Articles | Volume 17, issue 6
https://doi.org/10.5194/bg-17-1451-2020
© Author(s) 2020. 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-17-1451-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
23 Mar 2020
Research article |
| 23 Mar 2020
| 23 Mar 2020
The pH-based ecological coherence of active canonical methanotrophs in paddy soils
Jun Zhao
State Key Laboratory of Soil and Sustainable Agriculture, Institute
of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
Yuanfeng Cai
State Key Laboratory of Soil and Sustainable Agriculture, Institute
of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
Zhongjun Jia
CORRESPONDING AUTHOR
State Key Laboratory of Soil and Sustainable Agriculture, Institute
of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
Related authors
No articles found.
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.
Yu-Te Lin, Zhongjun Jia, Dongmei Wang, and Chih-Yu Chiu
Biogeosciences, 14, 4879–4889, https://doi.org/10.5194/bg-14-4879-2017, https://doi.org/10.5194/bg-14-4879-2017, 2017
Short summary
Short summary
We evaluated the bacterial composition and diversity of bamboo soils sampled at different elevations and incubated at different temperatures. Soil respiration was greater at higher elevation and temperature. Soil bacterial structure and diversity showed variable under different incubation times and temperatures. Increases in temperature increased soil respiration and consumption of soil soluble carbon and nitrogen, thus influencing the bacterial diversity and structure at different elevations.
Xiaoqi Zhou, Zhiying Guo, Chengrong Chen, and Zhongjun Jia
Biogeosciences, 14, 2101–2111, https://doi.org/10.5194/bg-14-2101-2017, https://doi.org/10.5194/bg-14-2101-2017, 2017
Short summary
Short summary
We selected three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and an eucalypt species to investigate the patterns of community structure of soil bacteria and eukaryotes. We found that soil pH and nutrient quality indicators like C : N and EOC : EON ratios were key factors determining the patterns of soil microbial communities. We introduced a key factor limitation hypothesis that gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus.
Y. Zheng, R. Huang, B. Z. Wang, P. L. E. Bodelier, and Z. J. Jia
Biogeosciences, 11, 3353–3368, https://doi.org/10.5194/bg-11-3353-2014, https://doi.org/10.5194/bg-11-3353-2014, 2014
M. S. Alam, G. D. Ren, L. Lu, Y. Zheng, X. H. Peng, and Z. J. Jia
Biogeosciences, 10, 5739–5753, https://doi.org/10.5194/bg-10-5739-2013, https://doi.org/10.5194/bg-10-5739-2013, 2013
Related subject area
Biodiversity and Ecosystem Function: Microbial Ecology & Geomicrobiology
Maximum summer temperatures predict the temperature adaptation of Arctic soil bacterial communities
Potential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China's estuarine and coastal areas
Aqueous system-level processes and prokaryote assemblages in the ferruginous and sulfate-rich bottom waters of a post-mining lake
Abundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonia compared to neighbouring oceans and Northern Hemisphere fjords
Determining the hierarchical order by which the variables of sampling period, dust outbreak occurrence, and sampling location can shape the airborne bacterial communities in the Mediterranean basin
The water column of the Yamal tundra lakes as a microbial filter preventing methane emission
Bioerosion and fungal colonization of the invasive foraminiferan Amphistegina lobifera in a Mediterranean seagrass meadow
Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove
Deep maxima of phytoplankton biomass, primary production and bacterial production in the Mediterranean Sea
Haplo-diplontic life cycle expands coccolithophore niche
The composition of endolithic communities in gypcrete is determined by the specific microhabitat architecture
Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences
Cryptic roles of tetrathionate in the sulfur cycle of marine sediments: microbial drivers and indicators
Lake mixing regime selects apparent methane oxidation kinetics of the methanotroph assemblage
The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth)
Biogeographical distribution of microbial communities along the Rajang River–South China Sea continuum
Microbial community composition and abundance after millennia of submarine permafrost warming
Cold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edge
Ecophysiological characteristics of red, green, and brown strains of the Baltic picocyanobacterium Synechococcus sp. – a laboratory study
Factors controlling the community structure of picoplankton in contrasting marine environments
Community composition and seasonal changes of archaea in coarse and fine air particulate matter
Microbial community structure in the western tropical South Pacific
Ecophysiological characterization of early successional biological soil crusts in heavily human-impacted areas
Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)
Plant n-alkane production from litterfall altered the diversity and community structure of alkane degrading bacteria in litter layer in lowland subtropical rainforest in Taiwan
Revisiting chlorophyll extraction methods in biological soil crusts – methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methods
Divergence of dominant factors in soil microbial communities and functions in forest ecosystems along a climatic gradient
Uncovering biological soil crusts: carbon content and structure of intact Arctic, Antarctic and alpine biological soil crusts
Antagonistic effects of drought and sand burial enable the survival of the biocrust moss Bryum argenteum in an arid sandy desert
Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic Sea
Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia
Effects of temperature on the composition and diversity of bacterial communities in bamboo soils at different elevations
Development of bacterial communities in biological soil crusts along a revegetation chronosequence in the Tengger Desert, northwest China
Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments
Diversity and mineral substrate preference in endolithic microbial communities from marine intertidal outcrops (Isla de Mona, Puerto Rico)
Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea
Mechanisms of Trichodesmium demise within the New Caledonian lagoon during the VAHINE mesocosm experiment
Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids
Effect of light on photosynthetic efficiency of sequestered chloroplasts in intertidal benthic foraminifera (Haynesina germanica and Ammonia tepida)
Seasonal and size-dependent variations in the phytoplankton growth and microzooplankton grazing in the southern South China Sea under the influence of the East Asian monsoon
Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest
Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China
Redox regime shifts in microbially mediated biogeochemical cycles
Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs
Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota
Diversity and seasonal dynamics of airborne archaea
Methanotrophic activity and diversity of methanotrophs in volcanic geothermal soils at Pantelleria (Italy)
Genotyping an Emiliania huxleyi (prymnesiophyceae) bloom event in the North Sea reveals evidence of asexual reproduction
High temperature decreases the PIC / POC ratio and increases phosphorus requirements in Coccolithus pelagicus (Haptophyta)
Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil
Ruud Rijkers, Mark Dekker, Rien Aerts, and James T. Weedon
Biogeosciences, 20, 767–780, https://doi.org/10.5194/bg-20-767-2023, https://doi.org/10.5194/bg-20-767-2023, 2023
Short summary
Short summary
Bacterial communities in the soils of the Arctic region decompose soil organic matter to CO2 from a large carbon pool. The amount of CO2 released is likely to increase under future climate conditions. Here, we study how temperature sensitive the growth of soil bacterial communties is for 12 sampling sites in the sub to high Arctic. We show that the optimal growth temperature varies between 23 and 34 °C and is influenced by the summer temperature.
Xiaofeng Dai, Mingming Chen, Xianhui Wan, Ehui Tan, Jialing Zeng, Nengwang Chen, Shuh-Ji Kao, and Yao Zhang
Biogeosciences, 19, 3757–3773, https://doi.org/10.5194/bg-19-3757-2022, https://doi.org/10.5194/bg-19-3757-2022, 2022
Short summary
Short summary
This study revealed the distinct distribution patterns of six key microbial functional genes and transcripts related to N2O sources and sinks in four estuaries spanning the Chinese coastline, which were significantly constrained by nitrogen and oxygen concentrations, salinity, temperature, and pH. The community structure of the nosZ clade II was distinctly different from those in the soil and marine OMZs. Denitrification may principally control the N2O emissions patterns across the estuaries.
Daniel A. Petrash, Ingrid M. Steenbergen, Astolfo Valero, Travis B. Meador, Tomáš Pačes, and Christophe Thomazo
Biogeosciences, 19, 1723–1751, https://doi.org/10.5194/bg-19-1723-2022, https://doi.org/10.5194/bg-19-1723-2022, 2022
Short summary
Short summary
We spectroscopically evaluated the gradients of dissolved C, N, S, Fe and Mn in a newly formed redox-stratified lake. The lake features an intermediate redox state between nitrogenous and euxinic conditions that encompasses vigorous open sulfur cycling fuelled by the reducible Fe and Mn stocks of the anoxic sediments. This results in substantial bottom water loads of dissolved iron and sulfate. Observations made in this ecosystem have relevance for deep-time paleoceanographic reconstructions.
Francisco Díaz-Rosas, Catharina Alves-de-Souza, Emilio Alarcón, Eduardo Menschel, Humberto E. González, Rodrigo Torres, and Peter von Dassow
Biogeosciences, 18, 5465–5489, https://doi.org/10.5194/bg-18-5465-2021, https://doi.org/10.5194/bg-18-5465-2021, 2021
Short summary
Short summary
Coccolithophores are important unicellular algae with a calcium carbonate covering that might be affected by ongoing changes in the ocean due to absorption of CO2, warming, and melting of glaciers. We used the southern Patagonian fjords as a natural laboratory, where chemical conditions are naturally highly variable. One variant of a widespread coccolithophore species can tolerate these conditions, suggesting it is highly adaptable, while others were excluded, suggesting they are less adaptable.
Riccardo Rosselli, Maura Fiamma, Massimo Deligios, Gabriella Pintus, Grazia Pellizzaro, Annalisa Canu, Pierpaolo Duce, Andrea Squartini, Rosella Muresu, and Pietro Cappuccinelli
Biogeosciences, 18, 4351–4367, https://doi.org/10.5194/bg-18-4351-2021, https://doi.org/10.5194/bg-18-4351-2021, 2021
Short summary
Short summary
The bacteria carried by winds over the island of Sardinia in the Mediterranean Sea were collected, and their identities were investigated by reading DNA sequences. The sampling period was the factor that most determined the airborne species composition as its role was stronger than that of dust-carrying storms and of the geographical position of the sampling station. The bacteria found when the sampling was performed in September had more species variety than those collected in May.
Alexander Savvichev, Igor Rusanov, Yury Dvornikov, Vitaly Kadnikov, Anna Kallistova, Elena Veslopolova, Antonina Chetverova, Marina Leibman, Pavel A. Sigalevich, Nikolay Pimenov, Nikolai Ravin, and Artem Khomutov
Biogeosciences, 18, 2791–2807, https://doi.org/10.5194/bg-18-2791-2021, https://doi.org/10.5194/bg-18-2791-2021, 2021
Short summary
Short summary
Microbial processes of the methane cycle were studied in four lakes of the central part of the Yamal Peninsula in an area of continuous permafrost: two large, deep lakes and two small and shallow ones. It was found that only small, shallow lakes contributed significantly to the overall diffusive methane emissions from the water surface during the warm summer season. The water column of large, deep lakes on Yamal acted as a microbial filter preventing methane emissions into the atmosphere.
Martin Vohník
Biogeosciences, 18, 2777–2790, https://doi.org/10.5194/bg-18-2777-2021, https://doi.org/10.5194/bg-18-2777-2021, 2021
Short summary
Short summary
Amphistegina lobifera (Foraminifera) has colonized the Mediterranean through the Suez Canal, often forming thick sediments altering the invaded environments. Little is known about postmortem fate of its shells, so I investigated their turnover in the rhizosphere of the dominant Mediterranean seagrass. Most were bioeroded, likely by cyanobacteria and algae but not fungi occurring in the seagrass roots. Bioerosion may counterbalance accumulation of A. lobifera shells in the seabed substrate.
Carolina Oliveira de Santana, Pieter Spealman, Vânia Maria Maciel Melo, David Gresham, Taíse Bomfim de Jesus, and Fabio Alexandre Chinalia
Biogeosciences, 18, 2259–2273, https://doi.org/10.5194/bg-18-2259-2021, https://doi.org/10.5194/bg-18-2259-2021, 2021
Short summary
Short summary
This study highlights the influence of
tidal zonationon the prokaryotic sediment communities of a pristine mangrove forest. We observed that the variability in environmental factors between tidal zones results in differences in structure, diversity, and the potential function of prokaryotic populations. This suggests that further work is needed in determining the role tidal microhabitat biodiversity has in mangroves.
Emilio Marañón, France Van Wambeke, Julia Uitz, Emmanuel S. Boss, Céline Dimier, Julie Dinasquet, Anja Engel, Nils Haëntjens, María Pérez-Lorenzo, Vincent Taillandier, and Birthe Zäncker
Biogeosciences, 18, 1749–1767, https://doi.org/10.5194/bg-18-1749-2021, https://doi.org/10.5194/bg-18-1749-2021, 2021
Short summary
Short summary
The concentration of chlorophyll is commonly used as an indicator of the abundance of photosynthetic plankton (phytoplankton) in lakes and oceans. Our study investigates why a deep chlorophyll maximum, located near the bottom of the upper, illuminated layer develops in the Mediterranean Sea. We find that the acclimation of cells to low light is the main mechanism involved and that this deep maximum represents also a maximum in the biomass and carbon fixation activity of phytoplankton.
Joost de Vries, Fanny Monteiro, Glen Wheeler, Alex Poulton, Jelena Godrijan, Federica Cerino, Elisa Malinverno, Gerald Langer, and Colin Brownlee
Biogeosciences, 18, 1161–1184, https://doi.org/10.5194/bg-18-1161-2021, https://doi.org/10.5194/bg-18-1161-2021, 2021
Short summary
Short summary
Coccolithophores are important calcifying phytoplankton with an overlooked life cycle. We compile a global dataset of marine coccolithophore abundance to investigate the environmental characteristics of each life cycle phase. We find that both phases contribute to coccolithophore abundance and that their different environmental preference increases coccolithophore habitat. Accounting for the life cycle of coccolithophores is thus crucial for understanding their ecology and biogeochemical impact.
María Cristina Casero, Victoria Meslier, Jocelyne DiRuggiero, Antonio Quesada, Carmen Ascaso, Octavio Artieda, Tomasz Kowaluk, and Jacek Wierzchos
Biogeosciences, 18, 993–1007, https://doi.org/10.5194/bg-18-993-2021, https://doi.org/10.5194/bg-18-993-2021, 2021
Short summary
Short summary
Endolithic microhabitats have been described as the last refuge for life in arid and hyper-arid deserts where life has to deal with harsh environmental conditions, such as those in the Atacama Desert. In this work, three different endolithic microhabitats occurring in gypcrete rocks of the Atacama Desert are characterized, using both microscopy and molecular techniques, to show if the architecture of each microhabitat has an influence on the microbial communities inhabiting each of them.
Jeffrey M. Dick, Miao Yu, and Jingqiang Tan
Biogeosciences, 17, 6145–6162, https://doi.org/10.5194/bg-17-6145-2020, https://doi.org/10.5194/bg-17-6145-2020, 2020
Short summary
Short summary
Many natural environments differ in their range of salt concentration (salinity). We developed a metric for the number of water molecules in formation reactions of different proteins and found that it decreases between freshwater and marine systems and also in laboratory experiments with increasing salinity. These results demonstrate a new type of link between geochemical conditions and the chemical composition of microbial communities that can be useful for models of microbial adaptation.
Subhrangshu Mandal, Sabyasachi Bhattacharya, Chayan Roy, Moidu Jameela Rameez, Jagannath Sarkar, Tarunendu Mapder, Svetlana Fernandes, Aditya Peketi, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 17, 4611–4631, https://doi.org/10.5194/bg-17-4611-2020, https://doi.org/10.5194/bg-17-4611-2020, 2020
Short summary
Short summary
Potential roles of polythionates as key sulfur cycle intermediates are less appreciated, apparently because, in most of the natural environments, they do not accumulate to easily detectable levels. Our exploration of the eastern Arabian Sea sediment horizons revealed microbe-mediated production and redox transformations of tetrathionate to be important modules of the in situ sulfur cycle, even as high biotic and abiotic reactivity of this polythionate keeps it hidden from geochemical detection.
Magdalena J. Mayr, Matthias Zimmermann, Jason Dey, Bernhard Wehrli, and Helmut Bürgmann
Biogeosciences, 17, 4247–4259, https://doi.org/10.5194/bg-17-4247-2020, https://doi.org/10.5194/bg-17-4247-2020, 2020
Massimiliano Molari, Felix Janssen, Tobias R. Vonnahme, Frank Wenzhöfer, and Antje Boetius
Biogeosciences, 17, 3203–3222, https://doi.org/10.5194/bg-17-3203-2020, https://doi.org/10.5194/bg-17-3203-2020, 2020
Short summary
Short summary
Industrial-scale mining of deep-sea polymetallic nodules will remove nodules in large areas of the sea floor. We describe community composition of microbes associated with nodules of the Peru Basin. Our results show that nodules provide a unique ecological niche, playing an important role in shaping the diversity of the benthic deep-sea microbiome and potentially in element fluxes. We believe that our findings are highly relevant to expanding our knowledge of the impact associated with mining.
Edwin Sien Aun Sia, Zhuoyi Zhu, Jing Zhang, Wee Cheah, Shan Jiang, Faddrine Holt Jang, Aazani Mujahid, Fuh-Kwo Shiah, and Moritz Müller
Biogeosciences, 16, 4243–4260, https://doi.org/10.5194/bg-16-4243-2019, https://doi.org/10.5194/bg-16-4243-2019, 2019
Short summary
Short summary
Microbial community composition and diversity in freshwater habitats are much less studied compared to marine and soil communities. This study presents the first assessment of microbial communities of the Rajang River, the longest river in Malaysia, expanding our knowledge of microbial ecology in tropical regions. Areas surrounded by oil palm plantations showed the lowest diversity and other signs of anthropogenic impacts included the presence of CFB groups as well as probable algal blooms.
Julia Mitzscherling, Fabian Horn, Maria Winterfeld, Linda Mahler, Jens Kallmeyer, Pier P. Overduin, Lutz Schirrmeister, Matthias Winkel, Mikhail N. Grigoriev, Dirk Wagner, and Susanne Liebner
Biogeosciences, 16, 3941–3958, https://doi.org/10.5194/bg-16-3941-2019, https://doi.org/10.5194/bg-16-3941-2019, 2019
Short summary
Short summary
Permafrost temperatures increased substantially at a global scale, potentially altering microbial assemblages involved in carbon mobilization before permafrost thaws. We used Arctic Shelf submarine permafrost as a natural laboratory to investigate the microbial response to long-term permafrost warming. Our work shows that millennia after permafrost warming by > 10 °C, microbial community composition and population size reflect the paleoenvironment rather than a direct effect through warming.
Blanca Rincón-Tomás, Jan-Peter Duda, Luis Somoza, Francisco Javier González, Dominik Schneider, Teresa Medialdea, Esther Santofimia, Enrique López-Pamo, Pedro Madureira, Michael Hoppert, and Joachim Reitner
Biogeosciences, 16, 1607–1627, https://doi.org/10.5194/bg-16-1607-2019, https://doi.org/10.5194/bg-16-1607-2019, 2019
Short summary
Short summary
Cold-water corals were found at active sites in Pompeia Province (Gulf of Cádiz). Since seeped fluids are harmful for the corals, we approached the environmental conditions that allow corals to colonize carbonates while seepage occurs. As a result, we propose that chemosynthetic microorganisms (i.e. sulfide-oxidizing bacteria and AOM-related microorganisms) play an important role in the colonization of the corals at these sites by feeding on the seeped fluids and avoiding coral damage.
Sylwia Śliwińska-Wilczewska, Agata Cieszyńska, Jakub Maculewicz, and Adam Latała
Biogeosciences, 15, 6257–6276, https://doi.org/10.5194/bg-15-6257-2018, https://doi.org/10.5194/bg-15-6257-2018, 2018
Short summary
Short summary
The present study describes responses of picocyanobacteria (PCY) physiology to different environmental conditions. The cultures were grown under 64 combinations of temperature, irradiance in a photosynthetically active spectrum (PAR), and salinity. The results show that each strain of Baltic Synechococcus sp. behaves differently in respective environmental scenarios. The study develops the knowledge on bloom-forming PCY and reasons further research on the smallest size fraction of phytoplankton.
Jose Luis Otero-Ferrer, Pedro Cermeño, Antonio Bode, Bieito Fernández-Castro, Josep M. Gasol, Xosé Anxelu G. Morán, Emilio Marañon, Victor Moreira-Coello, Marta M. Varela, Marina Villamaña, and Beatriz Mouriño-Carballido
Biogeosciences, 15, 6199–6220, https://doi.org/10.5194/bg-15-6199-2018, https://doi.org/10.5194/bg-15-6199-2018, 2018
Short summary
Short summary
The effect of inorganic nutrients on planktonic assemblages has been traditionally assessed by looking at concentrations rather than fluxes of nutrient supply. However, in near-steady-state systems such as subtropical gyres, nitrate concentrations are kept close to the detection limit due to phytoplankton uptake. Our results, based on direct measurements of nitrate diffusive fluxes, support the key role of nitrate supply in controlling the structure of marine picoplankton communities.
Jörn Wehking, Daniel A. Pickersgill, Robert M. Bowers, David Teschner, Ulrich Pöschl, Janine Fröhlich-Nowoisky, and Viviane R. Després
Biogeosciences, 15, 4205–4214, https://doi.org/10.5194/bg-15-4205-2018, https://doi.org/10.5194/bg-15-4205-2018, 2018
Short summary
Short summary
Archaea as a third domain of life play an important role in soils and marine environments. Although archaea have been found in air as a part of the atmospheric bioaerosol, little is known about their atmospheric dynamics due to their low number and challenging analysis.
Here we present a DNA-based study of airborne archaea, show seasonal dynamics, and discuss anthropogenic influences on the diversity, composition, and abundances of airborne archaea.
Nicholas Bock, France Van Wambeke, Moïra Dion, and Solange Duhamel
Biogeosciences, 15, 3909–3925, https://doi.org/10.5194/bg-15-3909-2018, https://doi.org/10.5194/bg-15-3909-2018, 2018
Short summary
Short summary
We report the distribution of major nano- and pico-plankton groups in the western tropical South Pacific. We found microbial community structure to be typical of highly stratified regions of the open ocean, with significant contributions to total biomass by picophytoeukaryotes, and N2 fixation playing a central role in regulating ecosystem processes. Our results also suggest a reduction in the importance of predation in regulating bacteria populations under nutrient-limited conditions.
Michelle Szyja, Burkhard Büdel, and Claudia Colesie
Biogeosciences, 15, 1919–1931, https://doi.org/10.5194/bg-15-1919-2018, https://doi.org/10.5194/bg-15-1919-2018, 2018
Short summary
Short summary
Ongoing human impact transforms habitats into surfaces lacking higher vegetation. Here, biological soil crusts (BSCs) provide ecosystem services like soil creation and carbon uptake. To understand the functioning of these areas, we examined the physiological capability of early successional BSCs. We found features enabling BSCs to cope with varying climatic stresses. BSCs are important carbon fixers independent of the dominating organism. We provide baseline data for modeling carbon fluxes.
Petr Kotas, Hana Šantrůčková, Josef Elster, and Eva Kaštovská
Biogeosciences, 15, 1879–1894, https://doi.org/10.5194/bg-15-1879-2018, https://doi.org/10.5194/bg-15-1879-2018, 2018
Short summary
Short summary
The soil microbial properties were investigated along altitudinal gradients in the Arctic. Systematic altitudinal shift in MCS resulting in high F / B ratios at the most elevated sites was observed. The changes in composition, size and activity of microbial communities were mainly controlled through the effect of vegetation on edaphic properties and by bedrock chemistry. The upward migration of vegetation due to global warming will likely diminish the spatial variability in microbial properties.
Tung-Yi Huang, Bing-Mu Hsu, Wei-Chun Chao, and Cheng-Wei Fan
Biogeosciences, 15, 1815–1826, https://doi.org/10.5194/bg-15-1815-2018, https://doi.org/10.5194/bg-15-1815-2018, 2018
Short summary
Short summary
The n-alkane in litterfall and the microbial community in litter layer in different habitats of lowland subtropical rainforest were studied. We revealed that the plant vegetation of forest not only dominated the n-alkane input of habitats but also governed the diversity of microbial community of litter layer. In this study, we found that the habitat which had high n-alkane input induced a shift of relative abundance toward phylum of Actinobacteria and the growth of alkB gene contained bacteria.
Jennifer Caesar, Alexandra Tamm, Nina Ruckteschler, Anna Lena Leifke, and Bettina Weber
Biogeosciences, 15, 1415–1424, https://doi.org/10.5194/bg-15-1415-2018, https://doi.org/10.5194/bg-15-1415-2018, 2018
Short summary
Short summary
In our study we analyzed the efficiency of different chlorophyll extraction solvents and investigated the effect of different preparatory steps to determine the optimal extraction method for biological soil crusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest to insert an intermediate shaking step for complete chlorophyll extraction.
Zhiwei Xu, Guirui Yu, Xinyu Zhang, Nianpeng He, Qiufeng Wang, Shengzhong Wang, Xiaofeng Xu, Ruili Wang, and Ning Zhao
Biogeosciences, 15, 1217–1228, https://doi.org/10.5194/bg-15-1217-2018, https://doi.org/10.5194/bg-15-1217-2018, 2018
Short summary
Short summary
Forest types with specific soil conditions supported the development of distinct soil microbial communities with variable functions. Our results indicate that the main controls on soil microbes and functions vary across forest ecosystems in different climatic zones. This information will add value to the modeling of microbial processes and will contribute to carbon cycling on a large scale.
Patrick Jung, Laura Briegel-Williams, Anika Simon, Anne Thyssen, and Burkhard Büdel
Biogeosciences, 15, 1149–1160, https://doi.org/10.5194/bg-15-1149-2018, https://doi.org/10.5194/bg-15-1149-2018, 2018
Short summary
Short summary
Arctic, Antarctic and alpine biological soil crusts (BSCs) are formed by adhesion of soil particles to cyanobacteria. BSCs influence ecosystems services like soil erodibility and chemical cycles. In cold environments degradation rates are low and BSCs increase soil organic carbon through photosynthesis, whereby these soils are considered as CO2 sinks. This work provides a novel method to visualize BSCs with a focus on cyanobacteria and their contribution to soil organic carbon.
Rongliang Jia, Yun Zhao, Yanhong Gao, Rong Hui, Haotian Yang, Zenru Wang, and Yixuan Li
Biogeosciences, 15, 1161–1172, https://doi.org/10.5194/bg-15-1161-2018, https://doi.org/10.5194/bg-15-1161-2018, 2018
Short summary
Short summary
Why can biocrust moss survive and flourish in these habitats when stressed simultaneously by drought and sand burial? A field experiment was conducted to assess the combined effects of the two stressors on Bryum argenteum within biocrust. The two stressors did not exacerbate the single negative effects; their mutually antagonistic effect on the physiological vigor of B. argenteum was found, and it provided an opportunity for it to overcome the two co-occurring stressors in arid sandy ecosystems.
Johanna Maltby, Lea Steinle, Carolin R. Löscher, Hermann W. Bange, Martin A. Fischer, Mark Schmidt, and Tina Treude
Biogeosciences, 15, 137–157, https://doi.org/10.5194/bg-15-137-2018, https://doi.org/10.5194/bg-15-137-2018, 2018
Short summary
Short summary
The activity and environmental controls of methanogenesis (MG) within the sulfate-reducing zone (0–30 cm below the seafloor) were investigated in organic-rich sediments of the seasonally hypoxic Eckernförde Bay, SW Baltic Sea. MG activity was mostly linked to non-competitive substrates. The major controls identified were organic matter availability, C / N, temperature, and O2 in the water column, revealing higher rates in warm, stratified, hypoxic seasons compared to colder, oxygenated seasons.
Rebecca Elizabeth Cooper, Karin Eusterhues, Carl-Eric Wegner, Kai Uwe Totsche, and Kirsten Küsel
Biogeosciences, 14, 5171–5188, https://doi.org/10.5194/bg-14-5171-2017, https://doi.org/10.5194/bg-14-5171-2017, 2017
Short summary
Short summary
In this study we show increasing organic matter (OM) content on ferrihydrite surfaces enhances Fe reduction by the model Fe reducer S. oneidensis and a microbial consortia extracted from peat. Similarities in reduction rates between S. oneidensis and the consortia suggest electron shuttling dominates in OM-rich soils. Community profile analyses showed enrichment of fermenters with pure ferrihydrite, whereas OM–mineral complexes favored enrichment of Fe-reducing Desulfobacteria and Pelosinus sp.
Yu-Te Lin, Zhongjun Jia, Dongmei Wang, and Chih-Yu Chiu
Biogeosciences, 14, 4879–4889, https://doi.org/10.5194/bg-14-4879-2017, https://doi.org/10.5194/bg-14-4879-2017, 2017
Short summary
Short summary
We evaluated the bacterial composition and diversity of bamboo soils sampled at different elevations and incubated at different temperatures. Soil respiration was greater at higher elevation and temperature. Soil bacterial structure and diversity showed variable under different incubation times and temperatures. Increases in temperature increased soil respiration and consumption of soil soluble carbon and nitrogen, thus influencing the bacterial diversity and structure at different elevations.
Lichao Liu, Yubing Liu, Peng Zhang, Guang Song, Rong Hui, Zengru Wang, and Jin Wang
Biogeosciences, 14, 3801–3814, https://doi.org/10.5194/bg-14-3801-2017, https://doi.org/10.5194/bg-14-3801-2017, 2017
Short summary
Short summary
We studied the development process of bacterial community structure of biological soil crusts (BSCs) along a revegetation chronosequence by Illumina MiSeq sequencing in the Tengger Desert. Our results indicated (1) a shift of bacterial composition related to their function in the crust development process; (2) bacterial diversity and richness consistent with the recovery phase of soil properties; and (3) bacteria as key contributors to the BSC succession process.
Sophie L. Nixon, Jon P. Telling, Jemma L. Wadham, and Charles S. Cockell
Biogeosciences, 14, 1445–1455, https://doi.org/10.5194/bg-14-1445-2017, https://doi.org/10.5194/bg-14-1445-2017, 2017
Short summary
Short summary
Despite their permanently cold and dark characteristics, subglacial environments (glacier ice–sediment interface) are known to harbour active microbial communities. However, the role of microbial iron cycling in these environments is poorly understood. Here we show that subglacial sediments harbour active iron-reducing microorganisms, and they appear to be cold-adapted. These results may have important implications for global biogeochemical iron cycling and export to marine ecosystems.
Estelle Couradeau, Daniel Roush, Brandon Scott Guida, and Ferran Garcia-Pichel
Biogeosciences, 14, 311–324, https://doi.org/10.5194/bg-14-311-2017, https://doi.org/10.5194/bg-14-311-2017, 2017
Short summary
Short summary
Endoliths are a prominent bioerosive component of intertidal marine habitats, traditionally thought to be formed by a few cyanobacteria, algae and fungi. Using molecular techniques, however, we found that endoliths from Mona Island, Puerto Rico, were of high diversity, well beyond that reported in traditional studies. We also found evidence for substrate specialization, in that closely related cyanobacteria seem to have diversified to specialize recurrently to excavate various mineral substrates
Yong Wang, Tie Gang Li, Meng Ying Wang, Qi Liang Lai, Jiang Tao Li, Zhao Ming Gao, Zong Ze Shao, and Pei-Yuan Qian
Biogeosciences, 13, 6405–6417, https://doi.org/10.5194/bg-13-6405-2016, https://doi.org/10.5194/bg-13-6405-2016, 2016
Short summary
Short summary
Mild eruption of hydrothermal solutions on deep-sea benthic floor can produce anhydrite crystal layers, where microbes are trapped and preserved for a long period of time. These embedded original inhabitants will be biomarkers for the environment when the hydrothermal eruption occurred. This study discovered a thick anhydrite layer in a deep-sea brine pool in the Red Sea. Oil-degrading bacteria were revealed in the crystals with genomic and microscopic evidence.
Dina Spungin, Ulrike Pfreundt, Hugo Berthelot, Sophie Bonnet, Dina AlRoumi, Frank Natale, Wolfgang R. Hess, Kay D. Bidle, and Ilana Berman-Frank
Biogeosciences, 13, 4187–4203, https://doi.org/10.5194/bg-13-4187-2016, https://doi.org/10.5194/bg-13-4187-2016, 2016
Short summary
Short summary
The marine cyanobacterium Trichodesmium spp. forms massive blooms important to carbon and nitrogen cycling in the oceans that often collapse abruptly. We investigated a Trichodesmium bloom in the lagoon waters of New Caledonia to specifically elucidate the cellular processes mediating the bloom decline. We demonstrate physiological, biochemical, and genetic evidence for nutrient and oxidative stress that induced a genetically controlled programmed cell death (PCD) pathway leading to bloom demise.
Lotta Purkamo, Malin Bomberg, Riikka Kietäväinen, Heikki Salavirta, Mari Nyyssönen, Maija Nuppunen-Puputti, Lasse Ahonen, Ilmo Kukkonen, and Merja Itävaara
Biogeosciences, 13, 3091–3108, https://doi.org/10.5194/bg-13-3091-2016, https://doi.org/10.5194/bg-13-3091-2016, 2016
Short summary
Short summary
The microbial communities of up to 2.3 km depth of Precambrian crystalline bedrock fractures share features with serpenization-driven microbial communities in alkaline springs and subsurface aquifers. This study suggests that phylotypes belonging to Burkholderiales and Clostridia are possible "keystone microbial species" in Outokumpu deep biosphere. Many of the keystone species belong to the rare biosphere with low abundance but a wide range of carbon substrates and a capacity for H2 oxidation.
Thierry Jauffrais, Bruno Jesus, Edouard Metzger, Jean-Luc Mouget, Frans Jorissen, and Emmanuelle Geslin
Biogeosciences, 13, 2715–2726, https://doi.org/10.5194/bg-13-2715-2016, https://doi.org/10.5194/bg-13-2715-2016, 2016
Short summary
Short summary
Some benthic foraminifera can incorporate chloroplasts from microalgae. We investigated chloroplast functionality of two benthic foraminifera (Haynesina germanica & Ammonia tepida) exposed to different light levels. Only H. germanica was capable of using the kleptoplasts, showing net oxygen production. Chloroplast functionality time was longer in darkness (2 weeks) than at high light (1 week). Kleptoplasts are unlikely to be completely functional, thus requiring continuous chloroplast resupply.
L. Zhou, Y. Tan, L. Huang, Z. Hu, and Z. Ke
Biogeosciences, 12, 6809–6822, https://doi.org/10.5194/bg-12-6809-2015, https://doi.org/10.5194/bg-12-6809-2015, 2015
Short summary
Short summary
We observed that phytoplankton biomass and growth rate (μ), microzooplankton grazing rate (m), and coupling (correlation) between the μ and m significantly varied between the summer and winter, and microzooplankton selectively grazed more on the larger-sized phytoplankton, and a low grazing impact on phytoplankton (m/μ < 50%) in the SSCS. The salient seasonal variations in μ and m, and their coupling were closely related to environmental variables under the influence of the East Asian monsoon.
A. M. Womack, P. E. Artaxo, F. Y. Ishida, R. C. Mueller, S. R. Saleska, K. T. Wiedemann, B. J. M. Bohannan, and J. L. Green
Biogeosciences, 12, 6337–6349, https://doi.org/10.5194/bg-12-6337-2015, https://doi.org/10.5194/bg-12-6337-2015, 2015
Short summary
Short summary
Fungi in the atmosphere can affect precipitation by nucleating the formation of clouds and ice. This process is important over the Amazon rainforest where precipitation is limited by the types and amount of airborne particles. We found that the total and metabolically active fungi communities were dominated by different taxonomic groups, and the active community unexpectedly contained many lichen fungi, which are effective at nucleating ice.
W. Y. Dong, X. Y. Zhang, X. Y. Liu, X. L. Fu, F. S. Chen, H. M. Wang, X. M. Sun, and X. F. Wen
Biogeosciences, 12, 5537–5546, https://doi.org/10.5194/bg-12-5537-2015, https://doi.org/10.5194/bg-12-5537-2015, 2015
Short summary
Short summary
We examined how N and P addition influenced soil microbial community composition and enzyme activities in subtropical China. The results showed that C and N cycling enzymes were more sensitive to nutrient additions than P cycling enzymes and Gram-positive bacteria were most closely related to soil nutrient cycling enzymes. Combined additions of N and P fertilizer are recommended to promote soil fertility and microbial activity in this kind of plantation.
T. Bush, I. B. Butler, A. Free, and R. J. Allen
Biogeosciences, 12, 3713–3724, https://doi.org/10.5194/bg-12-3713-2015, https://doi.org/10.5194/bg-12-3713-2015, 2015
Short summary
Short summary
Despite their global importance, redox reactions mediated by microorganisms are often crudely represented in biogeochemical models. We show that including the dynamics of microbial growth in such a model can cause sudden shifts between redox states in response to an environmental change. We identify the conditions required for these redox regime shifts, and predict that they are likely in the modern day sulfur and nitrogen cycles, and potentially the iron cycle in the ancient ocean.
P. K. Gao, G. Q. Li, H. M. Tian, Y. S. Wang, H. W. Sun, and T. Ma
Biogeosciences, 12, 3403–3414, https://doi.org/10.5194/bg-12-3403-2015, https://doi.org/10.5194/bg-12-3403-2015, 2015
Short summary
Short summary
Microbial communities in injected water are expected to have a significant influence on those of reservoir strata in long-term water-flooding petroleum reservoirs. We thereby investigated the similarities and differences in microbial communities in water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous reservoir and a heterogeneous reservoir using high-throughput sequencing.
V. Marteinsson, A. Klonowski, E. Reynisson, P. Vannier, B. D. Sigurdsson, and M. Ólafsson
Biogeosciences, 12, 1191–1203, https://doi.org/10.5194/bg-12-1191-2015, https://doi.org/10.5194/bg-12-1191-2015, 2015
Short summary
Short summary
Colonization of life on Surtsey has been observed systematically since the formation of the island. Microbial colonization and the influence of associate vegetation and birds on viable counts of environmental bacteria at the surface of the Surtsey was explored for the first time in diverse surface soils. Also, hot subsurface samples deep in the centre of this volcanic island were collected. Both uncultivated bacteria and archaea were found in the subsurface samples collected below 145 m.
J. Fröhlich-Nowoisky, C. Ruzene Nespoli, D. A. Pickersgill, P. E. Galand, I. Müller-Germann, T. Nunes, J. Gomes Cardoso, S. M. Almeida, C. Pio, M. O. Andreae, R. Conrad, U. Pöschl, and V. R. Després
Biogeosciences, 11, 6067–6079, https://doi.org/10.5194/bg-11-6067-2014, https://doi.org/10.5194/bg-11-6067-2014, 2014
Short summary
Short summary
We have investigated the presence of archaea as well as their amoA gene diversity in aerosol particles collected over 1 year in central Europe and found that, within the 16S and amoA gene, Thaumarchaeota prevail and experience a diversity peak in fall, while only few Euryarchaeota were detected primarily in spring. We also compared the results with airborne archaea from Cape Verde and observe that the proportions of Euryarchaeota seem to be enhanced in coastal air compared to continental air.
A. L. Gagliano, W. D'Alessandro, M. Tagliavia, F. Parello, and P. Quatrini
Biogeosciences, 11, 5865–5875, https://doi.org/10.5194/bg-11-5865-2014, https://doi.org/10.5194/bg-11-5865-2014, 2014
S. A. Krueger-Hadfield, C. Balestreri, J. Schroeder, A. Highfield, P. Helaouët, J. Allum, R. Moate, K. T. Lohbeck, P. I. Miller, U. Riebesell, T. B. H. Reusch, R. E. M. Rickaby, J. Young, G. Hallegraeff, C. Brownlee, and D. C. Schroeder
Biogeosciences, 11, 5215–5234, https://doi.org/10.5194/bg-11-5215-2014, https://doi.org/10.5194/bg-11-5215-2014, 2014
A. C. Gerecht, L. Šupraha, B. Edvardsen, I. Probert, and J. Henderiks
Biogeosciences, 11, 3531–3545, https://doi.org/10.5194/bg-11-3531-2014, https://doi.org/10.5194/bg-11-3531-2014, 2014
Y. Zheng, R. Huang, B. Z. Wang, P. L. E. Bodelier, and Z. J. Jia
Biogeosciences, 11, 3353–3368, https://doi.org/10.5194/bg-11-3353-2014, https://doi.org/10.5194/bg-11-3353-2014, 2014
Cited articles
Aigle, A., Prosser, J. I., and Gubry-Rangin, C.: The application of
high-throughput sequencing technology to analysis of amoA phylogeny and
environmental niche specialisation of terrestrial bacterial
ammonia-oxidisers, Environ. Microbiomes, 14, 3, https://doi.org/10.1186/s40793-019-0342-6,
2019.
Alam, M. S. and Jia, Z.: Inhibition of methane oxidation by nitrogenous
fertilizers in a paddy soil, Front. Microbiol., 3, 246,
https://doi.org/10.3389/fmicb.2012.00246, 2012.
Bedard, C. and Knowles, R.: Physiology, biochemistry, and specific
inhibitors of CH4,
Belova, S. E., Kulichevskaya, I. S., Bodelier, P. L. E., and Dedysh, S. N.:
Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and
emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al.
1993, Int. J. Syst. Evol. Micr., 63, 1096–1104,
https://doi.org/10.1099/ijs.0.043505-0, 2013.
Bodelier, P. L. E., Roslev, P., Henckel, T., and Frenzel, P.: Stimulation by
ammonium-based fertilizers of methane oxidation in soil around rice roots,
Nature, 403, 421–424, https://doi.org/10.1038/35000193, 2000.
Bridgham, S. D., Cadillo-Quiroz, H., Keller, J. K., and Zhuang, Q.: Methane
emissions from wetlands: Biogeochemical, microbial, and modeling
perspectives from local to global scales, Glob. Change Biol., 19, 1325–1346,
https://doi.org/10.1111/gcb.12131, 2013.
Cai, Y., Zheng, Y., Bodelier, P. L. E., Conrad, R., and Jia, Z.:
Conventional methanotrophs are responsible for atmospheric methane oxidation
in paddy soils, Nat. Commun., 7, 11728, https://doi.org/10.1038/ncomms11728, 2016.
Cai, Z. and Yan, X.: Kinetic model for methane oxidation by paddy soil as
affected by temperature, moisture and N addition, Soil Biol. Biochem., 31,
715–725, https://doi.org/10.1016/S0038-0717(98)00170-9, 1999.
Calhoun, A. and King, G. M.: Characterization of root-associated
methanotrophs from three freshwater macrophytes: Pontederia cordata, Sparganium eurycarpum, and Sagittaria latifolia, Appl. Environ.
Microb., 64, 1099–1105, 1998.
Caporaso, J., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.,
Costello, E., Fierer, N., Pena, A., Goodrich, J., Gordon, J., Huttley, G.,
Kelley, S., Knights, D., Koenig, J., Ley, R., Lozupone, C., McDonald, D.,
Muegge, B., Pirrung, M., Reeder, J., Sevinsky, J., Tumbaugh, P., Walters,
W., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R.: QIIME allows
analysis of high-throughput community sequencing data, Nat. Methods, 7,
335–336, https://doi.org/10.1038/nmeth.f.303, 2010.
Chen, Y., Dumont, M. G., McNamara, N. P., Chamberlain, P. M., Bodrossy, L.,
Stralis-Pavese, N., and Murrell, J. C.: Diversity of the active
methanotrophic community in acidic peatlands as assessed by mRNA and
SIP-PLFA analyses, Environ. Microbiol., 10, 446–459,
https://doi.org/10.1111/j.1462-2920.2007.01466.x, 2008a.
Chen, Y., Dumont, M. G., Neufeld, J. D., Bodrossy, L., Stralis-Pavese, N.,
McNamara, N. P., Ostle, N., Briones, M. J. I., and Murrell, J. C.: Revealing
the uncultivated majority: Combining DNA stable-isotope probing, multiple
displacement amplification and metagenomic analyses of uncultivated
Methylocystis in acidic peatlands, Environ. Microbiol., 10, 2609–2622,
https://doi.org/10.1111/j.1462-2920.2008.01683.x, 2008b.
Conrad, R. and Rothfuss, F.: Methane oxidation in the soil surface layer of
a flooded rice field and the effect of ammonium, Biol. Fert. Soils, 12,
28–32, https://doi.org/10.1007/BF00369384, 1991.
Costello, A. M. and Lidstrom, M. E.: Molecular characterization of
functional and phylogenetic genes from natural populations of methanotrophs
in lake sediments, Appl. Environ. Microb., 65, 5066–5074, 1999.
Daebeler, A., Bodelier, P. L. E., Yan, Z., Hefting, M. M., Jia, Z., and
Laanbroek, H. J.: Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate
autotrophic nitrification in volcanic grassland soil, ISME J., 8, 2397–2410,
https://doi.org/10.1038/ismej.2014.81, 2014.
Dedysh, S. N.: Exploring methanotroph diversity in acidic northern wetlands:
Molecular and cultivation-based studies, Microbiology, 78, 655–669,
https://doi.org/10.1134/S0026261709060010, 2009.
Dedysh, S. N., Liesack, W., Khmelenina, V. N., Suzina, N. E., Trotsenko, Y.
A., Semrau, J. D., Bares, A. M., Panikov, N. S., and Tiedje, J. M.:
Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from
peat bogs, representing a novel subtype of serine- pathway methanotrophs,
Int. J. Syst. Evol. Micr., 50, 955–969, https://doi.org/10.1099/00207713-50-3-955,
2000.
Dedysh, S. N., Belova, S. E., Bodelier, P. L. E., Smirnova, K. V.,
Khmelenina, V. N., Chidthaisong, A., Trotsenko, Y. A., Liesack, W., and
Dunfiel, P. F.: Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium
possessing “signature” fatty acids of type I methanotrophs, Int. J. Syst.
Evol. Micr., 57, 472–479, https://doi.org/10.1099/ijs.0.64623-0, 2007.
Degelmann, D. M., Borken, W., Drake, H. L., and Kolb, S.: Different
atmospheric methane-oxidizing communities in european beech and norway
spruce soils, Appl. Environ. Microb., 76, 3228–3235,
https://doi.org/10.1128/aem.02730-09, 2010.
Deng, W., Wang, Y., Liu, Z., Cheng, H., and Xue, Y.: HemI: A toolkit for
illustrating heatmaps, PLoS One, 9, e111988, https://doi.org/10.1371/journal.pone.0111988, 2014.
Deng, Y., Cui, X., and Dumont, M. G.: Identification of active aerobic
methanotrophs in plateau wetlands using DNA stable isotope probing, FEMS
Microbiol. Lett., 363, 1–8, https://doi.org/10.1093/femsle/fnw168, 2016.
Dumont, M. G., Lüke, C., Deng, Y., and Frenzel, P.: Classification of
pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in
MEGAN, Front. Microbiol., 5, 34, https://doi.org/10.3389/fmicb.2014.00034, 2014.
Edgar, R.: UPARSE: highly accurate OTU sequences from microbial amplicon
reads, Nat. Methods, 10, 996–998, https://doi.org/10.1038/nmeth.2604, 2013.
Eller, G. and Frenzel, P.: Changes in activity and community structure of
methane-oxidizing bacteria over the growth period of rice, Appl. Environ.
Microb., 67, 2395–2403, https://doi.org/10.1128/aem.67.6.2395-2403.2001, 2001.
Esson, K. C., Lin, X., Kumaresan, D., Chanton, J. P., Murrell, J. C., and
Kostka, E.: Alpha- and Gammaproteobacterial methanotrophs codominate the
active methane-oxidizing communities in an acidic boreal peat bog, Appl.
Environ. Microb., 82, 2363–2371, https://doi.org/10.1128/aem.03640-15, 2016.
Fierer, N., Strickland, M. S., Liptzin, D., Bradford, M. A., and Cleveland,
C. C.: Global patterns in belowground communities, Ecol. Lett., 12,
1238–1249, https://doi.org/10.1111/j.1461-0248.2009.01360.x, 2009.
Frenzel, P., Rothfuss, F., and Conrad, R.: Oxygen profiles and methane
turnover in a flooded rice microcosm, Biol. Fert. Soils, 14, 84–89, 1992.
Graham, D. W., Chaudhary, J. A., Hanson, R. S., and Arnold, R. G.: Factors
affecting competition between type I and type II methanotrophs in
two-organism, continuous-flow reactors, Microb. Ecol., 25, 1–17,
https://doi.org/10.1007/BF00182126, 1993.
Gubry-Rangin, C., Hai, B., Quince, C., Engel, M., Thomson, B. C., James, P.,
Schloter, M., Griffiths, R. I., Prosser, J. I., and Nicol, G. W.: Niche
specialization of terrestrial archaeal ammonia oxidizers, P. Natl. Acad.
Sci. USA, 108, 21206–21211, https://doi.org/10.1073/pnas.1109000108, 2011.
Gupta, V., Smemo, K. A., Yavitt, J. B., and Basiliko, N.: Active
methanotrophs in two contrasting North American peatland ecosystems revealed
using DNA-SIP, Microb. Ecol., 63, 438–445, https://doi.org/10.1007/s00248-011-9902-z,
2012.
Hanson, R. S. and Hanson, T. E.: Methanotrophic bacteria, Microbiol. Rev.,
60, 439–471, https://doi.org/10.1002/0471263397.env316, 1996.
He, R., Wooller, M. J., Pohlman, J. W., Quensen, J., Tiedje, J. M., and
Leigh, M. B.: Diversity of active aerobic methanotrophs along depth profiles
of arctic and subarctic lake water column and sediments, ISME J., 6,
1937–1948, https://doi.org/10.1038/ismej.2012.34, 2012.
Ho, A., Kerckhof, F. M., Luke, C., Reim, A., Krause, S., Boon, N., and
Bodelier, P. L. E.: Conceptualizing functional traits and ecological
characteristics of methane-oxidizing bacteria as life strategies, Env.
Microbiol. Rep., 5, 335–345, https://doi.org/10.1111/j.1758-2229.2012.00370.x, 2013.
Holmes, A. J., Costello, A., Lidstrom, M. E., and Murrell, J. C.: Evidence
that participate methane monooxygenase and ammonia monooxygenase may be
evolutionarily related, FEMS Microbiol. Lett., 132, 203–208,
https://doi.org/10.1016/0378-1097(95)00311-R, 1995.
Holmes, A. J., Roslev, P., McDonald, I. R., Iversen, N., Henriksen, K., and
Murrell, J. C.: Characterization of methanotrophic bacterial populations in
soils showing atmospheric methane uptake, Appl. Environ. Microb., 65,
3312–3318, 1999.
Kip, N., Fritz, C., Langelaan, E. S., Pan, Y., Bodrossy, L., Pancotto, V., Jetten, M. S. M., Smolders, A. J. P., and Op den Camp, H. J. M.: Methanotrophic activity and diversity in different Sphagnum magellanicum dominated habitats in the southernmost peat bogs of Patagonia, Biogeosciences, 9, 47–55, https://doi.org/10.5194/bg-9-47-2012, 2012.
Knief, C., Lipski, A., and Dunfield, P. F.: Diversity and activity of
methanotrophic bacteria in different upland soils, Appl. Environ.
Microb., 69, 6703–6714, https://doi.org/10.1128/aem.69.11.6703-6714.2003, 2003.
Kögel-Knabner, I., Amelung, W., Cao, Z., Fiedler, S., Frenzel, P., Jahn,
R., Kalbitz, K., Kölbl, A., and Schloter, M.: Biogeochemistry of paddy
soils, Geoderma, 157, 1–14, https://doi.org/10.1016/j.geoderma.2010.03.009, 2010.
Kolb, S., Knief, C., Stubner, S., and Conrad, R.: Quantitative detection of
methanotrophs in soil by novel pmoA-targeted real-time PCR assays, Appl.
Environ. Microb., 69, 2423–2429, https://doi.org/10.1128/aem.69.5.2423-2429.2003,
2003.
Lauber, C. L., Hamady, M., Knight, R., and Fierer, N.: Pyrosequencing-based
assessment of soil pH as a predictor of soil bacterial community structure
at the continental scale, Appl. Environ. Microb., 75, 5111–5120,
https://doi.org/10.1128/aem.00335-09, 2009.
Leng, L., Chang, J., Geng, K., Lu, Y., and Ma, K.: Uncultivated
Methylocystis species in paddy soil include facultative methanotrophs that utilize
acetate, Microbiol. Ecol., 70, 88–96, https://doi.org/10.1007/s00248-014-0540-0, 2015.
Liebner, S. and Wagner, D.: Abundance, distribution and potential activity
of methane oxidizing bacteria in permafrost soils from the Lena Delta,
Siberia, Environ. Microbiol., 9, 107–117,
https://doi.org/10.1111/j.1462-2920.2006.01120.x, 2007.
Lin, J. L., Radajewski, S., Eshinimaev, B. T., Trotsenko, Y. A., McDonald,
I. R., and Murrell, J. C.: Molecular diversity of methanotrophs in
Transbaikal soda lake sediments and identification of potentially active
populations by stable isotope probing, Environ. Microbiol., 6, 1049–1060,
https://doi.org/10.1111/j.1462-2920.2004.00635.x, 2004.
Liu, B., Mørkved, P. T., Frostegård, Å., and Bakken, L. R.:
Denitrification gene pools, transcription and kinetics of NO, N2O and
N2 production as affected by soil pH, FEMS Microbiol. Ecol., 72,
407–417, https://doi.org/10.1111/j.1574-6941.2010.00856.x, 2010.
Ma, K., Conrad, R., and Lu, Y.: Dry/wet cycles change the activity and
population dynamics of methanotrophs in rice field soil, Appl. Environ.
Microb., 79, 4932–4939, https://doi.org/10.1128/aem.00850-13, 2013.
Magoč, T. and Salzberg, S. L.: FLASH: Fast length adjustment of short
reads to improve genome assemblies, Bioinformatics, 27, 2957–2963,
https://doi.org/10.1093/bioinformatics/btr507, 2011.
Mohanty, S. R., Bodelier, P. L., Floris, V., and Conrad, R.: Differential
effects of nitrogenous fertilizers on methane-consuming microbes in rice
field and forest soils, Appl. Environ. Microb., 72, 1346–1354,
https://doi.org/10.1128/aem.72.2.1346-1354.2006, 2006.
Morris, S. A., Radajewski, S., Willison, T. W., and Murrell, J. C.:
Identification of the functionally active methanotroph population in a peat
soil microcosm by stable-isotope probing, Appl. Environ. Microb., 68,
1446–1453, https://doi.org/10.1128/aem.68.3.1446-1453.2002, 2002.
Murase, J. and Frenzel, P.: A methane-driven microbial food web in a
wetland rice soil, Environ. Microbiol., 9, 3025–3034,
https://doi.org/10.1111/j.1462-2920.2007.01414.x, 2007.
Noll, M., Frenzel, P., and Conrad, R.: Selective stimulation of type I
methanotrophs in a rice paddy soil by urea fertilization revealed by
RNA-based stable isotope probing, FEMS Microbiol. Ecol., 65, 125–132,
https://doi.org/10.1111/j.1574-6941.2008.00497.x, 2008.
Nouchi, I., Mariko, S., and Aoki, K.: Mechanism of methane transport from
the rhizosphere to the atmosphere through rice plants, Plant Physiol., 94,
59–66, https://doi.org/10.1104/pp.94.1.59, 1990.
Nouchi, I., Hosono, T., Aoki, K., and Minami, K.: Seasonal variation in
methane flux from rice paddies associated with methane concentration in soil
water, rice biomass and temperature, and its modelling, Plant Soil, 161,
195–208, https://doi.org/10.1007/BF00046390, 1994.
Qiu, Q., Noll, M., Abraham, W., Lu, Y., and Conrad, R.: Applying stable
isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field
to study activity and composition of the methanotrophic bacterial
communities in situ, ISME J., 2, 602–614, https://doi.org/10.1038/ismej.2008.34, 2008.
Reim, A., Lu, C., Krause, S., Pratscher, J., and Frenzel, P.: One millimetre
makes the difference: high-resolution analysis of methane-oxidizing bacteria
and their specific activity at the oxic-anoxic interface in a flooded paddy
soil, ISME J., 6, 2128–2139, https://doi.org/10.1038/ismej.2012.57, 2012.
Roslev, P. and Iversen, N.: Radioactive fingerprinting of microorganisms
that oxidize atmospheric methane in different soils, Appl. Environ.
Microb., 65, 4064–4070, 1999.
Semrau, J. D., DiSpirito, A. A., and Vuilleumier, S.: Facultative
methanotrophy: false leads, true results, and suggestions for future
research, FEMS Microbiol. Lett., 323, 1–12,
https://doi.org/10.1111/j.1574-6968.2011.02315.x, 2011.
Shiau, Y. J., Cai, Y., Jia, Z., Chen, C. L., and Chiu, C. Y.:
Phylogenetically distinct methanotrophs modulate methane oxidation in rice
paddies across Taiwan, Soil Biol. Biochem., 124, 59–69,
https://doi.org/10.1016/j.soilbio.2018.05.025, 2018.
Shrestha, M., Abraham, W. R., Shrestha, P. M., Noll, M., and Conrad, R.:
Activity and composition of methanotrophic bacterial communities in planted
rice soil studied by flux measurements, analyses of pmoA gene and stable isotope
probing of phospholipid fatty acids, Environ. Microbiol., 10, 400–412,
https://doi.org/10.1111/j.1462-2920.2007.01462.x, 2008.
Stubner, S.: Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice field soil by
real-time PCR with SybrGreen™ detection, J. Microbiol. Meth.,
50, 155–164, https://doi.org/10.1016/S0167-7012(02)00024-6, 2002.
Tripathi, B. M., Stegen, J. C., Kim, M., Dong, K., Adams, J. M., and Lee, Y.
K.: Soil pH mediates the balance between stochastic and deterministic
assembly of bacteria, ISME J., 12, 1072–1083, https://doi.org/10.1038/s41396-018-0082-4,
2018.
Trotsenko, Y. A. and Murrell, J. C.: Metabolic aspects of aerobic obligate
methanotrophy, Adv. App. Microbiol., 63, 183–229,
https://doi.org/10.1016/S0065-2164(07)00005-6, 2008.
Tveit, A. T., Hestnes, A. G., Robinson, S. L., Schintlmeister, A., Dedysh,
S. N., Jehmlich, N., von Bergen, M., Herbold, C., Wagner, M., Richter, A.,
and Svenning, M. M.: Widespread soil bacterium that oxidizes atmospheric
methane, P. Natl. Acad. Sci. USA, 116, 8515–8524,
https://doi.org/10.1073/pnas.1817812116, 2019.
van de Kamp, J., Hook, S. E., Williams, A., Tanner, J. E., and Bodrossy, L.:
Baseline characterization of aerobic hydrocarbon degrading microbial
communities in deep-sea sediments of the Great Australian Bight, Australia,
Environ. Microbiol., 21, 1782–1797, https://doi.org/10.1111/1462-2920.14559, 2019.
Wang, B., Zhao, J., Guo, Z., Ma, J., Xu, H., and Jia, Z.: Differential
contributions of ammonia oxidizers and nitrite oxidizers to nitrification in
four paddy soils, ISME J., 9, 1062–1075, https://doi.org/10.1038/ismej.2014.194, 2015.
Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R.: Naïve
Bayesian classifier for rapid assignment of rRNA sequences into the new
bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261–5267,
https://doi.org/10.1128/AEM.00062-07, 2007.
Wang, Q., Quensen, J. F. I., Fish, J. A., Lee, T. K., Sun, Y., Tiedje, J.
M., and Cole, J. R.: Ecological patterns of nifH genes in four terrestrial
climatic zones, MBio, 4, e00592-13, https://doi.org/10.1128/mBio.00592-13, 2013.
Wen, X., Yang, S., and Liebner, S.: Evaluation and update of cutoff values
for methanotrophic pmoA gene sequences, Arch. Microbiol., 198, 629–636,
https://doi.org/10.1007/s00203-016-1222-8, 2016.
Yang, S., Matsen, J. B., Konopka, M., Green-Saxena, A., Clubb, J., Sadilek,
M., Orphan, V. J., Beck, D., and Kalyuzhnaya, M. G.: Global molecular
analyses of methane metabolism in methanotrophic Alphaproteobacterium,
Methylosinus trichosporium OB3b. Part II. metabolomics and 13C-labeling study, Front. Microbiol., 4, 70,
https://doi.org/10.3389/fmicb.2013.00070, 2013.
Zhang, J., Cai, Z., Cheng, Y., and Zhu, T.: Denitrification and total
nitrogen gas production from forest soils of Eastern China, Soil Biol.
Biochem., 41, 2551–2557, https://doi.org/10.1016/j.soilbio.2009.09.016, 2009.
Zhao, J.: Methanotrophic bacterium clone, available at: https://www.ncbi.nlm.nih.gov/nuccore/MK613983-MK613993, last access: 9 March 2019a.
Zhao, J.: Uncultured methanotrophic bacterium clone, available at: https://www.ncbi.nlm.nih.gov/nuccore/MK621911-MK621913, last access: 12 March 2019b.
Zhao, J., Wang, B., and Jia, Z.: Phylogenetically distinct phylotypes
modulate nitrification in a paddy soil, Appl. Environ. Microb., 81,
3218–3227, https://doi.org/10.1128/aem.00426-15, 2015.
Zhao, J., Cai, Y. F., and Jia, Z. J.: Type II and I methanotrophs in paddy soils, ENA-LAST-UPDATE, 2017-08-23, ENA, available at: https://www.ebi.ac.uk/ena/data/view/PRJEB37235, last access: 23 August 2017a.
Zhao, J., Cai, Y. F., and Jia, Z. J.: Methanotrophs in wetland paddies, ENA-LAST-UPDATE, 2017-08-23, ENA, available at: https://www.ebi.ac.uk/ena/data/view/PRJEB40045, last access: 23 August 2017b.
Zheng, Y., Huang, R., Wang, B. Z., Bodelier, P. L. E., and Jia, Z. J.: Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil, Biogeosciences, 11, 3353–3368, https://doi.org/10.5194/bg-11-3353-2014, 2014.
Short summary
We show that soil pH is a key factor in selecting distinct phylotypes of methanotrophs in paddy soils. Type II methanotrophs dominated the methane oxidation in low-pH soils, while type I methanotrophs were more active in high-pH soils. This pH-based niche differentiation of active methanotrophs appeared to be independent of nitrogen fertilization, but the inhibition of type II methanotrophic rate in low-pH soils by the fertilization might aggravate the emission of methane from paddy soils.
We show that soil pH is a key factor in selecting distinct phylotypes of methanotrophs in paddy...
Altmetrics
Final-revised paper
Preprint