Articles | Volume 18, issue 11
https://doi.org/10.5194/bg-18-3331-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-18-3331-2021
© Author(s) 2021. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| Highlight paper
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04 Jun 2021
Research article | Highlight paper |
| 04 Jun 2021
| 04 Jun 2021
Microbial and geo-archaeological records reveal the growth rate, origin and composition of desert rock surface communities
Nimrod Wieler
Zuckerberg Institute for Water Research, Jacob Blaustein Institutes
for Desert Research, Ben-Gurion University of the Negev, Sede Boqer
Campus 8499000, Israel
Tali Erickson Gini
Southern Region, Israel Antiquities Authority, Omer 84965,
Israel
Osnat Gillor
CORRESPONDING AUTHOR
Zuckerberg Institute for Water Research, Jacob Blaustein Institutes
for Desert Research, Ben-Gurion University of the Negev, Sede Boqer
Campus 8499000, Israel
Soil and Water Research Infrastructure and Institute of Soil
Biology, Biology Centre CAS, České Budějovice, Czechia
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Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145, https://doi.org/10.5194/bg-16-1133-2019, https://doi.org/10.5194/bg-16-1133-2019, 2019
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In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Talia Gabay, Eva Petrova, Osnat Gillor, Yaron Ziv, and Roey Angel
SOIL, 9, 231–242, https://doi.org/10.5194/soil-9-231-2023, https://doi.org/10.5194/soil-9-231-2023, 2023
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This paper evaluates bacterial growth in biocrusts after a large-scale mining disturbance in a hyperarid desert, using a stable isotope probing assay.
We discovered that biocrust bacteria from both natural and post-mining plots resumed photosynthetic activity but did not grow following hydration. Our paper provides insights into the effects of a large-scale disturbance (mining) on biocrusts and their response to hydration, with implications for biocrust restoration practices in Zin mines.
Anne Daebeler, Eva Petrová, Elena Kinz, Susanne Grausenburger, Helene Berthold, Taru Sandén, Roey Angel, and the high-school students of biology project groups I, II, and
III from 2018–2019
SOIL, 8, 163–176, https://doi.org/10.5194/soil-8-163-2022, https://doi.org/10.5194/soil-8-163-2022, 2022
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In this citizen science project, we combined a standardised litter bag method (Tea Bag Index) with microbiome analysis of bacteria and fungi colonising the teabags to gain a holistic understanding of the carbon degradation dynamics in temperate European soils. Our method focuses only on the active part of the soil microbiome. The results show that about one-third of the prokaryotes and one-fifth of the fungal species (ASVs) in the soil were enriched in response to the presence of fresh OM.
Capucine Baubin, Arielle M. Farrell, Adam Št'ovíček, Lusine Ghazaryan, Itamar Giladi, and Osnat Gillor
SOIL, 7, 611–637, https://doi.org/10.5194/soil-7-611-2021, https://doi.org/10.5194/soil-7-611-2021, 2021
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In this paper, we describe changes in desert soil bacterial diversity and function when two ecosystem engineers, shrubs and ant nests, in an arid environment are present. The results show that bacterial activity increases when there are ecosystem engineers and that their impact is non-additive. This is one of a handful of studies that investigated the separate and combined effects of ecosystem engineers on soil bacterial communities investigating both composition and function.
Capucine Baubin, Noya Ran, Hagar Siebner, and Osnat Gillor
SOIL Discuss., https://doi.org/10.5194/soil-2021-88, https://doi.org/10.5194/soil-2021-88, 2021
Revised manuscript not accepted
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In this manuscript, we describe changes in desert biocrust bacterial community during drought, rainfall, and dehydration in the Negev Desert. We followed the active bacterial community composition and their potential activity and showed that rainfall changes the bacterial community, triggers photosynthesis in soil phototrophs, and induces the production of extracellular polymeric substances that retain water during dehydration allowing bacterial cells to persist during the dehydration stage.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145, https://doi.org/10.5194/bg-16-1133-2019, https://doi.org/10.5194/bg-16-1133-2019, 2019
Short summary
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In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
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Nitrous oxide (N2O) synthesis by the freshwater cyanobacterium Microcystis aeruginosa
Interdisciplinary strategy to assess the impact of meteorological variables on the biochemical composition of the rain and the dynamics of a small eutrophic lake under rain forcing
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Eddy-enhanced primary production sustains heterotrophic microbial activities in the Eastern Tropical North Atlantic
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Caitlyn A. Hall, Andre van Turnhout, Edward Kavazanjian Jr., Leon A. van Paassen, and Bruce Rittmann
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Earthquake-induced soil liquefaction poses a significant global threat. Microbially induced desaturation and precipitation (MIDP) via denitrification is a potentially sustainable, non-disruptive bacteria-driven ground improvement technique under existing structures. We developed a next-generation biogeochemical model to understand and predict the behavior of MIDP in the natural environment to design field-based hazard mitigation treatments.
Ze Ren, Shudan Ye, Hongxuan Li, Xilei Huang, and Luyao Chen
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Permafrost thaw initiates thermokarst landscape formation, resulting in distinct new habitats, including degraded permafrost soil, thermokarst lake sediments, and lake water. These distinct habitats harbored differentiated bacterial communities that originated from the same source, differing in diversity, assembly mechanisms, and environmental influences. The results implied ecological consequences of permafrost degradation in the face of further climate change.
Juan Pablo Almeida, Lorenzo Menichetti, Alf Ekblad, Nicholas P. Rosenstock, and Håkan Wallander
Biogeosciences, 20, 1443–1458, https://doi.org/10.5194/bg-20-1443-2023, https://doi.org/10.5194/bg-20-1443-2023, 2023
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In forests, trees allocate a significant amount of carbon belowground to support mycorrhizal symbiosis. In northern forests nitrogen normally regulates this allocation and consequently mycorrhizal fungi growth. In this study we demonstrate that in a conifer forest from Sweden, fungal growth is regulated by phosphorus instead of nitrogen. This is probably due to an increase in nitrogen deposition to soils caused by decades of human pollution that has altered the ecosystem nutrient regime.
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Biogeosciences, 20, 1299–1312, https://doi.org/10.5194/bg-20-1299-2023, https://doi.org/10.5194/bg-20-1299-2023, 2023
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We found that increasing light intensity compensates for the negative effects of low phosphorus (P) availability on cellular protein and nitrogen contents. Reduced P availability, increasing light intensity, and ocean acidification act synergistically to increase cellular contents of carbohydrate and POC and the allocation of POC to carbohydrate. These regulation mechanisms in Emiliania huxleyi could provide vital information for evaluating carbon cycle in marine ecosystems under global change.
Beatriz Gill-Olivas, Jon Telling, Mark Skidmore, and Martyn Tranter
Biogeosciences, 20, 929–943, https://doi.org/10.5194/bg-20-929-2023, https://doi.org/10.5194/bg-20-929-2023, 2023
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Microbial ecosystems have been found in all subglacial environments sampled to date. Yet, little is known of the sources of energy and nutrients that sustain these microbial populations. This study shows that crushing of sedimentary rocks, which contain organic carbon, carbonate and sulfide minerals, along with previously weathered silicate minerals, produces a range of compounds and nutrients which can be utilised by the diverse suite of microbes that inhabit glacier beds.
Federico Fabisik, Benoit Guieysse, Jonathan Procter, and Maxence Plouviez
Biogeosciences, 20, 687–693, https://doi.org/10.5194/bg-20-687-2023, https://doi.org/10.5194/bg-20-687-2023, 2023
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We show, for the first time, that pure cultures of the cyanobacterium Microcystis aeruginosa can synthesize the potent greenhouse gas N2O using nitrite as substrate. Our findings have broad environmental implications because M. aeruginosa is globally found in freshwater ecosystems and is often the dominant species found in algae blooms. Further research is now needed to determine the occurrence and significance of N2O emissions from ecosystems rich with M. aeruginosa.
Fanny Noirmain, Jean-Luc Baray, Frédéric Tridon, Philippe Cacault, Hermine Billard, Guillaume Voyard, Joël Van Baelen, and Delphine Latour
Biogeosciences, 19, 5729–5749, https://doi.org/10.5194/bg-19-5729-2022, https://doi.org/10.5194/bg-19-5729-2022, 2022
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We present a study linking rain, meteorology, and mountain lake phytoplankton dynamics on the basis of a case study at Aydat (France) in September 2020. The air mass origin mainly influences the rain chemical composition, which depends on the type of rain, convective or stratiform. Our results also highlighted a non-negligible presence of photosynthetic cells in rainwater. The impact of the atmospheric forcing on the lake could play a key role in phytoplankton dynamics in the temperate zone.
Sarah A. Brown, John Paul Balmonte, Adrienne Hoarfrost, Sherif Ghobrial, and Carol Arnosti
Biogeosciences, 19, 5617–5631, https://doi.org/10.5194/bg-19-5617-2022, https://doi.org/10.5194/bg-19-5617-2022, 2022
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Bacteria use extracellular enzymes to cut large organic matter to sizes small enough for uptake. We compared the enzymatic response of surface, mid-water, and deep-ocean bacteria to complex natural substrates. Bacteria in surface and mid-depth waters produced a much wider range of enzymes than those in the deep ocean and may therefore consume a broader range of organic matter. The extent to which organic matter is recycled by bacteria depends in part on its residence time at different depths.
Aaron Ferderer, Zanna Chase, Fraser Kennedy, Kai G. Schulz, and Lennart T. Bach
Biogeosciences, 19, 5375–5399, https://doi.org/10.5194/bg-19-5375-2022, https://doi.org/10.5194/bg-19-5375-2022, 2022
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Ocean alkalinity enhancement has the capacity to remove vast quantities of carbon from the atmosphere, but its effect on marine ecosystems is largely unknown. We assessed the effect of increased alkalinity on a coastal phytoplankton community when seawater was equilibrated and not equilibrated with atmospheric CO2. We found that the phytoplankton community was moderately affected by increased alkalinity and equilibration with atmospheric CO2 had little influence on this effect.
Quentin Devresse, Kevin W. Becker, Arne Bendinger, Johannes Hahn, and Anja Engel
Biogeosciences, 19, 5199–5219, https://doi.org/10.5194/bg-19-5199-2022, https://doi.org/10.5194/bg-19-5199-2022, 2022
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Eddies are ubiquitous in the ocean and alter physical, chemical, and biological processes. However, how they affect organic carbon production and consumption is largely unknown. Here we show how an eddy triggers a cascade effect on biomass production and metabolic activities of phyto- and bacterioplankton. Our results may contribute to the improvement of biogeochemical models used to estimate carbon fluxes in the ocean.
Sania Arif, Heiko Nacke, Elias Schliekmann, Andreas Reimer, Gernot Arp, and Michael Hoppert
Biogeosciences, 19, 4883–4902, https://doi.org/10.5194/bg-19-4883-2022, https://doi.org/10.5194/bg-19-4883-2022, 2022
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The natural enrichment of Chloroflexi (Ktedonobacteria) at the Kilianstollen Marsberg copper mine rocks being exposed to the acidic sulfate-rich leachate led to an investigation of eight metagenomically assembled genomes (MAGs) involved in copper and other transition heavy metal resistance in addition to low pH resistance and aromatic compounds degradation. The present study offers functional insights about a novel cold-adapted Ktedonobacteria MAG extremophily along with other phyla MAGs.
Chunmei Zhang, Huirong Li, Yinxin Zeng, Haitao Ding, Bin Wang, Yangjie Li, Zhongqiang Ji, Yonghong Bi, and Wei Luo
Biogeosciences, 19, 4639–4654, https://doi.org/10.5194/bg-19-4639-2022, https://doi.org/10.5194/bg-19-4639-2022, 2022
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The unique microbial eukaryotic community structure and lower diversity have been demonstrated in five freshwater lakes of the Fildes Peninsula, Antarctica. Stochastic processes and biotic co-occurrence patterns were shown to be important in shaping microbial eukaryotic communities in the area. Our study provides a better understanding of the dynamic patterns and ecological assembly processes of microbial eukaryotic communities in Antarctic oligotrophic lakes (Fildes Peninsula).
Juan Pablo Almeida, Nicholas P. Rosenstock, Susanne K. Woche, Georg Guggenberger, and Håkan Wallander
Biogeosciences, 19, 3713–3726, https://doi.org/10.5194/bg-19-3713-2022, https://doi.org/10.5194/bg-19-3713-2022, 2022
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Fungi living in symbiosis with tree roots can accumulate belowground, forming special tissues than can repel water. We measured the water repellency of organic material incubated belowground and correlated it with fungal growth. We found a positive association between water repellency and root symbiotic fungi. These results are important because an increase in soil water repellency can reduce the release of CO2 from soils into the atmosphere and mitigate the effects of greenhouse gasses.
Karen M. Brandenburg, Björn Rost, Dedmer B. Van de Waal, Mirja Hoins, and Appy Sluijs
Biogeosciences, 19, 3305–3315, https://doi.org/10.5194/bg-19-3305-2022, https://doi.org/10.5194/bg-19-3305-2022, 2022
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Reconstructions of past CO2 concentrations rely on proxy estimates, with one line of proxies relying on the CO2-dependence of stable carbon isotope fractionation in marine phytoplankton. Culturing experiments provide insights into which processes may impact this. We found, however, that the methods with which these culturing experiments are performed also influence 13C fractionation. Caution should therefore be taken when extrapolating results from these experiments to proxy applications.
Weilin Huang, Peter M. van Bodegom, Toni Viskari, Jari Liski, and Nadejda A. Soudzilovskaia
Biogeosciences, 19, 1469–1490, https://doi.org/10.5194/bg-19-1469-2022, https://doi.org/10.5194/bg-19-1469-2022, 2022
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This work focuses on one of the essential pathways of mycorrhizal impact on C cycles: the mediation of plant litter decomposition. We present a model based on litter chemical quality which precludes a conclusive examination of mycorrhizal impacts on soil C. It improves long-term decomposition predictions and advances our understanding of litter decomposition dynamics. It creates a benchmark in quantitatively examining the impacts of plant–microbe interactions on soil C dynamics.
Julie Dinasquet, Estelle Bigeard, Frédéric Gazeau, Farooq Azam, Cécile Guieu, Emilio Marañón, Céline Ridame, France Van Wambeke, Ingrid Obernosterer, and Anne-Claire Baudoux
Biogeosciences, 19, 1303–1319, https://doi.org/10.5194/bg-19-1303-2022, https://doi.org/10.5194/bg-19-1303-2022, 2022
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Saharan dust deposition of nutrients and trace metals is crucial to microbes in the Mediterranean Sea. Here, we tested the response of microbial and viral communities to simulated dust deposition under present and future conditions of temperature and pH. Overall, the effect of the deposition was dependent on the initial microbial assemblage, and future conditions will intensify microbial responses. We observed effects on trophic interactions, cascading all the way down to viral processes.
Ralf Conrad, Pengfei Liu, and Peter Claus
Biogeosciences, 18, 6533–6546, https://doi.org/10.5194/bg-18-6533-2021, https://doi.org/10.5194/bg-18-6533-2021, 2021
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Acetate is an important intermediate during the anaerobic degradation of organic matter. It is consumed by methanogenic and sulfidogenic microorganisms accompanied by stable carbon isotope fractionation. We determined isotope fractionation under different conditions in two paddy soils and two lake sediments and also determined the composition of the microbial communities. Despite a relatively wide range of experimental conditions, the range of fractionation factors was quite moderate.
Natalie R. Cohen, Abigail E. Noble, Dawn M. Moran, Matthew R. McIlvin, Tyler J. Goepfert, Nicholas J. Hawco, Christopher R. German, Tristan J. Horner, Carl H. Lamborg, John P. McCrow, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 18, 5397–5422, https://doi.org/10.5194/bg-18-5397-2021, https://doi.org/10.5194/bg-18-5397-2021, 2021
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A previous study documented an intense hydrothermal plume in the South Pacific Ocean; however, the iron release associated with this plume and the impact on microbiology were unclear. We describe metal concentrations associated with multiple hydrothermal plumes in this region and protein signatures of plume-influenced microbes. Our findings demonstrate that resources released from these systems can be transported away from their source and may alter the physiology of surrounding microbes.
Sabyasachi Bhattacharya, Tarunendu Mapder, Svetlana Fernandes, Chayan Roy, Jagannath Sarkar, Moidu Jameela Rameez, Subhrangshu Mandal, Abhijit Sar, Amit Kumar Chakraborty, Nibendu Mondal, Sumit Chatterjee, Bomba Dam, Aditya Peketi, Ranadhir Chakraborty, Aninda Mazumdar, and Wriddhiman Ghosh
Biogeosciences, 18, 5203–5222, https://doi.org/10.5194/bg-18-5203-2021, https://doi.org/10.5194/bg-18-5203-2021, 2021
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Physicochemical determinants of microbiome architecture across continental shelves–slopes are unknown, so we explored the geomicrobiology along 3 m sediment horizons of seasonal (shallow coastal) and perennial (deep sea) hypoxic zones of the Arabian Sea. Nature, concentration, and fate of the organic matter delivered to the sea floor were found to shape the microbiome across the western Indian margin, under direct–indirect influence of sedimentation rate and water column O2 level.
Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
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Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Cora Hörstmann, Eric J. Raes, Pier Luigi Buttigieg, Claire Lo Monaco, Uwe John, and Anya M. Waite
Biogeosciences, 18, 3733–3749, https://doi.org/10.5194/bg-18-3733-2021, https://doi.org/10.5194/bg-18-3733-2021, 2021
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Microbes are the main drivers of productivity and nutrient cycling in the ocean. We present a combined approach assessing C and N uptake and microbial community diversity across ecological provinces in the Southern Ocean and southern Indian Ocean. Provinces showed distinct genetic fingerprints, but microbial activity varied gradually across regions, correlating with nutrient concentrations. Our study advances the biogeographic understanding of microbial diversity across C and N uptake regimes.
Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, and Orit Sivan
Biogeosciences, 18, 2091–2106, https://doi.org/10.5194/bg-18-2091-2021, https://doi.org/10.5194/bg-18-2091-2021, 2021
Mindaugas Zilius, Irma Vybernaite-Lubiene, Diana Vaiciute, Donata Overlingė, Evelina Grinienė, Anastasija Zaiko, Stefano Bonaglia, Iris Liskow, Maren Voss, Agneta Andersson, Sonia Brugel, Tobia Politi, and Paul A. Bukaveckas
Biogeosciences, 18, 1857–1871, https://doi.org/10.5194/bg-18-1857-2021, https://doi.org/10.5194/bg-18-1857-2021, 2021
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In fresh and brackish waters, algal blooms are often dominated by cyanobacteria, which have the ability to utilize atmospheric nitrogen. Cyanobacteria are also unusual in that they float to the surface and are dispersed by wind-driven currents. Their patchy and dynamic distribution makes it difficult to track their abundance and quantify their effects on nutrient cycling. We used remote sensing to map the distribution of cyanobacteria in a large Baltic lagoon and quantify their contributions.
Saly Jaber, Muriel Joly, Maxence Brissy, Martin Leremboure, Amina Khaled, Barbara Ervens, and Anne-Marie Delort
Biogeosciences, 18, 1067–1080, https://doi.org/10.5194/bg-18-1067-2021, https://doi.org/10.5194/bg-18-1067-2021, 2021
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Our study is of interest to atmospheric scientists and environmental microbiologists, as we show that clouds can be considered a medium where bacteria efficiently degrade and transform amino acids, in competition with chemical processes. As current atmospheric multiphase models are restricted to chemical degradation of organic compounds, our conclusions motivate further model development.
Kahina Djaoudi, France Van Wambeke, Aude Barani, Nagib Bhairy, Servanne Chevaillier, Karine Desboeufs, Sandra Nunige, Mohamed Labiadh, Thierry Henry des Tureaux, Dominique Lefèvre, Amel Nouara, Christos Panagiotopoulos, Marc Tedetti, and Elvira Pulido-Villena
Biogeosciences, 17, 6271–6285, https://doi.org/10.5194/bg-17-6271-2020, https://doi.org/10.5194/bg-17-6271-2020, 2020
Romie Tignat-Perrier, Aurélien Dommergue, Alban Thollot, Olivier Magand, Timothy M. Vogel, and Catherine Larose
Biogeosciences, 17, 6081–6095, https://doi.org/10.5194/bg-17-6081-2020, https://doi.org/10.5194/bg-17-6081-2020, 2020
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The adverse atmospheric environmental conditions do not appear suited for microbial life. We conducted the first global comparative metagenomic analysis to find out if airborne microbial communities might be selected by their ability to resist these adverse conditions. The relatively higher concentration of fungi led to the observation of higher proportions of stress-related functions in air. Fungi might likely resist and survive atmospheric physical stress better than bacteria.
Yanhong Lu, Shunyan Cheung, Ling Chen, Shuh-Ji Kao, Xiaomin Xia, Jianping Gan, Minhan Dai, and Hongbin Liu
Biogeosciences, 17, 6017–6032, https://doi.org/10.5194/bg-17-6017-2020, https://doi.org/10.5194/bg-17-6017-2020, 2020
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Through a comprehensive investigation, we observed differential niche partitioning among diverse ammonia-oxidizing archaea (AOA) sublineages in a typical subtropical estuary. Distinct AOA communities observed at DNA and RNA levels suggested that a strong divergence in ammonia-oxidizing activity among different AOA groups occurs. Our result highlights the importance of identifying major ammonia oxidizers at RNA level in future studies.
Anna-Neva Visser, Scott D. Wankel, Pascal A. Niklaus, James M. Byrne, Andreas A. Kappler, and Moritz F. Lehmann
Biogeosciences, 17, 4355–4374, https://doi.org/10.5194/bg-17-4355-2020, https://doi.org/10.5194/bg-17-4355-2020, 2020
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This study focuses on the chemical reaction between Fe(II) and nitrite, which has been reported to produce high levels of the greenhouse gas N2O. We investigated the extent to which dead biomass and Fe(II) minerals might enhance this reaction. Here, nitrite reduction was highest when both additives were present but less pronounced if only Fe(II) minerals were added. Both reaction systems show distinct differences, rather low N2O levels, and indicated the abiotic production of N2.
Lisa Tanet, Séverine Martini, Laurie Casalot, and Christian Tamburini
Biogeosciences, 17, 3757–3778, https://doi.org/10.5194/bg-17-3757-2020, https://doi.org/10.5194/bg-17-3757-2020, 2020
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Bioluminescent bacteria, the most abundant light-emitting organisms in the ocean, can be free-living, be symbiotic or colonize organic particles. This review suggests that they act as a visual target and may indirectly influence the sequestration of biogenic carbon in oceans by increasing the attraction rate for consumers. We summarize the instrumentation available to quantify this impact in future studies and propose synthetic figures integrating these ecological and biogeochemical concepts.
Michael Lintner, Bianca Biedrawa, Julia Wukovits, Wolfgang Wanek, and Petra Heinz
Biogeosciences, 17, 3723–3732, https://doi.org/10.5194/bg-17-3723-2020, https://doi.org/10.5194/bg-17-3723-2020, 2020
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Foraminifera are unicellular marine organisms that play an important role in the marine element cycle. Changes of environmental parameters such as salinity or temperature have a significant impact on the faunal assemblages. Our experiments show that changing salinity in the German Wadden Sea immediately influences the foraminiferal community. It seems that A. tepida is better adapted to salinity fluctuations than H. germanica.
Kathrin Busch, Ulrike Hanz, Furu Mienis, Benjamin Mueller, Andre Franke, Emyr Martyn Roberts, Hans Tore Rapp, and Ute Hentschel
Biogeosciences, 17, 3471–3486, https://doi.org/10.5194/bg-17-3471-2020, https://doi.org/10.5194/bg-17-3471-2020, 2020
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Seamounts are globally abundant submarine structures that offer great potential to study the impacts and interactions of environmental gradients at a single geographic location. In an exemplary way, we describe potential mechanisms by which a seamount can affect the structure of pelagic and benthic (sponge-)associated microbial communities. We conclude that the geology, physical oceanography, biogeochemistry, and microbiology of seamounts are even more closely linked than currently appreciated.
Alexander Bratek, Justus E. E. van
Beusekom, Andreas Neumann, Tina Sanders, Jana Friedrich, Kay-Christian Emeis, and Kirstin Dähnke
Biogeosciences, 17, 2839–2851, https://doi.org/10.5194/bg-17-2839-2020, https://doi.org/10.5194/bg-17-2839-2020, 2020
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The following paper highlights the importance of benthic N-transformation rates in different sediment types in the southern North Sea as a source of fixed nitrogen for primary producers and also as a sink of fixed nitrogen. Sedimentary fluxes of dissolved inorganic nitrogen support ∼7 to 59 % of the average annual primary production. Semi-permeable and permeable sediments contribute ∼68 % of the total benthic N2 production rates, counteracting eutrophication in the southern North Sea.
Sabine Haalboom, David M. Price, Furu Mienis, Judith D. L. van Bleijswijk, Henko C. de Stigter, Harry J. Witte, Gert-Jan Reichart, and Gerard C. A. Duineveld
Biogeosciences, 17, 2499–2519, https://doi.org/10.5194/bg-17-2499-2020, https://doi.org/10.5194/bg-17-2499-2020, 2020
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Mineral mining in deep-sea hydrothermal settings will lead to the formation of plumes of fine-grained, chemically reactive, suspended matter. Understanding how natural hydrothermal plumes evolve as they disperse from their source, and how they affect their surrounding environment, may help in characterising the behaviour of the diluted part of mining plumes. The natural plume provided a heterogeneous, geochemically enriched habitat conducive to the development of a distinct microbial ecology.
Noelle A. Held, Eric A. Webb, Matthew M. McIlvin, David A. Hutchins, Natalie R. Cohen, Dawn M. Moran, Korinna Kunde, Maeve C. Lohan, Claire Mahaffey, E. Malcolm S. Woodward, and Mak A. Saito
Biogeosciences, 17, 2537–2551, https://doi.org/10.5194/bg-17-2537-2020, https://doi.org/10.5194/bg-17-2537-2020, 2020
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Trichodesmium is a globally important marine nitrogen fixer that stimulates primary production in the surface ocean. We surveyed metaproteomes of Trichodesmium populations across the North Atlantic and other oceans, and we found that they experience simultaneous phosphate and iron stress because of the biophysical limits of nutrient uptake. Importantly, nitrogenase was most abundant during co-stress, indicating the potential importance of this phenotype to global nitrogen and carbon cycling.
Helmke Hepach, Claire Hughes, Karen Hogg, Susannah Collings, and Rosie Chance
Biogeosciences, 17, 2453–2471, https://doi.org/10.5194/bg-17-2453-2020, https://doi.org/10.5194/bg-17-2453-2020, 2020
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Tropospheric iodine takes part in numerous atmospheric chemical cycles, including tropospheric ozone destruction and aerosol formation. Due to its significance for atmospheric processes, it is crucial to constrain its sources and sinks. This paper aims at investigating and understanding features of biogenic iodate-to-iodide reduction in microalgal monocultures. We find that phytoplankton senescence may play a crucial role in the release of iodide to the marine environment.
Roger D. Finlay, Shahid Mahmood, Nicholas Rosenstock, Emile B. Bolou-Bi, Stephan J. Köhler, Zaenab Fahad, Anna Rosling, Håkan Wallander, Salim Belyazid, Kevin Bishop, and Bin Lian
Biogeosciences, 17, 1507–1533, https://doi.org/10.5194/bg-17-1507-2020, https://doi.org/10.5194/bg-17-1507-2020, 2020
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Effects of biological activity on mineral weathering operate at scales ranging from short-term, microscopic interactions to global, evolutionary timescale processes. Microorganisms have had well-documented effects at large spatio-temporal scales, but to establish the quantitative significance of microscopic measurements for field-scale processes, higher-resolution studies of liquid chemistry at local weathering sites and improved upscaling to soil-scale dissolution rates are still required.
Christine Rooks, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann
Biogeosciences, 17, 1231–1245, https://doi.org/10.5194/bg-17-1231-2020, https://doi.org/10.5194/bg-17-1231-2020, 2020
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Sponge grounds are known as nutrient sources, providing nitrate and ammonium to the ocean. We found that they also can do the opposite: in six species from Arctic and North Atlantic sponge grounds, we measured high rates of denitrification, which remove these nutrients from the sea. Rates were highest when the sponge tissue got low in oxygen, which happens when sponges stop pumping because of stress. Sponge grounds may become nutrient sinks when exposed to stress.
Cheng Li, Clare E. Reimers, and Yvan Alleau
Biogeosciences, 17, 597–607, https://doi.org/10.5194/bg-17-597-2020, https://doi.org/10.5194/bg-17-597-2020, 2020
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Novel filamentous cable bacteria that grow in the top layer of intertidal mudflat sediment were attracted to electrodes poised at a positive electrical potential. Several diverse morphologies of Desulfobulbaceae filaments, cells, and colonies were observed on the electrode surface. These observations provide information to suggest conditions that will induce cable bacteria to perform electron donation to an electrode, informing future experiments that culture cable bacteria outside of sediment.
Marie Maßmig, Jan Lüdke, Gerd Krahmann, and Anja Engel
Biogeosciences, 17, 215–230, https://doi.org/10.5194/bg-17-215-2020, https://doi.org/10.5194/bg-17-215-2020, 2020
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Little is known about the rates of bacterial element cycling in oxygen minimum zones (OMZs). We measured bacterial production and rates of extracellular hydrolytic enzymes at various in situ oxygen concentrations in the OMZ off Peru. Our field data show unhampered bacterial activity at low oxygen concentrations. Meanwhile bacterial degradation of organic matter substantially contributed to the formation of the OMZ.
Anna T. Kunert, Mira L. Pöhlker, Kai Tang, Carola S. Krevert, Carsten Wieder, Kai R. Speth, Linda E. Hanson, Cindy E. Morris, David G. Schmale III, Ulrich Pöschl, and Janine Fröhlich-Nowoisky
Biogeosciences, 16, 4647–4659, https://doi.org/10.5194/bg-16-4647-2019, https://doi.org/10.5194/bg-16-4647-2019, 2019
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A screening of more than 100 strains from 65 different species revealed that the ice nucleation activity within the fungal genus Fusarium is more widespread than previously assumed. Filtration experiments suggest that the single cell-free Fusarium IN is smaller than 100 kDa (~ 6 nm) and that aggregates can be formed in solution. Exposure experiments, freeze–thaw cycles, and long-term storage tests demonstrate a high stability of Fusarium IN under atmospherically relevant conditions.
Qing Wang, Renbin Zhu, Yanling Zheng, Tao Bao, and Lijun Hou
Biogeosciences, 16, 4113–4128, https://doi.org/10.5194/bg-16-4113-2019, https://doi.org/10.5194/bg-16-4113-2019, 2019
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We investigated abundance, potential activity, and diversity of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) in five Antarctic tundra patches, including penguin colony, seal colony, and tundra marsh. We have found (1) sea animal colonization increased AOB population size.; (2) AOB contributed to ammonia oxidation rates more than AOA in sea animal colonies; (3) community structures of AOB and AOA were closely related to soil biogeochemical processes associated with animal activities.
Yalda Vasebi, Marco E. Mechan Llontop, Regina Hanlon, David G. Schmale III, Russell Schnell, and Boris A. Vinatzer
Biogeosciences, 16, 1675–1683, https://doi.org/10.5194/bg-16-1675-2019, https://doi.org/10.5194/bg-16-1675-2019, 2019
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Ice nucleation particles (INPs) help ice form at temperatures as high as −4 °C and contribute to the formation of precipitation. Leaf litter contains a high concentration of INPs, but the organisms that produce them are unknown. Here, we cultured two bacteria and one fungus from leaf litter that produce INPs similar to those found in leaf litter. This suggests that leaf litter may be an important habitat of these organisms and supports a role of these organisms as producers of atmospheric INPs.
Nimrod Wieler, Hanan Ginat, Osnat Gillor, and Roey Angel
Biogeosciences, 16, 1133–1145, https://doi.org/10.5194/bg-16-1133-2019, https://doi.org/10.5194/bg-16-1133-2019, 2019
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In stony deserts, when rocks are exposed to atmospheric conditions, they undergo weathering. The cavernous (honeycomb) weathering pattern is one of the most common, but it is still unclear exactly how it is formed. We show that microorganisms, which differ from the surrounding soil and dust, form biological crusts on exposed rock surfaces. These microbes secrete polymeric substances that mitigate weathering by reducing evaporation rates and, consequently, salt transport rates through the rock.
Yang Li, Zhaojun Wu, Xingchen Dong, Zifu Xu, Qixin Zhang, Haiyan Su, Zhongjun Jia, and Qingye Sun
Biogeosciences, 16, 573–583, https://doi.org/10.5194/bg-16-573-2019, https://doi.org/10.5194/bg-16-573-2019, 2019
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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.
Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin
Biogeosciences, 15, 7419–7433, https://doi.org/10.5194/bg-15-7419-2018, https://doi.org/10.5194/bg-15-7419-2018, 2018
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In this study, we provide first evidence of lipid biomarker patterns and phylogenetic identities of key microbes mediating anaerobic oxidation of methane (AOM) communities in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. Our lipid and 16S rRNA results indicate that archaea of the ANME-2c and ANME-3 clades are involved in AOM in the MVs investigated.
Joshua F. Dean, Jurgen R. van Hal, A. Johannes Dolman, Rien Aerts, and James T. Weedon
Biogeosciences, 15, 7141–7154, https://doi.org/10.5194/bg-15-7141-2018, https://doi.org/10.5194/bg-15-7141-2018, 2018
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Lakes, rivers, ponds and streams are significant contributors of the greenhouse gas carbon dioxide to the atmosphere. This is partly due to the decomposition of plant and soil organic matter transported through these aquatic systems by microbial communities. In determining how vulnerable this organic material is to decomposition during aquatic transport, we show that standardized treatments in experiments can affect the way microbial communities behave and potentially the experimental outcome.
Xi Wen, Viktoria Unger, Gerald Jurasinski, Franziska Koebsch, Fabian Horn, Gregor Rehder, Torsten Sachs, Dominik Zak, Gunnar Lischeid, Klaus-Holger Knorr, Michael E. Böttcher, Matthias Winkel, Paul L. E. Bodelier, and Susanne Liebner
Biogeosciences, 15, 6519–6536, https://doi.org/10.5194/bg-15-6519-2018, https://doi.org/10.5194/bg-15-6519-2018, 2018
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Rewetting drained peatlands may lead to prolonged emission of the greenhouse gas methane, but the underlying factors are not well described. In this study, we found two rewetted fens with known high methane fluxes had a high ratio of microbial methane producers to methane consumers and a low abundance of methane consumers compared to pristine wetlands. We therefore suggest abundances of methane-cycling microbes as potential indicators for prolonged high methane emissions in rewetted peatlands.
Kyle R. Frischkorn, Andreas Krupke, Cécile Guieu, Justine Louis, Mónica Rouco, Andrés E. Salazar Estrada, Benjamin A. S. Van Mooy, and Sonya T. Dyhrman
Biogeosciences, 15, 5761–5778, https://doi.org/10.5194/bg-15-5761-2018, https://doi.org/10.5194/bg-15-5761-2018, 2018
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Trichodesmium is a keystone genus of marine cyanobacteria that is estimated to supply nearly half of the ocean’s fixed nitrogen, fuelling primary productivity and the cycling of carbon and nitrogen in the ocean. In our study we characterize Trichodesmium ecology across the western tropical South Pacific using gene and genome sequencing and geochemistry. We detected genes for phosphorus reduction, providing a mechanism for the noted importance of this organism in the ocean's phosphorus cycle.
Audrey Lallement, Ludovic Besaury, Elise Tixier, Martine Sancelme, Pierre Amato, Virginie Vinatier, Isabelle Canet, Olga V. Polyakova, Viatcheslay B. Artaev, Albert T. Lebedev, Laurent Deguillaume, Gilles Mailhot, and Anne-Marie Delort
Biogeosciences, 15, 5733–5744, https://doi.org/10.5194/bg-15-5733-2018, https://doi.org/10.5194/bg-15-5733-2018, 2018
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The main objective of this work was to evaluate the potential degradation of phenol, a highly toxic pollutant, by cloud microorganisms. Phenol concentrations measured on five cloud samples collected at the PUY station in France were from 0.15 to 0.74 µg L−1. Metatranscriptomic analysis suggested that phenol could be biodegraded directly in clouds, likely by Gammaproteobacteria. A large screening showed that 93 % of 145 bacterial strains isolated from clouds were able to degrade phenol.
Sara J. Bender, Dawn M. Moran, Matthew R. McIlvin, Hong Zheng, John P. McCrow, Jonathan Badger, Giacomo R. DiTullio, Andrew E. Allen, and Mak A. Saito
Biogeosciences, 15, 4923–4942, https://doi.org/10.5194/bg-15-4923-2018, https://doi.org/10.5194/bg-15-4923-2018, 2018
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Phaeocystis antarctica is an important phytoplankter of the Antarctic coastal environment where it dominates the early season bloom after sea ice retreat. Iron nutrition was found to be an important factor that results in Phaeocystis colony formation and a large restructuring of the proteome, including changes associated with the flagellate to colonial transition and adaptive responses to iron scarcity. Analysis of Phaeocystis proteins from the Ross Sea revealed the presence of both cell types.
Cited articles
Alonso-Zarza, A. M. and Tanner, L. H. (Eds.): Paleoenvironmental record and applications of calcretes and palustrine carbonates (Vol. 416), Geological Society of America, 2006. a
Alonso-Zarza, A. M. and Wright, V. P.: Chapter 5 Calcretes, in:
Developments in Sedimentology, edited by: Alonso-Zarza, A. M. and Tanner,
L. H., vol. 61 of Carbonates in Continental Settings: Facies,
Environments, and Processes, 225–267, Elsevier, Amsterdam, the Netherlands, Oxford, UK,
https://doi.org/10.1016/S0070-4571(09)06105-6, 2010. a
Amit, R., Simhai, O., Ayalon, A., Enzel, Y., Matmon, A., Crouvi, O., Porat, N.,
and McDonald, E.: Transition from Arid to Hyper-Arid Environment in the
Southern Levant Deserts as Recorded by Early Pleistocene Cummulic
Aridisols, Quaternary Sci. Rev., 30, 312–323,
https://doi.org/10.1016/j.quascirev.2010.11.007, 2011. a
Angel, R.: Microbiome analysis code, Zenodo [code], https://doi.org/10.5281/zenodo.4747587, 2021a. a
Angel, R.: Rock metagenome (ID 381355) – BioProject – NCBI, available at: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA381355, last access: 2 June 2021b. a
Angel, R. and Conrad, R.: Elucidating the Microbial Resuscitation Cascade in
Biological Soil Crusts Following a Simulated Rain Event, Environ.
Microbiol., 15, 2799–2815, https://doi.org/10.1111/1462-2920.12140, 2013. a, b
Avni, G.: The Byzantine-Islamic Transition in Palestine: An
Archaeological Approach, Oxford University press, Oxford, UK, 2014. a
Brlek, M. and Glumac, B.: Stable Isotopic (δ13C and δ18O)
Signatures of Biogenic Calcretes Marking Discontinuity Surfaces: A Case Study
from Upper Cretaceous Carbonates of Central Dalmatia and Eastern
Istria, Croatia, Facies, 60, 773–788,
https://doi.org/10.1007/s10347-014-0403-7, 2014. a
Büdel, B. and Wessels, D. C. J.: Rock Inhabiting Blue-Green
Algae/Cyanobacteria from Hot Arid Regions, Algological Studies/Archiv für
Hydrobiologie, Supplement Volumes, 385–398, 1991. a
Cabello-Briones, C. and Viles, H. A.: Evaluating the Effects of Open
Shelters on Limestone Deterioration at Archaeological Sites in
Different Climatic Locations, Int. J. Archit.
Herit., 11, 816–828, https://doi.org/10.1080/15583058.2017.1300710, 2017. a
Chen, L., Reeve, J., Zhang, L., Huang, S., Wang, X., and Chen, J.: GMPR:
A Robust Normalization Method for Zero-Inflated Count Data with
Application to Microbiome Sequencing Data, PeerJ, 6, e4600,
https://doi.org/10.7717/peerj.4600, 2018. a
Clarke, L. J. and Jenkyns, H. C.: New Oxygen Isotope Evidence for Long-Term
Cretaceous Climatic Change in the Southern Hemisphere, Geology, 27,
699–702, https://doi.org/10.1130/0091-7613(1999)027<0699:NOIEFL>2.3.CO;2, 1999. a
Corenblit, D., Darrozes, J., Julien, F., Otto, T., Roussel, E., Steiger, J.,
and Viles, H.: The Search for a Signature of Life on Mars:
A Biogeomorphological Approach, Astrobiology, 19, 1279–1291,
https://doi.org/10.1089/ast.2018.1969, 2019. a
Crouvi, O., Amit, R., Enzel, Y., Porat, N., and Sandler, A.: Sand Dunes as a
Major Proximal Dust Source for Late Pleistocene Loess in the Negev
Desert, Israel, Quaternary Res., 70, 275–282,
https://doi.org/10.1016/j.yqres.2008.04.011, 2008. a
Dietrich, W. E. and Perron, J. T.: The Search for a Topographic Signature of
Life, Nature, 439, 411–418, https://doi.org/10.1038/nature04452, 2006. a
Dorn, R. I.: Desert Rock Coatings, in: Geomorphology of Desert
Environments, edited by: Parsons, A. J. and Abrahams, A. D., 153–186,
Springer Netherlands, Dordrecht, https://doi.org/10.1007/978-1-4020-5719-9_7, 2009. a
Edgar, R. C.: UPARSE: Highly Accurate OTU Sequences from Microbial
Amplicon Reads, Nat. Methods, 10, 996–998, https://doi.org/10.1038/nmeth.2604, 2013. a
Ferreira, J. A. and Zwinderman, A. H.: On the
Benjamini–Hochberg Method, Ann. Stat., 34,
1827–1849, https://doi.org/10.1214/009053606000000425, 2006. a
Friedmann, E. I. and Kibler, A. P.: Nitrogen Economy of Endolithic Microbial
Communities in Hot and Cold Deserts, Microb. Ecol., 6, 95–108,
https://doi.org/10.1007/BF02010548, 1980. a
Garcia-Pichel, F.: Plausible Mechanisms for the Boring on Carbonates by
Microbial Phototrophs, Sediment. Geol., 185, 205–213,
https://doi.org/10.1016/j.sedgeo.2005.12.013, 2006. a
Gorbushina, A. A.: Life on the Rocks, Environ. Microbiol., 9,
1613–1631, https://doi.org/10.1111/j.1462-2920.2007.01301.x, 2007. a, b, c
Holmes, A. J., Bowyer, J., Holley, M. P., O'Donoghue, M., Montgomery, M., and
Gillings, M. R.: Diverse, yet-to-Be-Cultured Members of the Rubrobacter
Subdivision of the Actinobacteria Are Widespread in Australian Arid
Soils, FEMS Microbiol. Ecol., 33, 111–120,
https://doi.org/10.1111/j.1574-6941.2000.tb00733.x, 2000. a, b
Horn, H. S.: Measurement of “Overlap” in Comparative Ecological Studies,
Am. Nat., 100, 419–424, https://doi.org/10.1086/282436, 1966. a
Idris, H., Goodfellow, M., Sanderson, R., Asenjo, J. A., and Bull, A. T.:
Actinobacterial Rare Biospheres and Dark Matter Revealed in
Habitats of the Chilean Atacama Desert, Sci. Rep.-UK, 7, 8373,
https://doi.org/10.1038/s41598-017-08937-4, 2017. a
Ji, M., Greening, C., Vanwonterghem, I., Carere, C. R., Bay, S. K., Steen,
J. A., Montgomery, K., Lines, T., Beardall, J., van Dorst, J., Snape, I.,
Stott, M. B., Hugenholtz, P., and Ferrari, B. C.: Atmospheric Trace Gases
Support Primary Production in Antarctic Desert Surface Soil, Nature, 552, 400–403,
https://doi.org/10.1038/nature25014, 2017. a
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., and
Glöckner, F. O.: Evaluation of General 16S Ribosomal RNA Gene
PCR Primers for Classical and Next-Generation Sequencing-Based Diversity
Studies, Nucleic Acids Res., 41, e1–e1, https://doi.org/10.1093/nar/gks808, 2013. a
Krumbein, W. E. and Jens, K.: Biogenic Rock Varnishes of the Negev Desert
(Israel) an Ecological Study of Iron and Manganese Transformation by
Cyanobacteria and Fungi, Oecologia, 50, 25–38, https://doi.org/10.1007/BF00378791,
1981. a
Kuske, C. R., Yeager, C. M., Johnson, S., Ticknor, L. O., and Belnap, J.:
Response and Resilience of Soil Biocrust Bacterial Communities to Chronic
Physical Disturbance in Arid Shrublands, ISME J., 6, 886–897,
https://doi.org/10.1038/ismej.2011.153, 2012. a
Lang-Yona, N., Maier, S., Macholdt, D. S., Müller-Germann, I., Yordanova,
P., Rodriguez-Caballero, E., Jochum, K. P., Al-Amri, A., Andreae, M. O.,
Fröhlich-Nowoisky, J., and Weber, B.: Insights into Microbial Involvement
in Desert Varnish Formation Retrieved from Metagenomic Analysis,
Env. Microbiol. Rep., 10, 264–271,
https://doi.org/10.1111/1758-2229.12634, 2018. a, b
Lange, O. L.: Twenty-Three Years of Growth Measurements on the
Crustose Lichen Caloplaca Aurantia in the Central Negev Desert,
Israel J. Bot., 39, 383–394, https://doi.org/10.1080/0021213X.1990.10677162,
1990. a
Langgut, D., Tepper, Y., Benzaquen, M., Erickson-Gini, T., and Bar-Oz, G.:
Environment and Horticulture in the Byzantine Negev Desert, Israel:
Sustainability, Prosperity and Enigmatic Decline, Quaternary Int.,
https://doi.org/10.1016/j.quaint.2020.08.056, online first, 2020. a
Lebre, P. H., De Maayer, P., and Cowan, D. A.: Xerotolerant Bacteria: Surviving
through a Dry Spell, Nat. Rev. Microbiol., 15, 285–296,
https://doi.org/10.1038/nrmicro.2017.16, 2017. a
Lenth, R., Buerkner, P., Herve, M., Love, J., Riebl, H., and Singmann, H.:
Emmeans: Estimated Marginal Means, Aka Least-Squares Means, available at: https://cran.r-project.org/web/packages/emmeans/index.html (last access: 2 June 2021), 2020. a
Liu, K.: Oxygen and Carbon Isotope Analysis of the Mooreville Chalk and
Late Santonian-Early Campanian Sea Level and Sea Surface Temperature
Changes, Northeastern Gulf of Mexico, U.S.A., Cretaceous
Res., 30, 980–990, https://doi.org/10.1016/j.cretres.2009.02.008, 2009. a
Liu, T. and Broecker, W. S.: How Fast Does Rock Varnish Grow?, Geology, 28,
183–186, https://doi.org/10.1130/0091-7613(2000)28<183:HFDRVG>2.0.CO;2, 2000. a
Mabbutt, J. A.: Desert Landforms, Australian National University Press, Canberra, Australia, 1977. a
Makhalanyane, T. P., Valverde, A., Gunnigle, E., Frossard, A., Ramond, J.-B.,
and Cowan, D. A.: Microbial Ecology of Hot Desert Edaphic Systems, FEMS
Microbiol. Rev., 39, 203–221, https://doi.org/10.1093/femsre/fuu011, 2015. a, b
Martin, B. D., Witten, D., and Willis, A. D.: Modeling Microbial Abundances and
Dysbiosis with Beta-Binomial Regression, arXiv [stat], arXiv:1902.02776, 7 February 2019. a
McArdle, B. H. and Anderson, M. J.: Fitting Multivariate Models to
Community Data: A Comment on Distance-Based Redundancy
Analysis, Ecology, 82, 290–297,
https://doi.org/10.1890/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2, 2001. a
Mcllroy de la Rosa, J. P., Warke, P. A., and Smith, B. J.: The Effects of
Lichen Cover upon the Rate of Solutional Weathering of Limestone,
Geomorphology, 220, 81–92, https://doi.org/10.1016/j.geomorph.2014.05.030, 2014. a, b
McMurdie, P. J. and Holmes, S.: Phyloseq: An R Package for Reproducible
Interactive Analysis and Graphics of Microbiome Census Data, PLOS
ONE, 8, e61217, https://doi.org/10.1371/journal.pone.0061217, 2013. a
Mummey, D., Holben, W., Six, J., and Stahl, P.: Spatial Stratification of
Soil Bacterial Populations in Aggregates of Diverse Soils,
Microb. Ecol., 51, 404–411, https://doi.org/10.1007/s00248-006-9020-5, 2006. a
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn,
D., Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P., Stevens, M.
H. H., Szoecs, E., and Wagner, H.: Vegan: Community Ecology Package, available at: https://cran.r-project.org/web/packages/vegan/index.html (last access: 2 June 2021),
2018. a
Owen, J. J., Amundson, R., Dietrich, W. E., Nishiizumi, K., Sutter, B., and
Chong, G.: The Sensitivity of Hillslope Bedrock Erosion to Precipitation,
Earth Surf. Proc. Land., 36, 117–135, https://doi.org/10.1002/esp.2083,
2011. a
Pepe-Ranney, C., Koechli, C., Potrafka, R., Andam, C., Eggleston, E.,
Garcia-Pichel, F., and Buckley, D. H.: Non-Cyanobacterial Diazotrophs
Mediate Dinitrogen Fixation in Biological Soil Crusts during Early Crust
Formation, ISME J., 10, 287–298, https://doi.org/10.1038/ismej.2015.106,
2016. a
Pointing, S. B. and Belnap, J.: Microbial Colonization and Controls in Dryland
Systems, Nat. Rev. Microbiol., 10, 551–562,
https://doi.org/10.1038/nrmicro2831, 2012. a, b, c, d
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P.,
Peplies, J., and Glockner, F. O.: The SILVA Ribosomal RNA Gene
Database Project: Improved Data Processing and Web-Based Tools, Nucleic Acids
Res., 41, D590–D596, https://doi.org/10.1093/nar/gks1219, 2013. a
Rainey, F. A., Ray, K., Ferreira, M., Gatz, B. Z., Nobre, M. F., Bagaley, D.,
Rash, B. A., Park, M.-J., Earl, A. M., Shank, N. C., Small, A. M., Henk,
M. C., Battista, J. R., Kämpfer, P., and da Costa, M. S.: Extensive
Diversity of Ionizing-Radiation-Resistant Bacteria Recovered
from Sonoran Desert Soil and Description of Nine New Species of
the Genus Deinococcus Obtained from a Single Soil Sample, Appl.
Environ. Microb., 71, 5225–5235, https://doi.org/10.1128/AEM.71.9.5225-5235.2005,
2005. a, b
R Core Team: R: A Language and Environment for Statistical Computing, R
Foundation for Statistical Computing, available at: https://www.R-project.org/ (last access: 2 June 2021), 2020. a
Sandler, A., Meunier, A., and Velde, B.: Mineralogical and Chemical Variability
of Mountain Red/Brown Mediterranean Soils, Geoderma, 239–240, 156–167,
https://doi.org/10.1016/j.geoderma.2014.10.008, 2015. a
Scherer, G. W.: Crystallization in Pores, Cement Concrete Res., 29,
1347–1358, https://doi.org/10.1016/S0008-8846(99)00002-2, 1999. a
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., Robinson,
C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J., and Weber,
C. F.: Introducing Mothur: Open Source, Platform-Independent,
Community-Supported Software for Describing and Comparing Microbial
Communities, Appl. Environ. Microb., 75, 7537–7541,
https://doi.org/10.1128/AEM.01541-09, 2009. a
Schütz, F., Norden, B., and Förster, A.: Thermal Properties of
Sediments in Southern Israel: A Comprehensive Data Set for Heat Flow and
Geothermal Energy Studies, Basin Res., 24, 357–376,
https://doi.org/10.1111/j.1365-2117.2011.00529.x, 2012. a
Searle, S. R., Speed, F. M., and Milliken, G. A.: Population Marginal Means
in the Linear Model: An Alternative to Least Squares Means,
Am. Stat., 34, 216–221, https://doi.org/10.1080/00031305.1980.10483031,
1980. a
Sneh, A., Avni, Y., Bartov, Y., Zilberman, E., Braun, M., Lasman, N., and
Weinberger, R.: The geological map of Israel, 1 : 50,000. Sheet 18-III: Shivta, available at:
https://www.gov.il/he/departments/general/shivta-map (last access: 2 June 2021), 2011. a
Tepper, Y., Erickson-Gini, T., Farhi, Y., and Bar-Oz, G.: Probing the
Byzantine/Early Islamic Transition in the Negev: The Renewed
Shivta Excavations, 2015–2016, Tel Aviv, 45, 120–152,
https://doi.org/10.1080/03344355.2018.1412058, 2018. a, b, c, d
Uemura, R., Nakamoto, M., Asami, R., Mishima, S., Gibo, M., Masaka, K.,
Jin-Ping, C., Wu, C.-C., Chang, Y.-W., and Shen, C.-C.: Precise Oxygen and
Hydrogen Isotope Determination in Nanoliter Quantities of Speleothem
Inclusion Water by Cavity Ring-down Spectroscopic Techniques, Geochim.
Cosmochim. Ac., 172, 159–176, https://doi.org/10.1016/j.gca.2015.09.017, 2016. a
Velasco Ayuso, S., Giraldo Silva, A., Nelson, C., Barger, N. N., and
Garcia-Pichel, F.: Microbial Nursery Production of High-Quality
Biological Soil Crust Biomass for Restoration of Degraded Dryland
Soils, Appl. Environ. Microb., 83, e02179-16,
https://doi.org/10.1128/AEM.02179-16, 2017.
a
Viles, H.: Biogeomorphology: Past, Present and Future, Geomorphology, 366,
106809, https://doi.org/10.1016/j.geomorph.2019.06.022, 2019. a
Viles, H. A.: Understanding Dryland Landscape Dynamics: Do Biological
Crusts Hold the Key?, Geography Compass, 2, 899–919,
https://doi.org/10.1111/j.1749-8198.2008.00099.x, 2008. a, b
Viles, H. A. and Gorbushina, A. A.: Soiling and Microbial Colonisation on Urban
Roadside Limestone: A Three Year Study in Oxford, England, Build. Environ., 38, 1217–1224, https://doi.org/10.1016/S0360-1323(03)00078-7, 2003. a, b
Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R.: Naive Bayesian
Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial
Taxonomy, Appl. Environ. Microb., 73, 5261–5267,
https://doi.org/10.1128/AEM.00062-07, 2007. a
Warscheid, T. and Braams, J.: Biodeterioration of Stone: A Review,
Int. Biodeter. Biodegr., 46, 343–368,
https://doi.org/10.1016/S0964-8305(00)00109-8, 2000. a
Weber, B., Büdel, B., and Belnap, J. (Eds.): Biological Soil Crusts:
An Organizing Principle in Drylands, Springer, New York, NY, 1st
Edn., 2016. a
Wickham, H.: Ggplot2: Elegant Graphics for Data Analysis,
Springer-Verlag, New York, USA, 2016. a
Wieler, N., Ginat, H., Gillor, O., and Angel, R.: The origin and role of biological rock crusts in rocky desert weathering, Biogeosciences, 16, 1133–1145, https://doi.org/10.5194/bg-16-1133-2019, 2019. a, b, c, d
Wierzchos, J., Davila, A. F., Artieda, O., Cámara-Gallego, B., de los
Ríos, A., Nealson, K. H., Valea, S., Teresa García-González,
M., and Ascaso, C.: Ignimbrite as a Substrate for Endolithic Life in the
Hyper-Arid Atacama Desert: Implications for the Search for Life on
Mars, Icarus, 224, 334–346, https://doi.org/10.1016/j.icarus.2012.06.009, 2013. a
Wobbrock, J. O., Findlater, L., Gergle, D., and Higgins, J. J.: The Aligned
Rank Transform for Nonparametric Factorial Analyses Using Only Anova
Procedures, in: Proceedings of the SIGCHI Conference on Human Factors
in Computing Systems, CHI '11, 143–146, Association for
Computing Machinery, New York, NY, USA, https://doi.org/10.1145/1978942.1978963,
2011. a
Zhang, Y., Duan, P., Zhang, P., and Li, M.: Variations in Cyanobacterial and
Algal Communities and Soil Characteristics under Biocrust Development under
Similar Environmental Conditions, Plant Soil, 429, 241–251,
https://doi.org/10.1007/s11104-017-3443-2, 2018. a
Short summary
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands. BRCs play a crucial role in arid environments because of the limited activity of plants and soil. Nevertheless, BRC development rates have never been dated. Here we integrated archaeological, microbiological and geological methods to provide a first estimation of the growth rate of BRCs under natural conditions. This can serve as an affordable dating tool in archaeological sites in arid regions.
Biological rock crusts (BRCs) are common microbial-based assemblages covering rocks in drylands....
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