perchlorate, chloride, DOC and bromide in the vadose zone pore water showed limited migration capacity of biologically consumable carbon and significant mobilization of perchlorate.
I. Bar-Or, E. Ben-Dov, A. Kushmaro, W. Eckert, and O. Sivan
Biogeosciences, 12, 2847–2860, https://doi.org/10.5194/bg-12-2847-2015, https://doi.org/10.5194/bg-12-2847-2015, 2015
Short summary
Short summary
This study attempted to correlate between the performed geochemical and microbial profiles in lake sediments. The geochemical data suggest three main depth related zones of electron acceptor activities in the sediment: sulfate reduction, methanogenesis and a novel, deep iron-driven AOM. The prokaryotic analysis provided clues regarding the microorganisms that may be involved in this novel process and the metabolic paths that occur throughout the microbial assemblage.
Related subject area
Biogeochemistry: Environmental Microbiology
Characteristics of bacterial and fungal communities and their associations with sugar compounds in atmospheric aerosols at a rural site in northern China
Responses of globally important phytoplankton species to olivine dissolution products and implications for carbon dioxide removal via ocean alkalinity enhancement
Differentiation of cognate bacterial communities in thermokarst landscapes: implications for ecological consequences of permafrost degradation
A multi-phase biogeochemical model for mitigating earthquake-induced liquefaction via microbially induced desaturation and calcium carbonate precipitation
Phosphorus regulates ectomycorrhizal fungi biomass production in a Norway spruce forest
Reallocation of elemental content and macromolecules in the coccolithophore Emiliania huxleyi to acclimate to climate change
Abrasion of sedimentary rocks as a source of hydrogen peroxide and nutrients to subglacial ecosystems
Nitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosa
Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
Depth-related patterns in microbial community responses to complex organic matter in the western North Atlantic Ocean
Assessing the influence of ocean alkalinity enhancement on a coastal phytoplankton community
Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic
Composition and niche-specific characteristics of microbial consortia colonizing Marsberg copper mine in the Rhenish Massif
Diversity and assembly processes of microbial eukaryotic communities in Fildes Peninsula Lakes (West Antarctica)
Nitrophobic ectomycorrhizal fungi are associated with enhanced hydrophobicity of soil organic matter in a Norway spruce forest
Physiological control on carbon isotope fractionation in marine phytoplankton
Implementation of mycorrhizal mechanisms into soil carbon model improves the prediction of long-term processes of plant litter decomposition
Impact of dust addition on the microbial food web under present and future conditions of pH and temperature
Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments
Hydrothermal trace metal release and microbial metabolism in the northeastern Lau Basin of the South Pacific Ocean
Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin
Disturbance triggers non-linear microbe–environment feedbacks
Hydrographic fronts shape productivity, nitrogen fixation, and microbial community composition in the southern Indian Ocean and the Southern Ocean
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Spatiotemporal patterns of N2 fixation in coastal waters derived from rate measurements and remote sensing
Biotic and abiotic transformation of amino acids in cloud water: experimental studies and atmospheric implications
Potential bioavailability of organic matter from atmospheric particles to marine heterotrophic bacteria
Microbial functional signature in the atmospheric boundary layer
New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem
Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics
Reviews and syntheses: Bacterial bioluminescence – ecology and impact in the biological carbon pump
Salinity-dependent algae uptake and subsequent carbon and nitrogen metabolisms of two intertidal foraminifera (Ammonia tepida and Haynesina germanica)
On giant shoulders: how a seamount affects the microbial community composition of seawater and sponges
Spatial variations in sedimentary N-transformation rates in the North Sea (German Bight)
Patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge
Co-occurrence of Fe and P stress in natural populations of the marine diazotroph Trichodesmium
Senescence as the main driver of iodide release from a diverse range of marine phytoplankton
Reviews and syntheses: Biological weathering and its consequences at different spatial levels – from nanoscale to global scale
Deep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic sponges
Inducing the attachment of cable bacteria on oxidizing electrodes
Bacterial degradation activity in the eastern tropical South Pacific oxygen minimum zone
Macromolecular fungal ice nuclei in Fusarium: effects of physical and chemical processing
Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica
Comprehensive characterization of an aspen (Populus tremuloides) leaf litter sample that maintained ice nucleation activity for 48 years
The origin and role of biological rock crusts in rocky desert weathering
Pyrite oxidization accelerates bacterial carbon sequestration in copper mine tailings
Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea
Filtration artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assays
Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions
Trichodesmium physiological ecology and phosphate reduction in the western tropical South Pacific
Mutong Niu, Shu Huang, Wei Hu, Yajie Wang, Wanyun Xu, Wan Wei, Qiang Zhang, Zihan Wang, Donghuan Zhang, Rui Jin, Libin Wu, Junjun Deng, Fangxia Shen, and Pingqing Fu
Biogeosciences, 20, 4915–4930, https://doi.org/10.5194/bg-20-4915-2023, https://doi.org/10.5194/bg-20-4915-2023, 2023
Short summary
Short summary
Sugar compounds in air can trace the source of bioaerosols that affect public health and climate. In rural north China, we observed increased fungal activity at night and less variable bacterial community diversity. Certain night-increasing sugar compounds were more closely related to fungi than bacteria. The fungal community greatly influenced sugar compounds, while bacteria played a limited role. Caution is advised when using sugar compounds to trace airborne microbes, particularly bacteria.
David A. Hutchins, Fei-Xue Fu, Shun-Chung Yang, Seth G. John, Stephen J. Romaniello, M. Grace Andrews, and Nathan G. Walworth
Biogeosciences, 20, 4669–4682, https://doi.org/10.5194/bg-20-4669-2023, https://doi.org/10.5194/bg-20-4669-2023, 2023
Short summary
Short summary
Applications of the mineral olivine are a promising means to capture carbon dioxide via coastal enhanced weathering, but little is known about the impacts on important marine phytoplankton. We examined the effects of olivine dissolution products on species from three major phytoplankton groups: diatoms, coccolithophores, and cyanobacteria. Growth and productivity were generally either unaffected or stimulated, suggesting the effects of olivine on key phytoplankton are negligible or positive.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
Biogeosciences, 20, 4241–4258, https://doi.org/10.5194/bg-20-4241-2023, https://doi.org/10.5194/bg-20-4241-2023, 2023
Short summary
Short summary
Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results imply ecological consequences of permafrost degradation in the face of further climate change.
Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
Biogeosciences, 20, 2903–2917, https://doi.org/10.5194/bg-20-2903-2023, https://doi.org/10.5194/bg-20-2903-2023, 2023
Short summary
Short summary
Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
Short summary
Short summary
In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
Yong Zhang, Yong Zhang, Shuai Ma, Hanbing Chen, Jiabing Li, Zhengke Li, Kui Xu, Ruiping Huang, Hong Zhang, Yonghe Han, and Jun Sun
Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
Short summary
Short summary
We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
Short summary
Short summary
Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulfide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693, https://doi.org/10.5194/bg-20-687-2023, https://doi.org/10.5194/bg-20-687-2023, 2023
Short summary
Short summary
We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749, https://doi.org/10.5194/bg-19-5729-2022, https://doi.org/10.5194/bg-19-5729-2022, 2022
Short summary
Short summary
We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631, https://doi.org/10.5194/bg-19-5617-2022, https://doi.org/10.5194/bg-19-5617-2022, 2022
Short summary
Short summary
Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399, https://doi.org/10.5194/bg-19-5375-2022, https://doi.org/10.5194/bg-19-5375-2022, 2022
Short summary
Short summary
Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219, https://doi.org/10.5194/bg-19-5199-2022, https://doi.org/10.5194/bg-19-5199-2022, 2022
Short summary
Short summary
Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902, https://doi.org/10.5194/bg-19-4883-2022, https://doi.org/10.5194/bg-19-4883-2022, 2022
Short summary
Short summary
The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
Short summary
Short summary
The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726, https://doi.org/10.5194/bg-19-3713-2022, https://doi.org/10.5194/bg-19-3713-2022, 2022
Short summary
Short summary
Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315, https://doi.org/10.5194/bg-19-3305-2022, https://doi.org/10.5194/bg-19-3305-2022, 2022
Short summary
Short summary
Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
Short summary
Short summary
This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
Short summary
Short summary
Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
Short summary
Short summary
Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
Short summary
Short summary
A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
Short summary
Short summary
Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
Short summary
Short summary
Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
Short summary
Short summary
Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Nimrod Wieler, Tali Erickson Gini, Osnat Gillor, and Roey Angel
Biogeosciences, 18, 3331–3342, https://doi.org/10.5194/bg-18-3331-2021, https://doi.org/10.5194/bg-18-3331-2021, 2021
Short summary
Short summary
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
Short summary
Short summary
In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
Short summary
Short summary
Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
Short summary
Short summary
The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
Short summary
Short summary
Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
Short summary
Short summary
This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
Short summary
Short summary
Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
Short summary
Short summary
Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
Short summary
Short summary
Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
Short summary
Short summary
The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
Short summary
Short summary
Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
Short summary
Short summary
Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
Short summary
Short summary
Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533, https://doi.org/10.5194/bg-17-1507-2020, https://doi.org/10.5194/bg-17-1507-2020, 2020
Short summary
Short summary
Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245, https://doi.org/10.5194/bg-17-1231-2020, https://doi.org/10.5194/bg-17-1231-2020, 2020
Short summary
Short summary
Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607, https://doi.org/10.5194/bg-17-597-2020, https://doi.org/10.5194/bg-17-597-2020, 2020
Short summary
Short summary
Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230, https://doi.org/10.5194/bg-17-215-2020, https://doi.org/10.5194/bg-17-215-2020, 2020
Short summary
Short summary
Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659, https://doi.org/10.5194/bg-16-4647-2019, https://doi.org/10.5194/bg-16-4647-2019, 2019
Short summary
Short summary
A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128, https://doi.org/10.5194/bg-16-4113-2019, https://doi.org/10.5194/bg-16-4113-2019, 2019
Short summary
Short summary
We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683, https://doi.org/10.5194/bg-16-1675-2019, https://doi.org/10.5194/bg-16-1675-2019, 2019
Short summary
Short summary
Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145, https://doi.org/10.5194/bg-16-1133-2019, https://doi.org/10.5194/bg-16-1133-2019, 2019
Short summary
Short summary
In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Yang Li, Zhaojun Wu, Xingchen Dong, Zifu Xu, Qixin Zhang, Haiyan Su, Zhongjun Jia, and Qingye Sun
Biogeosciences, 16, 573–583, https://doi.org/10.5194/bg-16-573-2019, https://doi.org/10.5194/bg-16-573-2019, 2019
Short summary
Short summary
This paper contributes to the study of bacterial carbon sequestration in mine tailings. Previous studies focused on carbonate mineral precipitation, while the role of autotrophs in carbon sequestration has been neglected. Carbon sequestration in two mine tailings treated with FeS2 was analyzed using 13C isotope labeling, pyrosequencing, and DNA SIP to identify carbon fixers. This paper is the first to investigate carbon sequestration by autotrophic groups in mine tailings.
Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin
Biogeosciences, 15, 7419–7433, https://doi.org/10.5194/bg-15-7419-2018, https://doi.org/10.5194/bg-15-7419-2018, 2018
Short summary
Short summary
In this study, we provide first evidence of lipid biomarker patterns and phylogenetic identities of key microbes mediating anaerobic oxidation of methane (AOM) communities in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. Our lipid and 16S rRNA results indicate that archaea of the ANME-2c and ANME-3 clades are involved in AOM in the MVs investigated.
Joshua F. Dean, Jurgen R. van Hal, A. Johannes Dolman, Rien Aerts, and James T. Weedon
Biogeosciences, 15, 7141–7154, https://doi.org/10.5194/bg-15-7141-2018, https://doi.org/10.5194/bg-15-7141-2018, 2018
Short summary
Short summary
Lakes, rivers, ponds and streams are significant contributors of the greenhouse gas carbon dioxide to the atmosphere. This is partly due to the decomposition of plant and soil organic matter transported through these aquatic systems by microbial communities. In determining how vulnerable this organic material is to decomposition during aquatic transport, we show that standardized treatments in experiments can affect the way microbial communities behave and potentially the experimental outcome.
Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, Michael E. Böttcher, Matthias Winkel, Paul L. E. Bodelier, and Susanne Liebner
Biogeosciences, 15, 6519–6536, https://doi.org/10.5194/bg-15-6519-2018, https://doi.org/10.5194/bg-15-6519-2018, 2018
Short summary
Short summary
Rewetting drained peatlands may lead to prolonged emission of the greenhouse gas methane, but the underlying factors are not well described. In this study, we found two rewetted fens with known high methane fluxes had a high ratio of microbial methane producers to methane consumers and a low abundance of methane consumers compared to pristine wetlands. We therefore suggest abundances of methane-cycling microbes as potential indicators for prolonged high methane emissions in rewetted peatlands.
Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, and Sonya T. Dyhrman
Biogeosciences, 15, 5761–5778, https://doi.org/10.5194/bg-15-5761-2018, https://doi.org/10.5194/bg-15-5761-2018, 2018
Short summary
Short summary
Trichodesmium is a keystone genus of marine cyanobacteria that is estimated to supply nearly half of the ocean’s fixed nitrogen, fuelling primary productivity and the cycling of carbon and nitrogen in the ocean. In our study we characterize Trichodesmium ecology across the western tropical South Pacific using gene and genome sequencing and geochemistry. We detected genes for phosphorus reduction, providing a mechanism for the noted importance of this organism in the ocean's phosphorus cycle.
Cited articles
Adhikari, R. Y., Malvankar, N. S., Tuominen, M. T., and Lovley, D. R.:
Conductivity of individual Geobacter pili, RSC Adv., 6, 8354–8357,
https://doi.org/10.1039/c5ra28092c, 2016.
Adler, M.: Geochemical Control Mechanisms Regulating the Initiation and
Limitation of Methanogenesis in Lacustrine and Estuarine Sediments: A Case
Study of Lake Kinneret and the Yarqon River, PhD thesis, Ben-Gurion
University of the Negev, Israel, 103 pp., 2015.
Adler, M., Eckert, W., and Sivan, O.: Quantifying rates of methanogenesis and
methanotrophy in Lake Kinneret sediments (Israel) using pore-water profiles,
Limnol. Oceanogr., 56, 1525–1535, https://doi.org/10.4319/lo.2011.56.4.1525,
2011.
Aepfler, R. F., Bühring, S. I., and Elvert, M.: Substrate characteristic
bacterial fatty acid production based on amino acid assimilation and
transformation in marine sediments, FEMS Microbiol. Ecol., 95, fiz131,
https://doi.org/10.1093/femsec/fiz131, 2019.
Almagro Armenteros, J. J., Tsirigos, K. D., Sønderby, C. K., Petersen, T.
N., Winther, O., Brunak, S., von Heijne, G., and Nielsen, H.: SignalP 5.0
improves signal peptide predictions using deep neural networks, Nat.
Biotechnol, 37, 420–423, https://doi.org/10.1038/s41587-019-0036-z, 2019.
Angle, J. C., Morin, T. H., Solden, L. M., Narrowe, A. B., Smith, G. J., Borton, M. A., Rey-Sanchez, C., Daly, R. A., Mirfenderesgi, G., Hoyt, D. W., Riley, W. J., Miller, C. S., Bohrer, G., and Wrighton, K. C.: Methanogenesis in
oxygenated soils is a substantial fraction of wetland methane emissions,
Nat. Commun., 8, 1567, https://doi.org/10.1038/s41467-017-01753-4, 2017.
Bai, Y. N., Wang, X. N., Wu, J., Lu, Y. Z., Fu, L., Zhang, F., Lau, T. C.,
and Zeng, R. J.: Humic substances as electron acceptors for anaerobic
oxidation of methane driven by ANME-2d, Water Res., 164, 114935,
https://doi.org/10.1016/j.watres.2019.114935, 2019.
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., and Pevzner, P. A.: SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol., 19, 455–477, https://doi.org/10.1089/cmb.2012.0021, 2012.
Bar-Or, I., Ben-Dov, E., Kushmaro, A., Eckert, W., and Sivan, O.: Methane-related changes in prokaryotes along geochemical profiles in sediments of Lake Kinneret (Israel), Biogeosciences, 12, 2847–2860, https://doi.org/10.5194/bg-12-2847-2015, 2015.
Bar-Or, I., Elvert, M., Eckert, W., Kushmaro, A., Vigderovich, H., Zhu, Q.,
Ben-Dov, E., and Sivan, O.: Iron-coupled anaerobic oxidation of methane
performed by a mixed bacterial-archaeal community based on poorly reactive
minerals, Environ. Sci. Technol., 51, 12293–12301,
https://doi.org/10.1021/acs.est.7b03126, 2017.
Bastviken, D., Tranvik, L. J., Downing, J. A., Crill, P. M., and
Enrich-Prast, A.: Freshwater methane emissions offset the continental carbon
sink, Science, 331, 50, https://doi.org/10.1126/science.1196808, 2011.
Beck, D. A. C., Kalyuzhnaya, M. G., Malfatti, S., Tringe, S. G., Glavina del
Rio, T., Ivanova, N., Lidstrom, M. E., and Chistoserdova L.: A metagenomic
insight into freshwater methane-utilizing communities and evidence for
cooperation between the Methylococcaceae and the Methylophilaceae, PeerJ, 1,
e23, https://doi.org/10.7717/peerj.23, 2013.
Bond, D. R. and Lovley, D. R.: Reduction of Fe(III) oxide by methanogens in
the presence and absence of extracellular quinones, Environ. Microbiol., 4,
115–124, https://doi.org/10.1046/j.1462-2920.2002.00279.x, 2002.
Boyd, J. A., Jungbluth, S. P., Leu, A. O., Evans, P. N., Woodcroft, B. J., Chadwick, G. L., Orphan, V. J., Amend, J. P., Rappé, M. S., and Tyson, G. W.: Divergent
methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi, ISME
J., 13, 1269–1279, https://doi.org/10.1038/s41396-018-0343-2, 2019.
Bräuer, S., Cadillo-Quiroz, H., Kyrpides, N., Woyke, T., Goodwin, L., Detter, C., Podell, S., Yavitt, J. B., and Zinder, S. H.: Genome of
Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland
environments, Microbiology+, 161, 1572–1581,
https://doi.org/10.1099/mic.0.000117, 2015.
Bray, M. S., Wu, J., Padilla, C. C., Stewart, F. J., Fowle, D. A., Henny, C., Simister, R. L., Thompson, K. J., Crowe, S. A., and Glass, J. B.: Phylogenetic and structural
diversity of aromatically dense pili from environmental metagenomes,
Environ. Microbiol. Rep., 12, 49–57,
https://doi.org/10.1111/1758-2229.12809, 2020.
Buckel, W. and Thauer, R. K.: Flavin-based electron bifurcation,
ferredoxin, flavodoxin, and anaerobic respiration with protons (Ech) or
NAD+ (Rnf) as electron acceptors: A historical review, Front. Microbiol.,
9, 401, https://doi.org/10.3389/fmicb.2018.00401, 2018.
Cai, C., Leu, A. O., Xie, G.-J., Guo, J., Feng, Y., Zhao, J.-X., Tyson, G. W., Yuan, Z., and Hu, S.: A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction, ISME J., 12, 1929–1939, https://doi.org/10.1038/s41396-018-0109-x, 2018.
Cao, Q., Liu, X., Li, N., Xie, Z., Li, Z., and Li, D.: Stable-isotopic
analysis and high-throughput pyrosequencing reveal the coupling process and
bacteria in microaerobic and hypoxic methane oxidation coupled to
denitrification, Environ. Pollut., 250, 863–872,
https://doi.org/10.1016/j.envpol.2019.04.111, 2019.
Carr, S. A., Schubotz, F., Dunbar, R. B., Mills, C. T., Dias, R., Summons,
R. E., and Mandernack, K. W.: Acetoclastic Methanosaeta are dominant
methanogens in organic-rich antarctic marine sediments, ISME J., 12,
330–342, https://doi.org/10.1038/ismej.2017.150, 2018.
Christensen, L. F. B., Hansen, L. M., Finster, K., Christiansen, G.,
Nielsen, P. H., Otzen, D. E., and Dueholm, M. S.: The sheaths of
Methanospirillum are made of a new type of amyloid protein, Front.
Microbiol., 9, 1–11, https://doi.org/10.3389/fmicb.2018.02729, 2018.
Dueholm, M. S., Larsen, P., Finster, K., Stenvang, M. R., Christiansen, G., Vad, B. S., Bøggild, A., Otzen, D. E., and Nielsen, P. H.: The tubular sheaths
encasing Methanosaeta thermophila filaments are functional amyloids, J.
Biol. Chem., 290, 20590–20600, https://doi.org/10.1074/jbc.M115.654780,
2015.
Eckert, W. and Conrad, R.: Sulfide and methane evolution in the hypolimnion
of a subtropical lake: A three-year study, Biogeochemistry, 82, 67–76,
https://doi.org/10.1007/s10533-006-9053-3, 2007.
Elul, M., Rubin-Blum, M., Ronen, Z., Bar-Or, I., Sivan, O., and Eckert, W.: Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret iron-rich methanic sediments, figshare, data set Collection, https://doi.org/10.6084/m9.figshare.c.5245157.v1, 2020.
Ettwig, K. F., Butler, M. K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M. M. M., Schreiber, F., Dutilh, B. E., Zedelius, J., de Beer, D., Gloerich, J., Wessels, H. J. C. T., van Alen, T., Luesken, F., Wu, M. L., van de Pas-Schoonen, K. T., Op den Camp, H. J. M., Janssen-Megens, E. M., Francoijs, K.-J., Stunnenberg, H., Weissenbach, J., Jetten, M. S. M., and Strous, M.: Nitrite-driven
anaerobic methane oxidation by oxygenic bacteria, Nature, 464, 543–548,
https://doi.org/10.1038/nature08883, 2010.
Ettwig, K. F., Zhu, B., Speth, D., Keltjens, J. T., Jetten, M. S. M., and
Kartal, B.: Archaea catalyze iron-dependent anaerobic oxidation of methane,
P. Natl. Acad. Sci. USA, 113, 12792–12796,
https://doi.org/10.1073/pnas.1609534113, 2016.
Evans, P. N., Parks, D. H., Chadwick, G. L., Robbins, S. J., Orphan, V. J.,
Golding, S. D., and Tyson, G. W.: Methane metabolism in the archaeal phylum
Bathyarchaeota revealed by genome-centric metagenomics, Science, 350,
434–438, https://doi.org/10.1126/science.aac7745, 2015.
Evans, P. N., Boyd, J. A., Leu, A. O., Woodcroft, B. J., Parks, D. H.,
Hugenholtz, P., and Tyson, G. W.: An evolving view of methane metabolism in
the Archaea, Nat. Rev. Microbiol., 17, 219–232,
https://doi.org/10.1038/s41579-018-0136-7, 2019.
Filman, D. J., Marino, S. F., Ward, J. E., Yang, L., Mester, Z., Bullitt,
E., Lovley, D. R., and Strauss, M.: Cryo-EM reveals the structural basis of
long-range electron transport in a cytochrome-based bacterial nanowire,
Commun. Biol., 2, 19–24, https://doi.org/10.1038/s42003-019-0448-9, 2019.
Frank, Y. A., Kadnikov, V. V., Lukina, A. P., Banks, D., Beletsky, A. V., Mardanov, A. V., Sen'kina, E. I., Avakyan, M. R., Karnachuk, O. V., and Ravin, N. V.: Characterization
and genome analysis of the first facultatively alkaliphilic
Thermodesulfovibrio isolated from the deep terrestrial subsurface, Front.
Microbiol., 7, 1–11, https://doi.org/10.3389/fmicb.2016.02000, 2016.
Froelich, P. N., Klinkhammer, G. P., Bender, M. L., Luedtke, N. A., Heath, G. R., Cullen, D., Dauphin, P., Hammond, D., Hartman, B., and Maynard, V.: Early
oxidation of organic matter in pelagic sediments of the eastern equatorial
Atlantic: suboxic diagenesis, Geochim. Cosmochim. Ac., 43, 1075–1090,
https://doi.org/10.1016/0016-7037(79)90095-4, 1979.
Fu, L., Li, S.-W., Ding, Z.-W., Ding, J., Lu, Y.-Z., and Zeng, R. J.: Iron
reduction in the DAMO/Shewanella oneidensis MR-1 coculture system and the
fate of Fe(II), Water Res., 88, 808–815,
https://doi.org/10.1016/J.WATRES.2015.11.011, 2016.
Glöckner, F. O., Yilmaz, P., Quast, C., Gerken, J., Beccati, A., Ciuprina, A., Bruns, G., Yarza, P., Peplies, J., Westram, R., and Ludwig, W.: 25 years of serving
the community with ribosomal RNA gene reference databases and tools, J.
Biotechnol., 261, 169–176, https://doi.org/10.1016/j.jbiotec.2017.06.1198,
2017.
Gralnick, J. A. and Newman. D. K.: Extracellular respiration, Mol.
Microbiol., 65, 1–11, https://doi.org/10.1111/j.1365-2958.2007.05778.x,
2007.
Gruber-Vodicka, H. R., Seah, B. K., and Pruesse, E.: phyloFlash – Rapid
SSU rRNA profiling and targeted assembly from metagenomes, bioRxiv, 521922,
https://doi.org/10.1101/521922, 2019.
Haroon, M. F., Hu, S., Shi, Y., Imelfort, M., Keller, J., Hugenholtz, P.,
Yuan, Z., and Tyson, G. W.: Anaerobic oxidation of methane coupled to
nitrate reduction in a novel archaeal lineage, Nature, 500, 567–570,
https://doi.org/10.1038/nature12375, 2013.
He, Q., Yu, L., Li, J., He, D., Cai, X., and Zhou, S.: Electron shuttles
enhance anaerobic oxidation of methane coupled to iron(III) reduction, Sci.
Total Environ., 688, 664–672,
https://doi.org/10.1016/J.SCITOTENV.2019.06.299, 2019.
He, Y., Li, M., Perumal, V., Feng, X., Fang, J., Xie, J., Sievert, S. M.,
and Wang, F.: Genomic and enzymatic evidence for acetogenesis among multiple
lineages of the archaeal phylum Bathyarchaeota widespread in marine
sediments, Nat. Microbiol., 1, 16035,
https://doi.org/10.1038/nmicrobiol.2016.35, 2016.
He, Z., Zhang, Q., Feng, Y., Luo, H., Pan, X., and Gadd, G. M.:
Microbiological and environmental significance of metal-dependent anaerobic
oxidation of methane, Sci. Total Environ., 610–611, 759–768,
https://doi.org/10.1016/j.scitotenv.2017.08.140, 2018.
Holler, T., Wegener, G., Niemann, H., Deusner, C., Ferdelman, T. G., Boetius,
A., Brunner, B., and Widdel, F.: Carbon and sulfur back flux during
anaerobic microbial oxidation of methane and coupled sulfate reduction,
P. Natl. Acad. Sci. USA, 108, E1484–E1490,
https://doi.org/10.1073/pnas.1106032108, 2011.
Holmes, D. E., Rotaru, A. E., Ueki, T., Shrestha, P. M., Ferry, J. G., and
Lovley, D. R.: Electron and proton flux for carbon dioxide reduction in
methanosarcina barkeri during direct interspecies electron transfer, Front.
Microbiol., 9, 1–11, https://doi.org/10.3389/fmicb.2018.03109, 2018.
Holmes, D. E., Ueki, T., Tang, H., Zhou, J., Smith, J. A., Chaput, G., and
Lovley, D. R.: A membrane-bound cytochrome enables Methanosarcina
acetivorans to conserve energy from extracellular electron transfer, MBio,
10, 1–12, https://doi.org/10.1128/mBio.00789-19, 2019.
Imachi, H. and Sakai, S.: Methanoregulaceae, in: Bergey's manual of systematics of Archaea and Bacteria, edited by: Bergey, D. H., Harrison, F. C., Breed, R. S., Hammer, B. W., Huntoon, F. M., Wiley, New York, NY, 1–4, https://doi.org/10.1002/9781118960608.fbm00271, 2016.
Inaba, R., Nagoya, M., Kouzuma, A., and Watanabe K.: Metatranscriptomic
evidence for magnetite nanoparticle-stimulated acetoclastic methanogenesis
under continuous agitation, Appl. Environ. Microb., 85, e01733-19, https://doi.org/10.1128/AEM.01733-19, 2019.
Kadnikov, V. V., Savvichev, A. S., Mardanov, A. V., Beletsky, A. V., Merkel,
A. Y., Ravin, N. V., and Pimenov, N. V.: Microbial communities involved in
the methane cycle in the near-bottom water layer and sediments of the
meromictic subarctic Lake Svetloe, Antonie van Leeuwenhoek, 112, 1801–1814, https://doi.org/10.1007/s10482-019-01308-1, 2019.
Kang, D. D., Froula, J., Egan, R., and Wang, Z.: MetaBAT, an efficient tool
for accurately reconstructing single genomes from complex microbial
communities, PeerJ, 3, e1165, https://doi.org/10.7717/peerj.1165, 2015.
Lang, K., Schuldes, J., Klingl, A., Poehlein, A., Daniel, R., and Brune, A.:
New mode of energy metabolism in the seventh order of methanogens as
revealed by comparative genome analysis of “Candidatus Methanoplasma
termitum.”, Appl. Environ. Microb., 81, 1338–1352,
https://doi.org/10.1128/AEM.03389-14, 2015.
Lazar, C. S., Biddle, J. F., Meador, T. B., Blair, N., Hinrichs, K. U., and
Teske, A. P.: Environmental controls on intragroup diversity of the
uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage
naturally enriched in anoxic sediments of the White Oak River estuary (North
Carolina, USA), Environ. Microbiol., 17, 2228–2238,
https://doi.org/10.1111/1462-2920.12659, 2015.
Lazar, C. S., Baker, B. J., Seitz, K. W., and Teske, A. P.: Genomic
reconstruction of multiple lineages of uncultured benthic archaea suggests
distinct biogeochemical roles and ecological niches, ISME J., 11, 1118–1129,
https://doi.org/10.1038/ismej.2016.189, 2017.
Leang, C., Coppi, M. V., and Lovley, D. R.: OmcB, a c-type polyheme
cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens, J.
Bacteriol., 185, 2096–2103, https://doi.org/10.1128/JB.185.7.2096-2103.2003,
2003.
Leu, A. O., Cai, C., McIlroy, S. J., Southam, G., Orphan, V. J., Yuan, Z.,
Hu, S., and Tyson, G. W.: Anaerobic methane oxidation coupled to manganese
reduction by members of the Methanoperedenaceae, ISME J., 1–12,
https://doi.org/10.1038/s41396-020-0590-x, 2020.
Liang, B., Wang, L.-Y., Mbadinga, S. M., Liu, J.-F., Yang, S.-Z., Gu, J.-D.,
and Mu, B.-Z.: Anaerolineaceae and Methanosaeta turned to be the dominant
microorganisms in alkanes-dependent methanogenic culture after long-term of
incubation, AMB Express, 5, 37, https://doi.org/10.1186/s13568-015-0117-4,
2015.
Liu, C., Sun, D., Zhao, Z., Dang, Y., and Holmes, D. E.: Methanothrix
enhances biogas upgrading in microbial electrolysis cell via direct electron
transfer, Bioresour. Technol., 291, 121877,
https://doi.org/10.1016/j.biortech.2019.121877, 2019a.
Liu, X., Ye, Y., Xiao, K., Rensing, C., and Zhou, S.: Molecular evidence for
the adaptive evolution of Geobacter sulfurreducens to perform dissimilatory
iron reduction in natural environments, Mol. Microbiol., 289, mmi.14443,
https://doi.org/10.1111/mmi.14443, 2019b.
Lovley, D. R.: Live wires: direct extracellular electron exchange for
bioenergy and the bioremediation of energy-related contamination, Energy
Environ. Sci., 4, 4896–4906, https://doi.org/10.1039/c1ee02229f, 2011.
Lovley, D. R. and Walker, D. J. F.: Geobacter protein nanowires, Front.
Microbiol., 10, 2078, https://doi.org/10.3389/fmicb.2019.02078, 2019.
Martinez-Cruz, K., Sepulveda-Jauregui, A., Casper, P., Anthony, K. W.,
Smemo, K. A., and Thalasso, F.: Ubiquitous and significant anaerobic
oxidation of methane in freshwater lake sediments, Water Res., 144, 332–340,
https://doi.org/10.1016/j.watres.2018.07.053, 2018.
Maus, I., Rumming, M., Bergmann, I., Heeg, K., Pohl, M., Nettmann, E., Jaenicke, S., Blom, J., Pühler, A., Schlüter, A., Sczyrba, A., and Klocke, M.: Characterization of
Bathyarchaeota genomes assembled from metagenomes of biofilms residing in
mesophilic and thermophilic biogas reactors, Biotechnol. Biofuels, 11, 167,
https://doi.org/10.1186/s13068-018-1162-4, 2018.
McGlynn, S. E., Chadwick, G. L., Kempes, C. P., and Orphan, V. J.: Single
cell activity reveals direct electron transfer in methanotrophic consortia,
Nature, 526, 531–535, https://doi.org/10.1038/nature15512, 2015.
Menzel, P., Ng, K. L., and Krogh, A.: Fast and sensitive taxonomic
classification for metagenomics with Kaiju, Nat. Commun. 7, 1–9,
https://doi.org/10.1038/ncomms11257, 2016.
Moller, S., Croning, M. D. R., and Apweiler, R..: Evaluation of methods for
the prediction of membrane spanning regions, Bioinformatics, 18, 218–218,
https://doi.org/10.1093/bioinformatics/18.1.218, 2002.
Moran, J. J., House, C. H., Freeman, K. H., and Ferry, J. G.: Trace methane
oxidation studied in several Euryarchaeota under diverse conditions, Archaea,
303–309, 2005.
Narihiro, T., Nobu, M. K., Tamaki, H., Kamagata, Y., Sekiguchi, Y., and Liu,
W. T.: Comparative genomics of syntrophic branched-chain fatty acid
degrading bacteria, Microbes Environ., 31, 288–292,
https://doi.org/10.1264/jsme2.ME16057, 2016.
Newman, D. K. and Kolter, R.: A role for excreted quinones in extracellular
electron transfer, Nature, 405, 94–97, https://doi.org/10.1038/35011098,
2000.
Nobu, M. K., Narihiro, T., Kuroda, K., Mei, R., and Liu, W.-T.: Chasing the
elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious
methyl-reducing methanogen, ISME J., 10, 2478–2487,
https://doi.org/10.1038/ismej.2016.33, 2016.
Norði, K. À., Thamdrup, B., and Schubert, C. J.: Anaerobic oxidation
of methane in an iron-rich Danish freshwater lake sediment, Limnol.
Oceanogr, 58, 546–554, https://doi.org/10.4319/lo.2013.58.2.0546, 2013.
Nurk, S., Bankevich, A., and Antipov, D.: Assembling genomes and
mini-metagenomes from highly chimeric reads, Res. Comput. Mol. Biol., 7821,
158–170, https://doi.org/10.1007/978-3-642-37195-0, 2013.
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., Astashyn, A., Badretdin, A., Bao, Y., Blinkova, O., Brover, V., Chetvernin, V., Choi, J., Cox, E., Ermolaeva, O., Farrell, C. F., Goldfarb, T., Gupta, T., Haft, D., Hatcher, E., Hlavina, W., Joardar, V. S., Kodali, V. K., Li, W., Maglott, D., Masterson, P., McGarvey, K. M., Murphy, M. R., O'Neill, K., Pujar, S., Rangwala, S. H., Rausch, D., Riddick, L. D., Schoch, C., Shkeda, A., Storz, S. S., Sun, H., Thibaud-Nissen, F., Tolstoy, I., Tully, R. E., Vatsan, A. R., Wallin, C., Webb, D., Wu, W., Landrum, M. J., Kimchi, A., Tatusova, T., DiCuccio, M., Kitts, P., Murphy, T. D., and Pruitt, K. D.: Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation, Nucleic Acids Res., 44, D733–D745, https://doi.org/10.1093/nar/gkv1189, 2016.
Paquete, C. M., Fonseca, B. M., Cruz, D. R., Pereira, T. M., Pacheco, I.,
Soares, C. M., and Louro, R. O.: Exploring the molecular mechanisms of
electron shuttling across the microbe/metal space, Front. Microbiol., 5,
1–12, https://doi.org/10.3389/fmicb.2014.00318, 2014.
Park, J., Park, S., and Kim, M.: Anaerobic degradation of amino acids
generated from the hydrolysis of sewage sludge, Environ. Technol., 35, 1133–1139, https://doi.org/10.1080/09593330.2013.863951, 2014.
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A.,
Chaumeil, P.-A., and Hugenholtz, P.: A standardized bacterial taxonomy based
on genome phylogeny substantially revises the tree of life, Nat. Biotechnol.,
36, 996–1004, 2018.
Patel, G. B., Sprott, G. D., Humphrey, R. W., and Beveridge, T. J.:
Comparative analyses of the sheath structures of Methanothrix concilii GP6
and Methanospirillum hungatei strains GP1 and JF1, Can. J. Microbiol., 32,
623–631, https://doi.org/10.1139/m86-117, 1986.
Pereira, I. A. C., Ramos, A. R., Grein, F., Marques, M. C., da Silva, S. M.,
and Venceslau, S. S.: A comparative genomic analysis of energy metabolism in
sulfate reducing Bacteria and Archaea, Front. Microbiol., 2, 1–22,
https://doi.org/10.3389/fmicb.2011.00069 2011.
Prestat, E., David, M. M., Hultman, J., Taş, N., Lamendella, R., Dvornik, J., Mackelprang, R., Myrold, D. D., Jumpponen, A., Tringe, S. G., Holman, E., Mavromatis, K., and Jansson, J. K: FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus, Nucleic Acids Res., 42, e145–e145, https://doi.org/10.1093/nar/gku702, 2014.
Raghoebarsing, A. A., Pol, A., Van De Pas-Schoonen, K. T., Smolders, A. J. P., Ettwig, K. F., Rijpstra, W. I. C., Schouten, S., Sinninghe Damsté, J. S., Op den Camp, H. J. M., Jetten, M. S. M., and Strous, M.: A
microbial consortium couples anaerobic methane oxidation to denitrification,
Nature, 440, 918–921, https://doi.org/10.1038/nature04617, 2006.
Ramos, A. R., Grein, F., Oliveira, G. P., Venceslau, S. S., Keller, K. L.,
Wall, J. D., and Pereira, I. A. C.: The FlxABCD-HdrABC proteins correspond
to a novel NADH dehydrogenase/heterodisulfide reductase widespread in
anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio
vulgaris Hildenborough, Environ. Microbiol., 17, 2288–2305,
https://doi.org/10.1111/1462-2920.12689, 2015.
Reguera, G., McCarthy, K. D., Mehta, T., Nicoll, J. S., Tuominen, M. T., and
Lovley, D. R.: Extracellular electron transfer via microbial nanowires,
Nature, 435, 1098–1101, https://doi.org/10.1038/nature03661, 2005.
Rotaru, A. E., Shrestha, P. M., Liu, F., Shrestha, M., Shrestha, D., Embree, M., Zengler, K., Wardman, C., Nevin, K. P., and Lovley, D. R.: A new model for
electron flow during anaerobic digestion: Direct interspecies electron
transfer to Methanosaeta for the reduction of carbon dioxide to methane,
Energy Environ. Sci. 7, 408–415, https://doi.org/10.1039/c3ee42189a, 2014.
Scheller, S., Yu, H., Chadwick, G. L., McGlynn, S. E., and Orphan, V. J.:
Artificial electron acceptors decouple archaeal methane oxidation from
sulfate reduction, Science, 351, 703–707,
https://doi.org/10.1126/SCIENCE.AAD7154, 2016.
Schwarz, J. I. K., Eckert, W., and Conrad, R.: Community structure of
Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel),
Syst. Appl. Microbiol., 30, 239–254,
https://doi.org/10.1016/J.SYAPM.2006.05.004, 2007.
Scully, S. M. and Orlygsson, J.: Branched-chain amino acid catabolism of
Thermoanaerobacter pseudoethanolicus reveals potential route to
branched-chain alcohol formation, Extremophiles, 24, 121–133,
https://doi.org/10.1007/s00792-019-01140-5, 2019.
Seah, B. K. B. and Gruber-Vodicka, H. R.: gbtools: Interactive
visualization of metagenome bins in R. Front, Microbiology+, 6, 1451,
https://doi.org/10.3389/fmicb.2015.01451, 2015.
Segarra, K. E. A., Schubotz, F., Samarkin, V., Yoshinaga, M. Y., Hinrichs,
K. U., and Joye, S. B.: High rates of anaerobic methane oxidation in
freshwater wetlands reduce potential atmospheric methane emissions, Nat.
Commun., 6, 1–8, https://doi.org/10.1038/ncomms8477, 2015.
Sekiguchi, Y., Muramatsu, M., Imachi, H., Narihiro, T., Ohashi, A., Harada,
H., Hanada, S., and Kamagata, Y.: Thermodesulfovibrio aggregans sp. nov. and
Thermodesulfovibrio thiophilus sp. nov., anaerobic,thermophilic,
sulfate-reducing bacteria isolated from thermophilic methanogenic sludge,
and emended description of the genus Thermodesulfovibrio, Int. J. Syst.
Evol. Microbiol., 58, 2541–2548,
https://doi.org/10.1099/ijs.0.2008/000893-0, 2008.
Shi, L., Dong, H., Reguera, G., Beyenal, H., Lu, A., Liu, J., Yu, H.-Q., and
Fredrickson, J. K.: Extracellular electron transfer mechanisms between
microorganisms and minerals, Nat. Rev. Microbiol., 14, 651–662,
https://doi.org/10.1038/nrmicro.2016.93, 2016.
Shi, L., Squier,T. C., Zachara, J. M., and Fredrickson, J. K.: Respiration
of metal (hydr)oxides by Shewanella and Geobacter: A key role for multihaem
c-type cytochromes, Mol. Microbiol., 65, 12–20,
https://doi.org/10.1111/j.1365-2958.2007.05783.x, 2007.
Sieber, C. M. K., Probst, A. J., Sharrar, A., Thomas, B. C., Hess, M.,
Tringe, S. G., and Banfield, J. F.: Recovery of genomes from metagenomes via
a dereplication, aggregation and scoring strategy, Nat. Microbiol., 3,
836–843, https://doi.org/10.1038/s41564-018-0171-1, 2018.
Sieber, J. R., McInerney, M. J., and Gunsalus, R. P.: Genomic insights into
syntrophy: The paradigm for anaerobic metabolic cooperation, Annu. Rev.
Microbiol., 66, 429–452,
https://doi.org/10.1146/annurev-micro-090110-102844, 2012.
Sivan, O., Adler, M., Pearson, A., Gelman, F., Bar-Or, I., John, S. G., and
Eckert, W.: Geochemical evidence for iron-mediated anaerobic oxidation of
methane, Limnol. Oceanogr., 56, 1536–1544,
https://doi.org/10.4319/lo.2011.56.4.1536, 2011.
Sivan, O., Shusta, S. S., and Valentine, D. L.: Methanogens rapidly
transition from methane production to iron reduction, Geobiology, 14,
190–203, https://doi.org/10.1111/gbi.12172, 2016.
Smith, K. S. and Ingram-Smith, C.: Methanosaeta, the forgotten methanogen?
Trends Microbiol., 15, 150–155, https://doi.org/10.1016/j.tim.2007.02.002,
2007.
Soo, V. W. C., McAnulty, M. J., Tripathi, A., Zhu, F., Zhang, L., Hatzakis, E., Smith, P. B., Agrawal, S., Nazem-Bokaee, H., Gopalakrishnan, S., Salis, H. M., Ferry, J. G., Maranas, C. D., Patterson, A. D., and Wood, T. K.: Reversing methanogenesis to capture methane for liquid biofuel precursors, Microb. Cell Fact., 15, 11, https://doi.org/10.1186/s12934-015-0397-z, 2016.
Tamames, J. and Puente-Sánchez, F.: SqueezeMeta, a highly portable,
fully automatic metagenomic analysis pipeline, Front. Microbiol., 10,
https://doi.org/10.3389/fmicb.2018.03349, 2019.
Tan, S., Liu, J., Fang, Y., Hedlund, B. P., Lian, Z.-H., Huang, L.-Y., Li, J.-T., Huang, L.-N., Li, W.-J., Jiang, H.-C., Dong, H.-L., and Shu, W.-S.: Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics, ISME J., 13, 2044–2057, https://doi.org/10.1038/s41396-019-0415-y, 2019.
Thauer, R. K. and Shima, S.: Methane as fuel for anaerobic microorganisms,
Ann. N.Y. Acad. Sci., 1125, 158–170,
https://doi.org/10.1196/annals.1419.000, 2008.
Valenzuela, E. I., Prieto-Davó, A., López-Lozano, N. E.,
Hernández-Eligio, A., Vega-Alvarado, L., Juárez, K., Sarahí García-González, A., López, M. G., and Cervantes, F. J.:
Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic
Matter in a Tropical Wetland, Appl. Environ. Microbiol., 83, e00645-17,
https://doi.org/10.1128/AEM.00645-17, 2017.
Valenzuela, E. I., Avendaño, K. A., Balagurusamy, N., Arriaga, S.,
Nieto-Delgado, C., Thalasso, F., and Cervantes, F. J.: Electron shuttling mediated by
humic substances fuels anaerobic methane oxidation and carbon burial in
wetland sediments, Sci. Total Environ., 650, 2674–2684,
https://doi.org/10.1016/J.SCITOTENV.2018.09.388, 2019.
Vigderovich, H., Liang, L., Herut, B., Wang, F., Wurgaft, E., Rubin-Blum, M., and Sivan, O.: Evidence for microbial iron reduction in the methanic sediments of the oligotrophic southeastern Mediterranean continental shelf, Biogeosciences, 16, 3165–3181, https://doi.org/10.5194/bg-16-3165-2019, 2019.
Vuillemin, A., Horn, F., Friese, A., Winkel, M., Alawi, M., Wagner, D., Henny, C., Orsi, W. D., Crowe, S. A., and Kallmeyer, J.: Metabolic potential of
microbial communities from ferruginous sediments, Environ. Microbiol., 20,
4297–4313, https://doi.org/10.1111/1462-2920.14343, 2018.
Wagner, T., Koch, J., Ermler U., and Shima, S.: Methanogenic heterodisulfide
reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for
reduction, Science, 357, 699–703, https://doi.org/10.1126/science.1252826,
2017.
Walker, D. J. F., Nevin, K. P., Holmes, D. E., Rotaru, A. E., Ward, J. E., Woodard, T. L., Zhu, J., Ueki, T., Nonnenmann, S. S., McInerney, M. J., and Lovley, D. R.: Syntrophus
conductive pili demonstrate that common hydrogen-donating syntrophs can have
a direct electron transfer option, ISME J., 1–10,
https://doi.org/10.1038/s41396-019-0575-9, 2020.
Wang, F., Gu, Y., O'Brien, J. P., Yi, S. M., Ebru Yalcin, S., Srikanth, V., Shen, C., Vu, D., Ing, N. L., Hochbaum, A. I., Egelman, E. H., and Malvankar, N. S.: Structure of microbial
nanowires reveals stacked hemes that transport electrons over micrometers,
Cell, 177, 361–369, https://doi.org/10.1016/j.cell.2019.03.029, 2019.
Wang, H., Byrne, J. M., Liu, P., Liu, J., Dong, X., and Lu, Y.: Redox
cycling of Fe(II) and Fe(III) in magnetite accelerates aceticlastic
methanogenesis by Methanosarcina mazei, Environ. Microbiol. Rep., 12,
97–109, https://doi.org/10.1111/1758-2229.12819, 2020.
Wang, L., Miao, X., Ali, J., Lyu, T., and Pan, G.: Quantification of oxygen
nanobubbles in particulate matters and potential applications in remediation
of anaerobic environment, ACS Omega, 3, 10624–10630,
https://doi.org/10.1021/acsomega.8b00784, 2018.
Wang, Y. and Newman, D. K.: Redox reactions of phenazine antibiotics with
ferric (hydr)oxides and molecular oxygen, Environ. Sci. Technol., 42,
2380–2386, https://doi.org/10.1021/es702290a, 2008.
Wegener, G., Krukenberg, V., Riedel, D., Tegetmeyer, H. E., and Boetius, A.:
Intercellular wiring enables electron transfer between methanotrophic
archaea and bacteria, Nature, 526, 587–590,
https://doi.org/10.1038/nature15733, 2015.
Wegener, G., Krukenberg, V., Ruff, S. E., Kellermann, M. Y., and Knittel,
K.: Metabolic capabilities of microorganisms involved in and associated with
the anaerobic oxidation of methane, Front. Microbiol., 7, 46,
https://doi.org/10.3389/fmicb.2016.00046, 2016.
Welte, C. and Deppenmeier, U.: Bioenergetics and anaerobic respiratory
chains of aceticlastic methanogens, Biochim. Biophys. Acta, 1837,
1130–1147, https://doi.org/10.1016/j.bbabio.2013.12.002, 2014.
Wu, Y. W., Simmons, B. A., and Singer, S. W.: MaxBin 2.0: an automated
binning algorithm to recover genomes from multiple metagenomic datasets,
Bioinformatics, 32, 605–607, https://doi.org/10.1093/bioinformatics/btv638,
2015.
Wuebbles, D. J. and Hayhoe, K.: Atmospheric methane and global change.
Earth-Sci. Rev., 57, 177–210,
https://doi.org/10.1016/S0012-8252(01)00062-9, 2002.
Xin, J. Y., Cui, J. R., Niu, J. Z., Hua, S. F., Xia, C. G., Ben Li, S., and
Zhu, L. M.: Production of methanol from methane by methanotrophic bacteria,
Biocatal. Biotransformation, 22, 225–229,
https://doi.org/10.1080/10242420412331283305, 2004.
Yan, Z. and Ferry, J. G.: Electron bifurcation and confurcation in
methanogenesis and reverse methanogenesis, Front. Microbiol., 9, 1322,
https://doi.org/10.3389/fmicb.2018.01322, 2018.
Yan, Z., Joshi, P., Gorski, C. A., and Ferry, J. G.: A biochemical framework
for anaerobic oxidation of methane driven by Fe(III)-dependent respiration,
Nat. Commun., 9, 1642, https://doi.org/10.1038/s41467-018-04097-9, 2018.
Yee, M. O., and Rotaru, A. E.: Extracellular electron uptake in
Methanosarcinales is independent of multiheme c-type cytochromes, Sci. Rep.-UK, 10, 372, https://doi.org/10.1038/s41598-019-57206-z, 2020.
Yu, T., Wu, W., Liang, W., Lever, M. A., Hinrichs, K. U., and Wang, F.:
Growth of sedimentary Bathyarchaeota on lignin as an energy source, P.
Natl. Acad. Sci. USA, 115, 6022–6027,
https://doi.org/10.1073/pnas.1718854115, 2018.
Zehnder, A. J. B. and Brock, T. D.: Methane formation and methane oxidation
by methanogenic Bacteria, J. Bacteriol., 137, 420–432, 1979.
Zhang, L., Zhao, T., Shen, T., and Gao G.: Seasonal and spatial variation in
the sediment bacterial community and diversity of Lake Bosten, China, J.
Basic Microbiol., 59, 224–233, https://doi.org/10.1002/jobm.201800452, 2019.
Zhao, Z., Wang, J., Li, Y., Zhu, T., Yu, Q., Wang, T., Liang, S., and Zhang,
Y.: Why do DIETers like drinking: Metagenomic analysis for methane and
energy metabolism during anaerobic digestion with ethanol, Water Res., 171,
115425, https://doi.org/10.1016/j.watres.2019.115425, 2020.
Zhou, Z., Pan, J., Wang, F., Gu, J.-D., and Li, M.: Bathyarchaeota: globally
distributed metabolic generalists in anoxic environments, FEMS Microbiol.
Rev., 023, 639–655, https://doi.org/10.1093/femsre/fuy023, 2018.
Zhu, Y., Purdy, K. J., Eyice, Ö., Shen, L., Harpenslager, S. F.,
Yvon-Durocher, G., Dumbrell, A. J., and Trimmer, M.: Disproportionate
increase in freshwater methane emissions induced by experimental warming,
Nat. Clim. Change, 10, 685–690, https://doi.org/10.1038/s41558-020-0824-y,
2020.
Ziels, R. M., Nobu, M. K., and Sousa, D. Z.: Elucidating syntrophic
butyrate-degrading populations in anaerobic digesters using
stable-isotope-informed genome-resolved metagenomics, mSystems, 4, 1–16,
https://doi.org/10.1128/msystems.00159-19, 2019.
Altmetrics
Final-revised paper
Preprint