Articles | Volume 10, issue 8
https://doi.org/10.5194/bg-10-5739-2013
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-10-5739-2013
© Author(s) 2013. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| 
30 Aug 2013
Research article |
| 30 Aug 2013
Conversion of upland to paddy field specifically alters the community structure of archaeal ammonia oxidizers in an acid soil
M. S. Alam
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
University of Chinese Academy of Sciences, Beijing, 100049, China
Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur – 1706, Bangladesh
G. D. Ren
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
University of Chinese Academy of Sciences, Beijing, 100049, China
L. Lu
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
University of Chinese Academy of Sciences, Beijing, 100049, China
Y. Zheng
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
University of Chinese Academy of Sciences, Beijing, 100049, China
X. H. Peng
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
Z. J. Jia
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
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Jun Zhao, Yuanfeng Cai, and Zhongjun Jia
Biogeosciences, 17, 1451–1462, https://doi.org/10.5194/bg-17-1451-2020, https://doi.org/10.5194/bg-17-1451-2020, 2020
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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.
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
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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
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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
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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
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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
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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
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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
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Jun Zhao, Yuanfeng Cai, and Zhongjun Jia
Biogeosciences, 17, 1451–1462, https://doi.org/10.5194/bg-17-1451-2020, https://doi.org/10.5194/bg-17-1451-2020, 2020
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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.
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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.
Cited articles
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Auguet, J. C., Triado-Margarit, X., Nomokonova, N., Camarero, L., and Casamayor, E. O.: Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake, ISME J., 6, 1786–1797, 2012.
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Bodelier, P., Libochant, J. A., Blom, C., and Laanbroek, H. J.: Dynamics of nitrification and denitrification in root-oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats, Appl. Environ. Microbiol., 62, 4100–4107, 1996.
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Chen, X., Zhang, L. M., Shen, J. P., Xu, Z., and He, J. Z.: Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils, J. Soils Sediments, 10, 1510–1516, 2010.
Chen, X., Zhang, L. M., Shen, J. P., Wei, W. X., and He, J. Z.: Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil, Biol. Fertil. Soils, 47, 323–331, 2011.
Chu, H., Fujii, T., Morimoto, S., Lin, X., Yagi, K., Hu, J., and Zhang, J.: Community Structure of Ammonia-Oxidizing Bacteria under Long-Term Application of Mineral Fertilizer and Organic Manure in a Sandy Loam Soil, Appl. Environ. Microbiol., 73, 485–491, 2007.
Chu, H., Morimoto, S., Fujii, T., Yagi, K., and Nishimura, S.: Soil ammonia-oxidizing bacterial communities in paddy rice fields as affected by upland conversion history, Soil Sci. Soc. Am. J., 73, 2026–2031, 2009.
Erguder, T. H., Boon, N., Wittebolle, L., Marzorati, M., and Verstraete, W.: Environmental factors shaping the ecological niches of ammonia-oxidizing archaea, FEMS Microbiol. Rev., 33, 855–869, 2009.
Fan, F., Yang, Q., Li, Z., Wei, D., Cui, X. A., and Liang, Y.: Impacts of Organic and Inorganic Fertilizers on Nitrification in a Cold Climate Soil are Linked to the Bacterial Ammonia Oxidizer Community, Microb. Ecol., 62, 982–990, 2011.
Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., and Oakley, B. B.: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean, P. Natl. Aca. Sci. USA, 102, 14683–14688, 2005.
French, E., Kozlowski, J. A., Mukherjee, M., Bullerjahn, G., and Bollmann, A.: Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater, Appl. Environ. Microbiol., 78, 5773–5780, 2012.
Garbeva, P., van Veen, J. A., and van Elsas, J. D.: Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness, Annu. Rev. Phytopathol., 42, 243–270, 2004.
Geets, J., Boon, N., and Verstraete, W.: Strategies of aerobic ammonia-oxidizing bacteria for coping with nutrient and oxygen fluctuations, FEMS Microbiol. Ecol., 58, 1–13, 2006.
Gleeson, D. B., Muller, C., Banerjee, S., Ma, W., Siciliano, S. D., and Murphy, D. V.: Response of ammonia oxidizing archaea and bacteria to changing water filled pore space, Soil Biol. Biochem., 42, 1888–1891, 2010.
Griffiths, R. I., Whiteley, A. S., O'Donnell, A. G., and Bailey, M. J.: Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition, Appl. Environ. Microbiol., 66, 5488–5491, 2000.
Hatzenpichler, R.: Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea, Appl. Environ. Microbiol., 78, 7501–7510, 2012.
He, J. Z., Shen, J. P., Zhang, L. M., Zhu, Y. G., Zheng, Y. M., Xu, M. G., and Di, H. J.: Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices, Environ. Microbiol., 9, 2364–2374, 2007.
Herrmann, M., Saunders, A. M., and Schramm, A.: Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora, Appl. Environ. Microbiol., 74, 3279–3283, 2008.
Horz, H. P., Barbrook, A., Field, C. B., and Bohannan, B. J.: Ammonia-oxidizing bacteria respond to multifactorial global change, P. Natl. Acad. Sci. USA, 101, 15136–15141, 2004.
Innerebner, G., Knapp, B., Vasara, T., Romantschuk, M., and Insam, H.: Traceability of ammonia-oxidizing bacteria in compost-treated soils, Soil Biol. Biochem., 38, 1092–1100, 2006.
Jia, Z. and Conrad, R.: Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil, Environ. Microbiol., 11, 1658–1671, 2009.
Jung, M. Y., Park, S. J., Min, D., Kim, J. S., Rijpstra, W. I. C., Sinninghe Damsté, J. S., Kim, G. J., Madsen, E. L., and Rhee, S. K.: Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil, Appl. Environ. Microbiol., 77, 8635–8647, 2011.
Ke, X. and Lu, Y.: Adaptation of ammonia-oxidizing microorganisms to environment shift of paddy field soil, FEMS Microbiol. Ecol., 80, 87–97, 2012.
Kim, J. G., Jung, M. Y., Park, S. J., Rijpstra, W. I. C., Sinninghe Damsté, J. S., Madsen, E. L., Min, D., Kim, J. S., Kim, G. J., and Rhee, S.K.: Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil, Environ. Microbiol., 14, 1528–1543, 2012.
Könneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., and Stahl, D. A.: Isolation of an autotrophic ammonia-oxidizing marine archaeon, Nature, 437, 543–546, 2005.
Kowalchuk, G. A. and Stephen, J. R.: AMMONIA-OXIDIZING BACTERIA: A Model for Molecular Microbial Ecology, Annu. Rev. Microbiol., 55, 485–529, 2001.
Kowalchuk, G. A., Bodelier, P. L. E., Heilig, G. H. J., Stephen, J. R., and Laanbroek, H. J.: Community analysis of ammonia-oxidising bacteria, in relation to oxygen availability in soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridization, FEMS Microbiol. Ecol., 27, 339–350, 1998.
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Lehtovirta-Morley, L. E., Stoecker, K., Vilcinskas, A., Prosser, J. I., and Nicol, G. W.: Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil, P. Natl. Acad. Sci. USA, 108, 15892–15897, 2011.
Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G. W., Prosser, J. I., Schuster, S. C., and Schleper, C.: Archaea predominate among ammonia-oxidizing prokaryotes in soils, Nature, 442, 806–809, 2006.
Levičnik-Höfferle, Š., Nicol, G. W., Ausec, L., Mandić-Mulec, I., and Prosser, J. I.: Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not added inorganic nitrogen, FEMS Microbiol. Ecol., 80, 114–123, 2012.
Lu, L. and Jia, Z.: Urease gene-containing Archaea dominate autotrophic ammonia oxidation in two acid soils, Environ. Microbiol., 15, 1795–1809, https://doi.org/10.1111/1462-2920.12071, 2013.
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Mao, Y., Yannarell, A. C., and Mackie, R. I.: Changes in N-Transforming Archaea and Bacteria in Soil during the Establishment of Bioenergy Crops, PLoS ONE, 6, e24750, https://doi.org/10.1371/journal.pone.0024750, 2011.
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Park, H. D., Wells, G. F., Bae, H., Criddle, C. S., and Francis, C. A.: Occurrence of ammonia oxidizing archaea in wastewater treatment plant bioreactors, Appl. Environ. Microbiol., 72, 5643–5647, 2006.
Pett-Ridge J., Petersen, D. G., Nuccio, E., and Firestone M. K.: Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil, FEMS Microbiol. Ecol., 85, 179–194, 2013.
Prosser, J. I. and Nicol, G. W.: Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation, Trends Microbiol., 20, 523–531, 2012.
Rotthauwe, J., Witzel, K., and Liesack, W.: The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations, Appl. Environ. Microbiol., 63, 4704–4712, 1997.
Santoro, A. E., Francis, C. A., de Sieyes, N. R., and Boehm, A. B.: Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary, Environ. Microbiol., 10, 1068–1079, 2008.
Schleper, C.: Ammonia oxidation: different niches for bacteria and archaea, ISME J., 4, 1092–1094, 2010.
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