Articles | Volume 13, issue 10
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids
VTT Technical Research Centre of Finland Ltd., Espoo, Finland
Geological Survey of Finland (GTK), Espoo, Finland
VTT Technical Research Centre of Finland Ltd., Espoo, Finland
VTT Technical Research Centre of Finland Ltd., Espoo, Finland
VTT Technical Research Centre of Finland Ltd., Espoo, Finland
Geological Survey of Finland (GTK), Espoo, Finland
Geological Survey of Finland (GTK), Espoo, Finland
now at: Department of Physics, University of Helsinki, Helsinki, Finland
VTT Technical Research Centre of Finland Ltd., Espoo, Finland
No articles found.
Nikita Afonin, Elena Kozlovskaya, Ilmo Kukkonen, and DAFNE/FINLAND Working Group
Solid Earth, 8, 531–544,
Hanna K. Lappalainen, Veli-Matti Kerminen, Tuukka Petäjä, Theo Kurten, Aleksander Baklanov, Anatoly Shvidenko, Jaana Bäck, Timo Vihma, Pavel Alekseychik, Meinrat O. Andreae, Stephen R. Arnold, Mikhail Arshinov, Eija Asmi, Boris Belan, Leonid Bobylev, Sergey Chalov, Yafang Cheng, Natalia Chubarova, Gerrit de Leeuw, Aijun Ding, Sergey Dobrolyubov, Sergei Dubtsov, Egor Dyukarev, Nikolai Elansky, Kostas Eleftheriadis, Igor Esau, Nikolay Filatov, Mikhail Flint, Congbin Fu, Olga Glezer, Aleksander Gliko, Martin Heimann, Albert A. M. Holtslag, Urmas Hõrrak, Juha Janhunen, Sirkku Juhola, Leena Järvi, Heikki Järvinen, Anna Kanukhina, Pavel Konstantinov, Vladimir Kotlyakov, Antti-Jussi Kieloaho, Alexander S. Komarov, Joni Kujansuu, Ilmo Kukkonen, Ella-Maria Duplissy, Ari Laaksonen, Tuomas Laurila, Heikki Lihavainen, Alexander Lisitzin, Alexsander Mahura, Alexander Makshtas, Evgeny Mareev, Stephany Mazon, Dmitry Matishov, Vladimir Melnikov, Eugene Mikhailov, Dmitri Moisseev, Robert Nigmatulin, Steffen M. Noe, Anne Ojala, Mari Pihlatie, Olga Popovicheva, Jukka Pumpanen, Tatjana Regerand, Irina Repina, Aleksei Shcherbinin, Vladimir Shevchenko, Mikko Sipilä, Andrey Skorokhod, Dominick V. Spracklen, Hang Su, Dmitry A. Subetto, Junying Sun, Arkady Y. Terzhevik, Yuri Timofeyev, Yuliya Troitskaya, Veli-Pekka Tynkkynen, Viacheslav I. Kharuk, Nina Zaytseva, Jiahua Zhang, Yrjö Viisanen, Timo Vesala, Pertti Hari, Hans Christen Hansson, Gennady G. Matvienko, Nikolai S. Kasimov, Huadong Guo, Valery Bondur, Sergej Zilitinkevich, and Markku Kulmala
Atmos. Chem. Phys., 16, 14421–14461,Short summary
After kick off in 2012, the Pan-Eurasian Experiment (PEEX) program has expanded fast and today the multi-disciplinary research community covers ca. 80 institutes and a network of ca. 500 scientists from Europe, Russia, and China. Here we introduce scientific topics relevant in this context. This is one of the first multi-disciplinary overviews crossing scientific boundaries, from atmospheric sciences to socio-economics and social sciences.
Malin Bomberg, Tiina Lamminmäki, and Merja Itävaara
Biogeosciences, 13, 6031–6047,Short summary
Over 95 % of the microbial communities in isolated groundwater in Olkiluoto bedrock, Finland, is composed of only a few common species. The remaining rare microbiome contains over 3- and 6-fold more microbial diversity. The rare microbiome is an unlimited source of genomic functionality in the ecosystem. These microorganisms can respond to change caused by physical or biological factors that may lead to alterations in the diversity and function of the microbial communities in crystalline bedrock.
T. L. Kieft, T. C. Onstott, L. Ahonen, V. Aloisi, F. S. Colwell, B. Engelen, S. Fendrihan, E. Gaidos, U. Harms, I. Head, J. Kallmeyer, B. Kiel Reese, L.-H. Lin, P. E. Long, D. P. Moser, H. Mills, P. Sar, D. Schulze-Makuch, H. Stan-Lotter, D. Wagner, P.-L. Wang, F. Westall, and M. J. Wilkins
Sci. Dril., 19, 43–53,
Related subject area
Biodiversity and Ecosystem Function: Microbial Ecology & GeomicrobiologyImpact of metabolism and temperature on 2H ∕ 1H fractionation in lipids of the marine bacterium Shewanella piezotolerans WP3Maximum summer temperatures predict the temperature adaptation of Arctic soil bacterial communitiesPotential contributions of nitrifiers and denitrifiers to nitrous oxide sources and sinks in China's estuarine and coastal areasAqueous system-level processes and prokaryote assemblages in the ferruginous and sulfate-rich bottom waters of a post-mining lakeAbundances and morphotypes of the coccolithophore Emiliania huxleyi in southern Patagonia compared to neighbouring oceans and Northern Hemisphere fjordsDetermining 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 basinThe water column of the Yamal tundra lakes as a microbial filter preventing methane emissionBioerosion and fungal colonization of the invasive foraminiferan Amphistegina lobifera in a Mediterranean seagrass meadowEffects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangroveDeep maxima of phytoplankton biomass, primary production and bacterial production in the Mediterranean SeaHaplo-diplontic life cycle expands coccolithophore nicheThe composition of endolithic communities in gypcrete is determined by the specific microhabitat architectureUncovering chemical signatures of salinity gradients through compositional analysis of protein sequencesCryptic roles of tetrathionate in the sulfur cycle of marine sediments: microbial drivers and indicatorsLake mixing regime selects apparent methane oxidation kinetics of the methanotroph assemblageThe contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth)The pH-based ecological coherence of active canonical methanotrophs in paddy soilsBiogeographical distribution of microbial communities along the Rajang River–South China Sea continuumMicrobial community composition and abundance after millennia of submarine permafrost warmingCold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edgeEcophysiological characteristics of red, green, and brown strains of the Baltic picocyanobacterium Synechococcus sp. – a laboratory studyFactors controlling the community structure of picoplankton in contrasting marine environmentsCommunity composition and seasonal changes of archaea in coarse and fine air particulate matterMicrobial community structure in the western tropical South PacificEcophysiological characterization of early successional biological soil crusts in heavily human-impacted areasSoil 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 TaiwanRevisiting chlorophyll extraction methods in biological soil crusts – methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methodsDivergence of dominant factors in soil microbial communities and functions in forest ecosystems along a climatic gradientUncovering biological soil crusts: carbon content and structure of intact Arctic, Antarctic and alpine biological soil crustsAntagonistic effects of drought and sand burial enable the survival of the biocrust moss Bryum argenteum in an arid sandy desertMicrobial methanogenesis in the sulfate-reducing zone of sediments in the Eckernförde Bay, SW Baltic SeaFerrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortiaEffects of temperature on the composition and diversity of bacterial communities in bamboo soils at different elevationsDevelopment of bacterial communities in biological soil crusts along a revegetation chronosequence in the Tengger Desert, northwest ChinaViable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environmentsDiversity 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 SeaMechanisms of Trichodesmium demise within the New Caledonian lagoon during the VAHINE mesocosm experimentEffect 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 monsoonCharacterization of active and total fungal communities in the atmosphere over the Amazon rainforestResponses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical ChinaRedox regime shifts in microbially mediated biogeochemical cyclesDifferences in microbial community composition between injection and production water samples of water flooding petroleum reservoirsMicrobial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiotaDiversity and seasonal dynamics of airborne archaeaMethanotrophic 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 reproductionHigh temperature decreases the PIC / POC ratio and increases phosphorus requirements in Coccolithus pelagicus (Haptophyta)
Xin Chen, Weishu Zhao, Liang Dong, Huahua Jian, Lewen Liang, Jing Wang, and Fengping Wang
Biogeosciences, 20, 1491–1504,Short summary
Here, we studied the effects of metabolism and growth temperature on 2H/1H fractionation between fatty acids and growth water (εFA/water) by Shewanella piezotolerans WP3. Our results show that the εFA/water values display considerable variations for cultures grown on different substrates. Combined with metabolic model analysis, our results indicate that the central metabolic pathways exert a fundamental effect on the hydrogen isotope composition of lipids in heterotrophs.
Ruud Rijkers, Mark Dekker, Rien Aerts, and James T. Weedon
Biogeosciences, 20, 767–780,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,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,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,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,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,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.
Biogeosciences, 18, 2777–2790,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,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,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,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,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,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,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,
Massimiliano Molari, Felix Janssen, Tobias R. Vonnahme, Frank Wenzhöfer, and Antje Boetius
Biogeosciences, 17, 3203–3222,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.
Jun Zhao, Yuanfeng Cai, and Zhongjun Jia
Biogeosciences, 17, 1451–1462,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.
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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.
Thierry Jauffrais, Bruno Jesus, Edouard Metzger, Jean-Luc Mouget, Frans Jorissen, and Emmanuelle Geslin
Biogeosciences, 13, 2715–2726,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,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,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,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,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,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,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,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,
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,
A. C. Gerecht, L. Šupraha, B. Edvardsen, I. Probert, and J. Henderiks
Biogeosciences, 11, 3531–3545,
Ahonen, L., Kietäväinen, R., Kortelainen, N., Kukkonen, I. T., Pullinen, A., Toppi, T., Bomberg, M., Itävaara, M., Nousiainen, A., Nyyssönen, M., and Öster, M.: Hydrogeological characteristics of the Outokumpu Deep Drill Hole, edited by: Kukkonen, I. T., Geological Survey of Finland, Special Paper, 51, 151–168, 2011.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J.: Basic local alignment search tool, J. Mol. Biol., 215, 403–410, 1990.
Amend, J. P. and Teske, A.: Expanding frontiers in deep subsurface microbiology, Palaeogeogr. Palaeocl., 219, 131–155, 2005.
Baker, B. J., Moser, D. P., MacGregor, B. J., Fishbain, S., Wagner, M., Fry, N. K., Jackson, B., Speolstra, N., Loos, S., and Takai, K.: Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State, Environ. Microbiol., 5, 267–277, 2003.
Baker, B. J., Saw, J. H., Lind, A. E., Lazar C. S., Hinrichs, K.-U., Teske, A. P., and Ettema, T. J. G.: Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea, Nat. Microbiol., 16002, https://doi.org/10.1038/nmicrobiol.2016.2, 2016.
Bano, N., Ruffin, S., Ransom, B., and Hollibaugh, J. T.: Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages, Appl. Environ. Microbiol., 70, 781–789, 2004.
Barberan, A., Bates, S., T., Casamayor, E., O., and Fierer, N.: Using network analysis to explore co-occurrence patterns in soil microbial communities, ISME J., 6, 343–351, 2012.
Barns, S. M., Fundyga, R. E., Jeffries, M. W., and Pace, N. R.: Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment, P. Natl. Acad. Sci. USA, 91, 1609–1613, 1994.
Bastian, M., Heymann, S., and Jacomy, M.: Gephi: an open source software for exploring and manipulating networks, ICWSM, 8, 361–362, 2009.
Biddle, J. F., Lipp, J. S., Lever, M. A, Lloyd, K. G., Sørensen, K. B., Anderson, R., Fredricks, H. F., Elvert, M., Kelly, T. J., Schrag, D. P., Sogin, M. L., Brenchley, J. E., Teske, A., House, C. H., and Hinrichs, K.-U.: Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru, P. Natl. Acad. Sci. USA, 10, 3846–3851, 2006.
Biddle, J. F., Fitz-Gibbon, S., Schuster, S. C., Brenchley, J. E., and House, C. H.: Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment, P. Natl. Acad. Sci. USA, 105, 10583–10588, 2008.
Biddle, J. F., White, J. R., Teske, A. P., and House, C. H.: Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes, ISME J., 5, 1038–1047, 2011.
Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., and Taylor, J.: Galaxy: a web-based genome analysis tool for experimentalists, Curr. Protoc. Mol. Biol., 19, 19.10.1–19.10.21, https://doi.org/10.1002/0471142727.mb1910s89, 2010.
Blondel, V. D., Guillaume, J.-L., Lambiotte, R., and Lefebvre, E.: Fast unfolding of communities in large networks, Journal of Statistical Mechanics: Theory and Experiment, 2008.
Bomberg, M., Nyyssönen, M., Nousiainen, A., Hultman, J., Paulin, L., Auvinen, P., and Itävaara, M.: Evaluation of Molecular Techniques in Characterization of Deep Terrestrial Biosphere, Open Journal of Ecology, 4, 468–487, 2014.
Bomberg, M., Nyyssönen, M., Pitkänen, P., Lehtinen, A., and Itävaara, M.: Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland, BioMed Research International, 2015a.
Bomberg, M., Lamminmäki, T., and Itävaara, M.: Estimation of microbial metabolism and co-occurrence patterns in fracture groundwaters of deep crystalline bedrock at Olkiluoto, Finland, Biogeosciences Discuss., 12, 13819–13857, https://doi.org/10.5194/bgd-12-13819-2015, 2015b.
Brandes, U.: A Faster Algorithm for Betweenness Centrality, J. Math. Sociol., 25, 163–177, 2001.
Brazelton, W. J., Nelson, B., and Schrenk, M. O.: Metagenomic evidence for H2 oxidation and H2 production by serpentinite-hosted subsurface microbial communities, Front. Microbiol., 2, 268, https://doi.org/10.3389/fmicb.2011.00268, 2012.
Brazelton, W. J., Morrill, P. L., Szponar, N., and Schrenk, M. O.: Bacterial communities associated with subsurface geochemical processes in continental serpentinite springs, Appl. Environ. Microbiol., 79, 3906–3916, https://doi.org/10.1128/AEM.00330-13, 2013.
Brown, M. V., Philip, G. K., Bunge, J. A., Smith, M. C., Bissett, A., Lauro, F. M., Fuhrman, J. A., and Donachie, S. P.: Microbial community structure in the North Pacific ocean, ISME J. 3, 1374–1386, https://doi.org/10.1038/ismej.2009.86, 2009.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Pena, A. G., Goodrich, J. K., and Gordon, J. I.: QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335–336, 2010.
Chivian, D., Brodie, E. L., Alm, E. J., Culley, D. E., Dehal, P. S., DeSantis, T. Z., Gihring, T. M., Lapidus, A., Lin, L. H., Lowry, S. R., Moser, D. P., Richardson, P. M., Southam, G., Wanger, G., Pratt, L. M., Andersen, G. L., Hazen, T. C., Brockman, F. J., Arkin, A. P., and Onstott, T. C.: Environmental genomics reveals a single-species ecosystem deep within Earth, Science, 322, 275–278, https://doi.org/10.1126/science.1155495, 2008.
Dworkin, E., Falkow, S., Rosenberg, E., Schleifer, K.-H., Stackebrandt, E. (Eds.): The Prokaryotes, A Handbook on the Biology of Bacteria, Springer, New York, NY, USA, 2006.
Edwars, U., Rogall, T., Blocker, H., Emde, M., and Bottger, E. C.: Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA, Nucleic Acids Res., 17, 7843–7853, 1989.
Etiope, G. and Sherwood Lollar, B.: Abiotic methane on Earth, Rev. Geophys., 51, 276–299, 2013.
Fish, J. A., Chai, B., Wang, Q., Sun, Y., Brown, C. T., Tiedje, J. M., and Cole, J. R.: FunGene: the Functional Gene Pipeline and Repository, Front. Microbiol., 4, 291, https://doi.org/10.3389/fmicb.2013.00291, 2013.
Geets, J., Borremans, B., Diels, L., Springael, D., Vangronsveld, J., van der Lelie, D., and Vanbroekhoven, K.: DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria, J. Microbiol. Methods, 66, 194–205, 2006.
Giardine, B., Riemer, C., Hardison, R. C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W. J., and Nekrutenko, A.: Galaxy: a platform for interactive large-scale genome analysis, Genome Res., 15, 1451–1455, 2005.
Gihring, T., Moser, D., Lin, L. H., Davidson, M., Onstott, T., Morgan, L., Milleson, M., Kieft, T., Trimarco, E., and Balkwill, D.: The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa, Geomicrobiol. J., 23, 415–430, 2006.
Goecks, J., Nekrutenko, A., Taylor, J., and The Galaxy Team: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol., 11, R86, https://doi.org/10.1186/gb-2010-11-8-r86, 2010.
Gold, T.: The deep, hot biosphere, P. Natl. Acad. Sci. USA, 89, 6045–6049, 1992.
Grosskopf, R., Janssen, P. H., and Liesack, W.: Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval, Appl. Environ. Microbiol., 64, 960–969, 1998.
Hales, B. A., Edwards, C., Ritchie, D. A., Hall, G., Pickup, R. W., and Saunders, J. R.: Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis, Appl. Environ. Microbiol., 62, 668–675, 1996.
Hallbeck, L. and Pedersen, K.: Characterization of microbial processes in deep aquifers of the Fennoscandian Shield, Appl. Geochem., 23, 1796–1819, 2008.
Hallbeck, L. and Pedersen, K.: Culture-dependent comparison of microbial diversity in deep granitic groundwater from two sites considered for a Swedish final repository of spent nuclear fuel, FEMS Microbiol. Ecol., 81, 66–77, 2012.
Hammer, Ø., Harper, D., and Ryan, P.: Past: Paleontological Statistics Software Package for education and data analysis, Paleontología Electrónica, 4, 1–9, 2001.
Itävaara, M., Nyyssönen, M., Kapanen, A., Nousiainen, A., Ahonen, L., and Kukkonen, I.: Characterization of bacterial diversity to a depth of 1500 m in the Outokumpu deep borehole, Fennoscandian Shield, FEMS Microbiol. Ecol., 77, 295–309, 2011.
Kietäväinen, R. and Purkamo, L.: The origin, source and cycling of methane in deep crystalline rock biosphere, Front. Microbiol., 6, 725, https://doi.org/10.3389/fmicb.2015.00725, 2015.
Kietäväinen, R., Ahonen, L., Kukkonen, I. T., Hendriksson, N., Nyyssönen, M., and Itävaara, M.: Characterisation and isotopic evolution of saline waters of the Outokumpu Deep Drill Hole, Finland–Implications for water origin and deep terrestrial biosphere, Appl. Geochem., 32, 37–51, 2013.
Kukkonen, I. T., Rath, V., Kivekäs, L., Šafanda, J., and Čermák, V.: Geothermal studies of the Outokumpu deep drill hole, Outokumpu Deep Drilling Project 2003–2010, edited by: Kukkonen, I. T., Geological Survey of Finland, Special Paper, 51, 181–198, 2011.
Lambiotte, R., Delvenne, J.-C., and Barahona, M.: Laplacian Dynamics and Multiscale Modular Structure, Networks, 2009.
Langille, M. G., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Thurber, R. L. V., and Knight, R.: Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol., 31, 814–821, 2013.
Lau, M. C., Cameron, C., Magnabosco, C., Brown, C. T., Schilkey, F., Grim, S., Hendrickson, S., Pullin, M., Lollar, B. S., and van Heerden, E.: Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships, Front. Microbiol., 5, 531, https://doi.org/10.3389/fmicb.2014.00531, 2014.
Lin, L., Hall, J., Lippmann-Pipke, J., Ward, J. A., Sherwood Lollar, B., DeFlaun, M., Rothmel, R., Moser, D., Gihring, T. M., and Mislowack, B.: Radiolytic H2 in continental crust: nuclear power for deep subsurface microbial communities, Geochem. Geophys. Geosyst., 6, Q07003, https://doi.org/10.1029/2004GC000907, 2005.
Lin, L., Hall, J., Onstott, T., Gihring, T., Lollar, B. S., Boice, E., Pratt, L., Lippmann-Pipke, J., and Bellamy, R. E.: Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa, Geomicrobiol. J., 23, 475–497, 2006.
Lupatini, M., Suleiman, A. K., Jacques, R. J., Antoniolli, Z. I., de Siqueira Ferreira, A., Kuramae, E. E., and Roesch, L. F.: Network topology reveals high connectance levels and few key microbial genera within soils, Front. Environ. Sci., 2, 10, https://doi.org/10.3389/fenvs.2014.00010, 2014.
Magnabosco, C., Ryan, K., Lau, M. C., Kuloyo, O., Sherwood Lollar, B., Kieft, T. L., van Heerden, E., and Onstott, T.: A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust, ISME J., 10, 730–741, 2016.
McCollom, T. M.: Laboratory simulations of abiotic hydrocarbon formation in Earth's deep subsurface, Rev. Mineral. Geochem., 75, 467–494, https://doi.org/10.2138/rmg.2013.75.15, 2013.
McCollom, T. M., Lollar, B. S., Lacrampe-Couloume, G., and Seewald, J. S.: The influence of carbon source on abiotic organic synthesis and carbon isotope fractionation under hydrothermal conditions, Geochim. Cosmochim. Ac., 74, 2717–2740, 2010.
McMahon, S. and Parnell, J.: Weighing the deep continental biosphere, FEMS Microbiol. Ecol., 87, 113–120, https://doi.org/10.1111/1574-6941.12196, 2014.
Moser, D., Onstott, T., Fredrickson, J., Brockman, F., Balkwill, D., Drake, G., Pfiffner, S., White, D., Takai, K., and Pratt, L.: Temporal shifts in microbial community structure and geochemistry of an ultradeep South African gold mine borehole, Geomicrobiol. J., 20, 517–548, 2003.
Moser, D. P., Gihring, T. M., Brockman, F. J., Fredrickson, J. K., Balkwill, D. L., Dollhopf, M. E., Lollar, B. S., Pratt, L. M., Boice, E., Southam, G., Wanger, G., Baker, B. J., Pfiffner, S. M., Lin, L. H., and Onstott, T. C.: Desulfotomaculum and Methanobacterium spp. dominate a 4- to 5-kilometer-deep fault, Appl. Environ. Microbiol., 71, 8773–8783, 2005.
Mu, A., Boreham, C., Leong, H. X., Haese, R. R., and Moreau, J. W.: Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment, Front. Microbiol., 5, 209, https://doi.org/10.3389/fmicb.2014.00209, 2014.
Muyzer, G., de Waal, E. C., and Uitterlinden, A. G.: Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Appl. Environ. Microbiol., 59, 695–700, 1993.
Nealson, K., H., Inagaki, F., and Takai, K.: Hydrogen-driven subsurface lithoautotrophic microbial ecosystems (SLiMEs): do they exist and why should we care?, Trends Microbiol., 13, 405–410, https://doi.org/10.1016/j.tim.2005.07.010, 2005.
Nyyssönen, M., Bomberg, M., Kapanen, A., Nousiainen, A., Pitkänen, P., and Itävaara, M.: Methanogenic and sulphate-reducing microbial communities in deep groundwater of crystalline rock fractures in Olkiluoto, Finland, Geomicrobiol. J., 29, 863–878, 2012.
Nyyssönen, M., Hultman, J., Ahonen, L., Kukkonen, I., Paulin, L., Laine, P., Itävaara, M., and Auvinen, P.: Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield, ISME J., 8, 126–138, https://doi.org/10.1038/ismej.2013.125, 2014.
Osburn, M. R., LaRowe, D. E., Momper, L. M., and Amend, J. P.: Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA, Front. Microbiol., 5, 610, https://doi.org/10.3389/fmicb.2014.00610, 2014.
Paine, R. T.: A Conversation on Refining the Concept of Keystone Species, Conserv. Biol., 9, 962–964, 1995.
Pedersen, K.: Microbial life in deep granitic rock, FEMS Microbiol. Rev., 20, 399–414, 1997.
Pedersen, K.: Exploration of deep intraterrestrial microbial life: current perspectives, FEMS Microbiol. Lett., 185, 9–16, 2000.
Pedersen, K.: Investigations of subterranean bacteria in deep crystalline bedrock and their importance for the disposal of nuclear waste, Can. J. Microbiol., 42, 382–391, 1996.
Pedersen, K., Arlinger, J., Eriksson, S., Hallbeck, A., Hallbeck, L., and Johansson, J.: Numbers, biomass and cultivable diversity of microbial populations relate to depth and borehole-specific conditions in groundwater from depths of 4–450 m in Olkiluoto, Finland, ISME J., 2, 760–775, 2008.
Power, M. E., Tilman D., Estes, J. A., Menge, B. A., Bond, W. J., Mills, L. S., Gretchen, D., Castilla, J. C., Lubchenco, J., and Paine, R. T.: Challenges in the quest for keystones, BioScience, 4, 609–620, 1996.
Proskurowski, G., Lilley, M. D., Seewald, J. S., Fruh-Green, G. L., Olson, E. J., Lupton, J. E., Sylva, S. P., and Kelley, D. S.: Abiogenic hydrocarbon production at lost city hydrothermal field, Science, 319, 604–607, https://doi.org/10.1126/science.1151194, 2008.
Purkamo, L., Bomberg, M., Nyyssönen, M., Kukkonen, I., Ahonen, L., Kietäväinen, R., and Itävaara, M.: Dissecting the deep biosphere: retrieving authentic microbial communities from packer-isolated deep crystalline bedrock fracture zones, FEMS Microbiol. Ecol., 85, 324–337, 2013.
Purkamo, L., Bomberg, M., Nyyssönen, M., Kukkonen, I., Ahonen, L., and Itävaara, M.: Heterotrophic Communities Supplied by Ancient Organic Carbon Predominate in Deep Fennoscandian Bedrock Fluids, Microb. Ecol., 69, 319–332, https://doi.org/10.1007/s00248-014-0490-6, 2015.
Quince, C., Lanzén, A., Curtis, T. P., Davenport, R. J., Hall, N., Head, I. M., Read, L. F., and Sloan, W. T.: Accurate determination of microbial diversity from 454 pyrosequencing data, Nat. Methods, 6, 639–641, 2009.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., and Robinson, C. J.: Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 75, 7537–7541, 2009.
Schrenk, M. O., Brazelton, W. J., and Lang, S. Q.: Serpentinization, carbon, and deep life, Rev. Mineral. Geochem., 75, 575–606, https://doi.org/10.2138/rmg.2013.75.18, 2013.
Silver, B., Onstott, T., Rose, G., Lin, L. H., Ralston, C., Sherwood-Lollar, B., Pfiffner, S., Kieft, T., and McCuddy, S.: In situ cultivation of subsurface microorganisms in a deep mafic sill: implications for SLiMEs, Geomicrobiol. J., 27, 329–348, 2010.
Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D., Huse, S. M., Neal, P. R., Arrieta, J. M., and Herndl, G. J.: Microbial diversity in the deep sea and the underexplored “rare biosphere”, P. Natl. Acad. Sci. USA, 103, 12115–12120, 2006.
Sorokin, D. Y., Tourova, T. P., Mußmann, M., and Muyzer, G.: Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes, Extremophiles, 12, 431–439, 2008.
Stahl, D.: Development and application of nucleic acid probes, Nucleic acid techniques in bacterial systematics, 1991.
Steele, J. A., Countway, P. D., Xia, L., Vigil, P. D., Beman, J. M., Kim, D. Y., Chow, C. E., Sachdeva, R., Jones, A. C., Schwalbach M. S., Rose, J. M., Hewson, I., Patel, A., Sun, F., Caron, D. A., and Fuhrman, J. A.: Marine bacterial, archaeal and protistan association networks reveal ecological linkages, ISME J., 9, 1414–1425, 2011.
Szponar, N., Brazelton, W. J., Schrenk, M. O., Bower, D. M., Steele, A., and Morrill, P. L.: Geochemistry of a continental site of serpentinization, the Tablelands Ophiolite, Gros Morne National Park: a Mars analogue, Icarus, 224, 286–296, 2013.
Teske, A. and Sørensen, K. B.: Uncultured archaea in deep marine subsurface sediments: have we caught them all?, ISME J., 2, 3–18, 2008.
Tiago, I. and Veríssimo, A.: Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization, Environ. Microbiol., 15, 1687–1706, 2013.
Wang, Y. and Qian, P.-Y.: Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies, PLoS ONE, 4, e7401, https://doi.org/10.1371/journal.pone.0007401 , 2009.
Wagner, M., Roger, A. J., Flax, J. L., Brusseau, G. A., and Stahl, D. A.: Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration, J. Bacteriol., 180, 2975–2982, 1998.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J.: Prokaryotes: The unseen majority, P. Natl. Acad. Sci. USA, 95, 657–6583,1998.
Willems, A., De Ley, J., Gillis, M., and Kersters, K.: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov. comb. nov. for Alcaligenes paradoxus (Davis 1969), Int. J. Syst. Bact, 445–450, 1991.
Zhou, J., Deng, Y., Luo, F., He, Z., and Yang, Y.: Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2, MBio, 2, https://doi.org/10.1128/mBio.00122-11, 2011.
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.
The microbial communities of up to 2.3 km depth of Precambrian crystalline bedrock fractures...