Articles | Volume 17, issue 23
Research article 08 Dec 2020
Research article | 08 Dec 2020
Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences
Jeffrey M. Dick et al.
Related subject area
Biodiversity and Ecosystem Function: Microbial Ecology & GeomicrobiologyCryptic 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 composition of endolithic communities in gypcrete is determined by the specific microhabitat architectureDeep maxima of phytoplankton biomass, primary production and bacterial production in the Mediterranean Sea during late springThe contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth)The haplo-diplontic life cycle expands niche space of coccolithophoresThe 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 experimentMicrobial co-occurrence patterns in deep Precambrian bedrock fracture fluidsEffect 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)Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soilMicrobial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlandsResponse of benthic foraminifera to ocean acidification in their natural sediment environment: a long-term culturing experimentSummer and winter living coccolithophores in the Yellow Sea and the East China SeaConversion of upland to paddy field specifically alters the community structure of archaeal ammonia oxidizers in an acid soilHigh diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern ChinaDynamics of microbial communities during decomposition of litter from pioneering plants in initial soil ecosystemsInterconnectivity vs. isolation of prokaryotic communities in European deep-sea mud volcanoesMicrobial colonisation of chasmoendolithic habitats in the hyper-arid zone of the Atacama Desert
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,
María Cristina Casero, Victoria Meslier, Jocelyne DiRuggiero, Antonio Quesada, Carmen Ascaso, Tomasz Kowaluk, and Jacek Wierzchos
Revised manuscript accepted for BGShort 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, as those in the Atacama Desert. In this work, 3 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 in the microbial communities inhabiting each of them.
Emilio Marañón, France Van Wambeke, Julia Uitz, Emmanuel S. Boss, María Pérez-Lorenzo, Julie Dinasquet, Nils Haëntjens, Céline Dimier, and Vincent Taillandier
Revised manuscript accepted for BGShort 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.
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.
Joost de Vries, Fanny Monteiro, Glen Wheeler, Alex Poulton, Jelena Godrijan, Federica Cerino, Elisa Malinverno, Gerald Langer, and Colin Brownlee
Revised manuscript accepted for BGShort 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.
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.
Lotta Purkamo, Malin Bomberg, Riikka Kietäväinen, Heikki Salavirta, Mari Nyyssönen, Maija Nuppunen-Puputti, Lasse Ahonen, Ilmo Kukkonen, and Merja Itävaara
Biogeosciences, 13, 3091–3108,Short summary
The microbial communities of up to 2.3 km depth of Precambrian crystalline bedrock fractures share features with serpenization-driven microbial communities in alkaline springs and subsurface aquifers. This study suggests that phylotypes belonging to Burkholderiales and Clostridia are possible "keystone microbial species" in Outokumpu deep biosphere. Many of the keystone species belong to the rare biosphere with low abundance but a wide range of carbon substrates and a capacity for H2 oxidation.
Thierry Jauffrais, Bruno Jesus, Edouard Metzger, Jean-Luc Mouget, Frans Jorissen, and Emmanuelle Geslin
Biogeosciences, 13, 2715–2726,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,
Y. Zheng, R. Huang, B. Z. Wang, P. L. E. Bodelier, and Z. J. Jia
Biogeosciences, 11, 3353–3368,
S. Mishra, W. A. Lee, A. Hooijer, S. Reuben, I. M. Sudiana, A. Idris, and S. Swarup
Biogeosciences, 11, 1727–1741,
K. Haynert, J. Schönfeld, R. Schiebel, B. Wilson, and J. Thomsen
Biogeosciences, 11, 1581–1597,
J. Sun, X. Y. Gu, Y. Y. Feng, S. F. Jin, W. S. Jiang, H. Y. Jin, and J. F. Chen
Biogeosciences, 11, 779–806,
M. S. Alam, G. D. Ren, L. Lu, Y. Zheng, X. H. Peng, and Z. J. Jia
Biogeosciences, 10, 5739–5753,
X. S. Tai, W. L. Mao, G. X. Liu, T. Chen, W. Zhang, X. K. Wu, H. Z. Long, B. G. Zhang, and Y. Zhang
Biogeosciences, 10, 5589–5600,
J. Esperschütz, C. Zimmermann, A. Dümig, G. Welzl, F. Buegger, M. Elmer, J. C. Munch, and M. Schloter
Biogeosciences, 10, 5115–5124,
M. G. Pachiadaki and K. A. Kormas
Biogeosciences, 10, 2821–2831,
J. DiRuggiero, J. Wierzchos, C. K. Robinson, T. Souterre, J. Ravel, O. Artieda, V. Souza-Egipsy, and C. Ascaso
Biogeosciences, 10, 2439–2450,
Bjellqvist, B., Hughes, G. J., Pasquali, C., Paquet, N., Ravier, F., Sanchez, J.-C., Frutiger, S., and Hochstrasser, D.: The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences, Electrophoresis, 14, 1023–1031, https://doi.org/10.1002/elps.11501401163, 1993. a, b
Bjellqvist, B., Basse, B., Olsen, E., and Celis, J. E.: Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions, Electrophoresis, 15, 529–539, https://doi.org/10.1002/elps.1150150171, 1994. a, b, c
Boyd, E. S., Hamilton, T. L., Swanson, K. D., Howells, A. E., Baxter, B. K., Meuser, J. E., Posewitz, M. C., and Peters, J. W.: [FeFe]-hydrogenase abundance and diversity along a vertical redox gradient in Great Salt Lake, USA, Int. J. Mol. Sci., 15, 21947–21966, https://doi.org/10.3390/ijms151221947, 2014. a, b, c
Chirife, J., Fontan, C. F., and Scorza, O. C.: The intracellular water activity of bacteria in relation to the water activity of the growth medium, J. Appl. Bacteriol., 50, 475–479, https://doi.org/10.1111/j.1365-2672.1981.tb04250.x, 1981. a
Dupont, C. L., Larsson, J., Yooseph, S., Ininbergs, K., Goll, J., Asplund-Samuelsson, J., McCrow, J. P., Celepli, N., Allen, L. Z., Ekman, M., Lucas, A. J., Hagström, Å., Thiagarajan, M., Brindefalk, B., Richter, A. R., Andersson, A. F., Tenney, A., Lundin, D., Tovchigrechko, A., Nylander, J. A. A., Brami, D., Badger, J. H., Allen, A. E., Rusch, D. B., Hoffman, J., Norrby, E., Friedman, R., Pinhassi, J., Venter, J. C., and Bergman, B.: Functional tradeoffs underpin salinity-driven divergence in microbial community composition, PLOS One, 9, e89549, https://doi.org/10.1371/journal.pone.0089549, 2014. a, b, c, d, e
Eiler, A., Zaremba-Niedzwiedzka, K., Martínez-García, M., McMahon, K. D., Stepanauskas, R., Andersson, S. G. E., and Bertilsson, S.: Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics, Environ. Microbiol., 16, 2682–2698, https://doi.org/10.1111/1462-2920.12301, 2014. a, b
Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Hatzimanikatis, V., and Palsson, B. Ø.: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information, Mol. Syst. Biol., 3, 121, https://doi.org/10.1038/msb4100155, 2007. a
Fernandez, A. B., Ghai, R., Martin-Cuadrado, A. B., Sanchez-Porro, C., Rodriguez-Valera, F., and Ventosa, A.: Metagenome sequencing of prokaryotic microbiota from two hypersaline ponds of a marine saltern in Santa Pola, Spain, Genome Announcements, 1, e00933-13, https://doi.org/10.1128/genomea.00933-13, 2013. a, b
Finn, S., Rogers, L., Händler, K., McClure, P., Amézquita, A., Hinton, J. C. D., and Fanning, S.: Exposure of Salmonella enterica serovar Typhimurium to three humectants used in the food industry induces different osmoadaptation systems, Appl. Environ. Microbiol., 81, 6800–6811, https://doi.org/10.1128/AEM.01379-15, 2015. a, b, c, d, e, f
Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M. R., Appel, R. D., and Bairoch, A.: Protein identification and analysis tools on the ExPASy server, in: The Proteomics Protocols Handbook, edited by: Walker, J. M., Humana Press, Totowa, NJ, 571–607, https://doi.org/10.1385/1-59259-890-0:571, 2005. a
Ghai, R., Pašić, L., Fernández, A. B., Martin-Cuadrado, A.-B., Mizuno, C. M., McMahon, K. D., Papke, R. T., Stepanauskas, R., Rodriguez-Brito, B., Rohwer, F., Sánchez-Porro, C., Ventosa, A., and Rodríguez-Valera, F.: New abundant microbial groups in aquatic hypersaline environments, Sci. Rep., 1, 135, https://doi.org/10.1038/srep00135, 2011. a, b, c
Han, Y., Zhou, D., Pang, X., Zhang, L., Song, Y., Tong, Z., Bao, J., Dai, E., Wang, J., Guo, Z., Zhai, J., Du, Z., Wang, X., Wang, J., Huang, P., and Yang, R.: Comparative transcriptome analysis of Yersinia pestis in response to hyperosmotic and high-salinity stress, Res. Microbiol., 156, 403–415, https://doi.org/10.1016/j.resmic.2004.10.004, 2005. a, b
Kohler, C., Lourenço, R. F., Bernhardt, J., Albrecht, D., Schüler, J., Hecker, M., and Gomes, S. L.: A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive α-proteobacterium, BMC Microbiol., 15, 71, https://doi.org/10.1186/s12866-015-0404-x, 2015. a, b, c, d
Kunin, V., Raes, J., Harris, J. K., Spear, J. R., Walker, J. J., Ivanova, N., von Mering, C., Bebout, B. M., Pace, N. R., Bork, P., and Hugenholtz, P.: Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat, Mol. Syst. Biol., 4, 198, https://doi.org/10.1038/msb.2008.35, 2008. a, b, c, d
Ley, R. E., Harris, J. K., Wilcox, J., Spear, J. R., Miller, S. R., Bebout, B. M., Maresca, J. A., Bryant, D. A., Sogin, M. L., and Pace, N. R.: Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat, Appl. Environ. Microbiol., 72, 3685–3695, https://doi.org/10.1128/AEM.72.5.3685-3695.2006, 2006. a
Lindsay, M. R., Amenabar, M. J., Fecteau, K. M., Debes II, R. V., Fernandes Martins, M. C., Fristad, K. E., Xu, H., Hoehler, T. M., Shock, E. L., and Boyd, E. S.: Subsurface processes influence oxidant availability and chemoautotrophic hydrogen metabolism in Yellowstone hot springs, Geobiology, 16, 674–692, https://doi.org/10.1111/gbi.12308, 2018. a
Morowitz, H. J.: A theory of biochemical organization, metabolic pathways, and evolution, Complexity, 4, 39–53, https://doi.org/10.1002/(SICI)1099-0526(199907/08)4:6<39::AID-CPLX8>3.0.CO;2-2, 1999. a, b
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., Astashyn, A., Badretdin, A., Bao, Y., Blinkova, O., Brover, V., Chetvernin, V., Choi, J., Cox, E., Ermolaeva, O., Farrell, C. M., Goldfarb, T., Gupta, T., Haft, D., Hatcher, E., Hlavina, W., Joardar, V. S., Kodali, V. K., Li, W., Maglott, D., Masterson, P., McGarvey, K. M., Murphy, M. R., O'Neill, K., Pujar, S., Rangwala, S. H., Rausch, D., Riddick, L. D., Schoch, C., Shkeda, A., Storz, S. S., Sun, H., Thibaud-Nissen, F., Tolstoy, I., Tully, R. E., Vatsan, A. R., Wallin, C., Webb, D., Wu, W., Landrum, M. J., Kimchi, A., Tatusova, T., DiCuccio, M., Kitts, P., Murphy, T. D., and Pruitt, K. D.: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucl. Acid. Res., 44, D733–D745, https://doi.org/10.1093/nar/gkv1189, 2016. a
Poudel, S., Colman, D. R., Fixen, K. R., Ledbetter, R. N., Zheng, Y., Pence, N., Seefeldt, L. C., Peters, J. W., Harwood, C. S., and Boyd, E. S.: Electron transfer to nitrogenase in different genomic and metabolic backgrounds, J. Bacteriol., 200, e00757, https://doi.org/10.1128/JB.00757-17, 2018. a, b, c, d, e, f, g, h, i
Qiao, J., Huang, S., Te, R., Wang, J., Chen, L., and Zhang, W.: Integrated proteomic and transcriptomic analysis reveals novel genes and regulatory mechanisms involved in salt stress responses in Synechocystis sp. PCC 6803, Appl. Microbiol. Biotechnol., 97, 8253–8264, https://doi.org/10.1007/s00253-013-5139-8, 2013. a, b, c
R Core Team: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org, last access: 21 October 2020. a
Reveillaud, J., Reddington, E., McDermott, J., Algar, C., Meyer, J. L., Sylva, S., Seewald, J., German, C. R., and Huber, J. A.: Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise, Environ. Microbiol., 18, 1970–1987, https://doi.org/10.1111/1462-2920.13173, 2016. a, b
Rodriguez-Brito, B., Li, L., Wegley, L., Furlan, M., Angly, F., Breitbart, M., Buchanan, J., Desnues, C., Dinsdale, E., Edwards, R., Felts, B., Haynes, M., Liu, H., Lipson, D., Mahaffy, J., Martin-Cuadrado, A. B., Mira, A., Nulton, J., Pašić, L., Rayhawk, S., Rodriguez-Mueller, J., Rodriguez-Valera, F., Salamon, P., Srinagesh, S., Thingstad, T. F., Tran, T., Thurber, R. V., Willner, D., Youle, M., and Rohwer, F.: Viral and microbial community dynamics in four aquatic environments, ISME J., 4, 739–751, https://doi.org/10.1038/ismej.2010.1, 2010. a, b, c, d
Satinsky, B. M., Zielinski, B. L., Doherty, M., Smith, C. B., Sharma, S., Paul, J. H., Crump, B. C., and Moran, M. A.: The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010, Microbiome, 2, 17, https://doi.org/10.1186/2049-2618-2-17, 2014. a, b, c
Satinsky, B. M., Fortunato, C. S., Doherty, M., Smith, C. B., Sharma, S., Ward, N. D., Krusche, A. V., Yager, P. L., Richey, J. E., Moran, M. A., and Crump, B. C.: Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011, Microbiome, 3, 39, https://doi.org/10.1186/s40168-015-0099-0, 2015. a, b, c
Shock, E. L., Holland, M., Meyer-Dombard, D. R., Amend, J. P., Osburn, G. R., and Fischer, T. P.: Quantifying inorganic sources of geochemical energy in hydrothermal ecosystems, Yellowstone National Park, USA, Geochim. Cosmochim. Ac., 74, 4005–4043, https://doi.org/10.1016/j.gca.2009.08.036, 2010. a, b
Swingley, W. D., Meyer-Dombard, D. R., Shock, E. L., Alsop, E. B., Falenski, H. D., Havig, J. R., and Raymond, J.: Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem, PLOS One, 7, e38108, https://doi.org/10.1371/journal.pone.0038108, 2012. a, b, c, d
Vavourakis, C. D., Ghai, R., Rodriguez-Valera, F., Sorokin, D. Y., Tringe, S. G., Hugenholtz, P., and Muyzer, G.: Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines, Front. Microbiol., 7, 211, https://doi.org/10.3389/fmicb.2016.00211, 2016. a, b
Wang, Y., Bryan, C., Xu, H., and Gao, H.: Nanogeochemistry: Geochemical reactions and mass transfers in nanopores, Geology, 31, 387–390, https://doi.org/10.1130/0091-7613(2003)031<0387:NGRAMT>2.0.CO;2, 2003. a, b
Warn, J. R. W. and Peters, A. P. H.: Concise Chemical Thermodynamics, CRC Press, 2nd Edn., 1996. a
Zhang, Y., Li, Y., Zhang, Y., Wang, Z., Zhao, M., Su, N., Zhang, T., Chen, L., Wei, W., Luo, J., Zhou, Y., Xu, Y., Xu, P., Li, W., and Tao, Y.: Quantitative proteomics reveals membrane protein-mediated hypersaline sensitivity and adaptation in halophilic Nocardiopsis xinjiangensis, J. Proteome Res., 15, 68–85, https://doi.org/10.1021/acs.jproteome.5b00526, 2016. a
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.
Many natural environments differ in their range of salt concentration (salinity). We developed a...