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Baran R, Lau R, Bowen BP, Diamond S, Jose N, Garcia-Pichel F, Northen TR. Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D 2O) Stable Isotope Probing. ACS Chem Biol 2017; 12:674-681. [PMID: 28068058 DOI: 10.1021/acschembio.6b00890] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria are important primary producers of organic matter in diverse environments on a global scale. While mechanisms of CO2 fixation are well understood, the distribution of the flow of fixed organic carbon within individual cells and complex microbial communities is less well characterized. To obtain a general overview of metabolism, we describe the use of deuterium oxide (D2O) to measure deuterium incorporation into the intracellular metabolites of two physiologically diverse cyanobacteria: a terrestrial filamentous strain (Microcoleus vaginatus PCC 9802) and a euryhaline unicellular strain (Synechococcus sp. PCC 7002). D2O was added to the growth medium during different phases of the diel cycle. Incorporation of deuterium into metabolites at nonlabile positions, an indicator of metabolite turnover, was assessed using liquid chromatography mass spectrometry. Expectedly, large differences in turnover among metabolites were observed. Some metabolites, such as fatty acids, did not show significant turnover over 12-24 h time periods but did turn over during longer time periods. Unexpectedly, metabolites commonly regarded to act as compatible solutes, including glutamate, glucosylglycerol, and a dihexose, showed extensive turnover compared to most other metabolites already after 12 h, but only during the light phase in the cycle. The observed extensive turnover is surprising considering the conventional view on compatible solutes as biosynthetic end points given the relatively slow growth and constant osmotic conditions. This suggests the possibility of a metabolic sink for some compatible solutes (e.g., into glycogen) that allows for rapid modulation of intracellular osmolarity. To investigate this, uniformly 13C-labeled Synechococcus sp. PCC 7002 were exposed to 12C glucosylglycerol. Following metabolite extraction, amylase treatment of methanol-insoluble polymers revealed 12C labeling of glycogen. Overall, our work shows that D2O probing is a powerful method for analysis of cyanobacterial metabolism including discovery of novel metabolic processes.
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Affiliation(s)
- Richard Baran
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rebecca Lau
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Benjamin P. Bowen
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Spencer Diamond
- Center
for Circadian Biology and Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States
| | - Nick Jose
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ferran Garcia-Pichel
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- School
of Life Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Trent R. Northen
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- School
of Life Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Joint Genome Institute, Walnut Creek, California 94598, United States
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102
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Kolton M, Graber ER, Tsehansky L, Elad Y, Cytryn E. Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere. THE NEW PHYTOLOGIST 2017; 213:1393-1404. [PMID: 27780299 DOI: 10.1111/nph.14253] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/01/2016] [Indexed: 05/03/2023]
Abstract
The 'biochar effect' depicts a phenomenon in which biochar soil amendment enhances plant performance by promoting growth and suppressing disease. Although this phenomenon has been observed in numerous studies, the mode of action that explains it is currently unknown. In order to elucidate mechanisms responsible for the 'biochar effect', we comprehensively monitored tomato plant development and resistance to the foliar fungal pathogen Botrytis cinerea, in biochar-amended and nonamended soils using native biochar and washed biochar, striped of labile chemical constituents. We concomitantly assessed bacterial community succession in the rhizosphere by high-throughput 16S rRNA gene amplicon sequencing and carbon-source utilization profiling. Biochar had little impact on plant physiological parameters. However, both native and washed biochar treatments were characterized by higher rhizosphere bacterial diversity and enhanced carbohydrate and phenolic compound utilization rates coupled to stimulation of bacteria known to degrade phenolic compounds. This study indicates that the 'biochar effect' is at least partially dictated by increased diversity and changes in metabolic potential in the rhizosphere microbiome, which is primarily triggered by the recalcitrant carbon backbone of the biochar and tightly bound compounds. It corresponds to the growing consensus that soil amendments which enhance microbial diversity have important benefits to ecosystem functioning.
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Affiliation(s)
- Max Kolton
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Ellen R Graber
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
| | - Ludmila Tsehansky
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, PO Box 15159, Rishon Lezion, 7528809, Israel
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103
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Erbilgin O, Bowen BP, Kosina SM, Jenkins S, Lau RK, Northen TR. Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. BMC Bioinformatics 2017; 18:57. [PMID: 28114881 PMCID: PMC5259839 DOI: 10.1186/s12859-017-1478-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 01/07/2017] [Indexed: 12/14/2022] Open
Abstract
Background Mixed cultures of different microbial species are increasingly being used to carry out a specific biochemical function in lieu of engineering a single microbe to do the same task. However, knowing how different species’ metabolisms will integrate to reach a desired outcome is a difficult problem that has been studied in great detail using steady-state models. However, many biotechnological processes, as well as natural habitats, represent a more dynamic system. Examining how individual species use resources in their growth medium or environment (exometabolomics) over time in batch culture conditions can provide rich phenotypic data that encompasses regulation and transporters, creating an opportunity to integrate the data into a predictive model of resource use by a mixed community. Results Here we use exometabolomic profiling to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by two Pseudomonas and one Bacillus species isolated from ground water. Contrary to studies in model organisms, we found surprisingly few correlations between resource preferences and maximal growth rate or biomass composition. We then modeled patterns of substrate depletion, and used these models to examine if substrate usage preferences and substrate depletion kinetics of individual isolates can be used to predict the metabolism of a co-culture of the isolates. We found that most of the substrates fit the model predictions, except for glucose and histidine, which were depleted more slowly than predicted, and proline, glycine, glutamate, lysine and arginine, which were all consumed significantly faster. Conclusions Our results indicate that a significant portion of a model community’s overall metabolism can be predicted based on the metabolism of the individuals. Based on the nature of our model, the resources that significantly deviate from the prediction highlight potential metabolic pathways affected by species-species interactions, which when further studied can potentially be used to modulate microbial community structure and/or function. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1478-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Onur Erbilgin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stefan Jenkins
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Present Address: Intrexon Corporation, 1750 Kraft Dr, Blacksburg, VA, 24060, USA
| | - Rebecca K Lau
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA. .,Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA.
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104
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Murik O, Oren N, Shotland Y, Raanan H, Treves H, Kedem I, Keren N, Hagemann M, Pade N, Kaplan A. What distinguishes cyanobacteria able to revive after desiccation from those that cannot: the genome aspect. Environ Microbiol 2016; 19:535-550. [PMID: 27501380 DOI: 10.1111/1462-2920.13486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/04/2016] [Indexed: 01/15/2023]
Abstract
Filamentous cyanobacteria are the main founders and primary producers in biological desert soil crusts (BSCs) and are likely equipped to cope with one of the harshest environmental conditions on earth including daily hydration/dehydration cycles, high irradiance and extreme temperatures. Here, we resolved and report on the genome sequence of Leptolyngbya ohadii, an important constituent of the BSC. Comparative genomics identified a set of genes present in desiccation-tolerant but not in dehydration-sensitive cyanobacteria. RT qPCR analyses showed that the transcript abundance of many of them is upregulated during desiccation in L. ohadii. In addition, we identified genes where the orthologs detected in desiccation-tolerant cyanobacteria differs substantially from that found in desiccation-sensitive cells. We present two examples, treS and fbpA (encoding trehalose synthase and fructose 1,6-bisphosphate aldolase respectively) where, in addition to the orthologs present in the desiccation-sensitive strains, the resistant cyanobacteria also possess genes with different predicted structures. We show that in both cases the two orthologs are transcribed during controlled dehydration of L. ohadii and discuss the genetic basis for the acclimation of cyanobacteria to the desiccation conditions in desert BSC.
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Affiliation(s)
- Omer Murik
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nadav Oren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Yoram Shotland
- Department of Chemical Engineering, Shamoon College of Engineering, Beer Sheva, 84100, Israel
| | - Hagai Raanan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Haim Treves
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Isaac Kedem
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Martin Hagemann
- Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, A.-Einstein-Str. 3, Rostock, D-18059, Germany
| | - Nadin Pade
- Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, A.-Einstein-Str. 3, Rostock, D-18059, Germany
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
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105
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Nitrogen fixation in a non-heterocystous cyanobacterial mat from a mountain river. Sci Rep 2016; 6:30920. [PMID: 27476439 PMCID: PMC4967917 DOI: 10.1038/srep30920] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/11/2016] [Indexed: 11/08/2022] Open
Abstract
In situ nitrogen fixation was investigated in a cyanobacterial mat growing on the bed of rocks of the Muga River, Spain. The filamentous non-heterocystous cyanobacterium Schizothrix dominated the mat, showing nitrogenase activity in the light at similar rates to those found in nearby heterocystous Rivularia colonies. N2 fixation in the light was significantly increased by an inhibitor of PSII and oxygen evolution, DCMU (3-[3,4-dichlorophenyl]-1,1-dimethylurea), and anaerobic conditions. However, no nitrogenase activity was found in the dark. Addition of fructose as a respiratory substrate induced nitrogenase activity in samples incubated under aerobic conditions in the dark but not in anaerobic conditions. Microelectrode oxygen profiles showed internal microaerobic microzones where nitrogen fixation might concentrate. Analyses of the 16S rRNA gene revealed only the presence of sequences belonging to filamentous non-heterocystous cyanobacteria. nifH gene diversity showed that the major phylotypes also belonged to this group. One of the three strains isolated from the Schizothrix mat was capable of fixing N2 and growing in the absence of combined N. This was consistent with the nifH gene analysis. These results suggest a relevant contribution of non-heterocystous cyanobacteria to nitrogen fixation in these mats.
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106
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Abstract
UNLABELLED Although it is becoming clear that many microbial primary producers can also play a role as organic consumers, we know very little about the metabolic regulation of photoautotroph organic matter consumption. Cyanobacteria in phototrophic biofilms can reuse extracellular organic carbon, but the metabolic drivers of extracellular processes are surprisingly complex. We investigated the metabolic foundations of organic matter reuse by comparing exoproteome composition and incorporation of (13)C-labeled and (15)N-labeled cyanobacterial extracellular organic matter (EOM) in a unicyanobacterial biofilm incubated using different light regimes. In the light and the dark, cyanobacterial direct organic C assimilation accounted for 32% and 43%, respectively, of all organic C assimilation in the community. Under photosynthesis conditions, we measured increased excretion of extracellular polymeric substances (EPS) and proteins involved in micronutrient transport, suggesting that requirements for micronutrients may drive EOM assimilation during daylight hours. This interpretation was supported by photosynthesis inhibition experiments, in which cyanobacteria incorporated N-rich EOM-derived material. In contrast, under dark, C-starved conditions, cyanobacteria incorporated C-rich EOM-derived organic matter, decreased excretion of EPS, and showed an increased abundance of degradative exoproteins, demonstrating the use of the extracellular domain for C storage. Sequence-structure modeling of one of these exoproteins predicted a specific hydrolytic activity that was subsequently detected, confirming increased EOM degradation in the dark. Associated heterotrophic bacteria increased in abundance and upregulated transport proteins under dark relative to light conditions. Taken together, our results indicate that biofilm cyanobacteria are successful competitors for organic C and N and that cyanobacterial nutrient and energy requirements control the use of EOM. IMPORTANCE Cyanobacteria are globally distributed primary producers, and the fate of their fixed C influences microbial biogeochemical cycling. This fate is complicated by cyanobacterial degradation and assimilation of organic matter, but because cyanobacteria are assumed to be poor competitors for organic matter consumption, regulation of this process is not well tested. In mats and biofilms, this is especially relevant because cyanobacteria produce an extensive organic extracellular matrix, providing the community with a rich source of nutrients. Light is a well-known regulator of cyanobacterial metabolism, so we characterized the effects of light availability on the incorporation of organic matter. Using stable isotope tracing at the single-cell level, we quantified photoautotroph assimilation under different metabolic conditions and integrated the results with proteomics to elucidate metabolic status. We found that cyanobacteria effectively compete for organic matter in the light and the dark and that nutrient requirements and community interactions contribute to cycling of extracellular organic matter.
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107
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Young KE, Grover HS, Bowker MA. Altering biocrusts for an altered climate. THE NEW PHYTOLOGIST 2016; 210:18-22. [PMID: 26919695 DOI: 10.1111/nph.13910] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Kristina E Young
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, PO Box 15018, Flagstaff, AZ 86011, USA
| | - Henry S Grover
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, PO Box 15018, Flagstaff, AZ 86011, USA
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, PO Box 15018, Flagstaff, AZ 86011, USA
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108
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Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen BP, Lim HC, Nico PS, Holman HY, Gilbert B, Silver WL, Northen TR, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Front Microbiol 2016; 7:323. [PMID: 27014243 PMCID: PMC4791749 DOI: 10.3389/fmicb.2016.00323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/29/2016] [Indexed: 01/29/2023] Open
Abstract
Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the production of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots.
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Affiliation(s)
- Nicholas J Bouskill
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Tana E Wood
- International Institute of Tropical Forestry, United States Department of Agriculture Forest ServiceRio Piedras, PR, USA; Fundación Puertorriqueña de ConservaciónSan Juan, PR, USA
| | - Richard Baran
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zhao Hao
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zaw Ye
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Ben P Bowen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hsiao Chien Lim
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Peter S Nico
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hoi-Ying Holman
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Benjamin Gilbert
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management, University of California, Berkeley Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eoin L Brodie
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA
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109
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Garcia-Pichel F, Felde VJMNL, Drahorad SL, Weber B. Microstructure and Weathering Processes Within Biological Soil Crusts. BIOLOGICAL SOIL CRUSTS: AN ORGANIZING PRINCIPLE IN DRYLANDS 2016. [DOI: 10.1007/978-3-319-30214-0_13] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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110
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Patterns and Controls on Nitrogen Cycling of Biological Soil Crusts. BIOLOGICAL SOIL CRUSTS: AN ORGANIZING PRINCIPLE IN DRYLANDS 2016. [DOI: 10.1007/978-3-319-30214-0_14] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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